Starting phenix.real_space_refine on Fri Jul 3 14:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud2_64059/07_2026/9ud2_64059.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud2_64059/07_2026/9ud2_64059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ud2_64059/07_2026/9ud2_64059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud2_64059/07_2026/9ud2_64059.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud2_64059/07_2026/9ud2_64059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud2_64059/07_2026/9ud2_64059.cif" } resolution = 2.59 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= 0.002 sd= 0.178 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 3 5.49 5 S 93 5.16 5 C 9543 2.51 5 N 2414 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 14763 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: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1950 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'FMN': 1, 'LMT': 1, 'RBF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 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: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9136 SG CYS D 112 42.490 49.575 88.247 1.00 11.00 S ATOM 10102 SG CYS E 26 44.745 52.431 86.883 1.00 9.03 S ATOM 8497 SG CYS D 29 43.266 55.502 90.952 1.00 11.41 S ATOM 10824 SG CYS E 120 41.688 52.795 92.669 1.00 6.78 S ATOM 11950 SG CYS F 79 39.354 34.607 58.385 1.00141.61 S ATOM 12189 SG CYS F 111 39.783 35.647 61.954 1.00145.38 S ATOM 11903 SG CYS F 70 45.702 34.231 60.915 1.00157.13 S Time building chain proxies: 3.36, per 1000 atoms: 0.23 Number of scatterers: 14763 At special positions: 0 Unit cell: (89.76, 124.08, 154, 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 93 16.00 P 3 15.00 O 2705 8.00 N 2414 7.00 C 9543 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: 1.30 Conformation dependent library (CDL) restraints added in 687.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 76 " Number of angles added : 12 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 11 sheets defined 54.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.833A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.613A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.775A pdb=" N THR A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) 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 removed outlier: 3.799A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.981A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.790A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 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 425 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.885A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 removed outlier: 3.708A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.575A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.523A pdb=" N ALA B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.552A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.356A pdb=" N VAL B 275 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.735A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.720A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.824A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 333 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.584A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.744A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'C' and resid 7 through 33 Processing helix chain 'C' and resid 33 through 54 removed outlier: 4.209A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 67 Processing helix chain 'C' and resid 92 through 99 removed outlier: 3.952A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.563A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'D' and resid 12 through 17 removed outlier: 4.233A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 37 through 62 removed outlier: 3.686A pdb=" N ILE D 62 " --> pdb=" O PHE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.812A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.951A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.598A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.018A 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 removed outlier: 3.704A pdb=" N PHE E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.681A pdb=" N MET E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.539A pdb=" N GLY E 110 " --> pdb=" O TYR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 117 Proline residue: E 114 - end of helix removed outlier: 3.522A pdb=" N THR E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 117' Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.811A 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 24 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 54 through 63 Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.548A pdb=" N ASP F 96 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 124 through 130 removed outlier: 3.635A pdb=" N PHE F 128 " --> pdb=" O PRO F 124 " (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 189 through 196 Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.956A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.802A pdb=" N MET F 317 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 343 through 347 removed outlier: 3.525A pdb=" N ASN F 347 " --> pdb=" O PRO F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.360A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 8.118A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.294A 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 32 removed outlier: 6.626A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY A 74 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.964A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.571A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.327A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'F' and resid 46 through 47 removed outlier: 4.156A pdb=" N ILE F 37 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER F 85 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.629A pdb=" N TYR F 167 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN F 169 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER F 139 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 178 Processing sheet with id=AB2, first strand: chain 'F' and resid 333 through 339 removed outlier: 3.638A pdb=" N VAL F 334 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU F 275 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TYR F 376 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL F 277 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS F 378 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE F 279 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU F 402 " --> pdb=" O CYS F 373 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2094 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: 2.51 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.39: 6013 1.39 - 1.60: 8914 1.60 - 1.80: 130 1.80 - 2.01: 32 2.01 - 2.21: 8 Bond restraints: 15097 Sorted by residual: bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.384 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " ideal model delta sigma weight residual 1.676 1.604 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4A FMN B 501 " pdb=" N5 FMN B 501 " ideal model delta sigma weight residual 1.300 1.370 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C10 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.443 1.385 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" C10 FMN B 501 " pdb=" N1 FMN B 501 " ideal model delta sigma weight residual 1.317 1.373 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 15092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 20057 2.09 - 4.18: 364 4.18 - 6.27: 54 6.27 - 8.36: 7 8.36 - 10.44: 2 Bond angle restraints: 20484 Sorted by residual: angle pdb=" C ALA F 231 " pdb=" N THR F 232 " pdb=" CA THR F 232 " ideal model delta sigma weight residual 120.49 130.66 -10.17 1.42e+00 4.96e-01 5.13e+01 angle pdb=" N GLY C 144 " pdb=" CA GLY C 144 " pdb=" C GLY C 144 " ideal model delta sigma weight residual 113.18 102.74 10.44 2.37e+00 1.78e-01 1.94e+01 angle pdb=" N SER E 20 " pdb=" CA SER E 20 " pdb=" C SER E 20 " ideal model delta sigma weight residual 109.85 104.37 5.48 1.58e+00 4.01e-01 1.20e+01 angle pdb=" C TYR C 225 " pdb=" N LEU C 226 " pdb=" CA LEU C 226 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 119.42 -5.82 1.90e+00 2.77e-01 9.40e+00 ... (remaining 20479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7987 17.81 - 35.63: 754 35.63 - 53.44: 172 53.44 - 71.25: 44 71.25 - 89.07: 18 Dihedral angle restraints: 8975 sinusoidal: 3594 harmonic: 5381 Sorted by residual: dihedral pdb=" CA ALA F 25 " pdb=" C ALA F 25 " pdb=" N LYS F 26 " pdb=" CA LYS F 26 " ideal model delta harmonic sigma weight residual 180.00 149.84 30.16 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" N GLY C 144 " pdb=" CA GLY C 144 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LEU E 19 " pdb=" C LEU E 19 " pdb=" N SER E 20 " pdb=" CA SER E 20 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1433 0.041 - 0.082: 647 0.082 - 0.122: 204 0.122 - 0.163: 32 0.163 - 0.204: 6 Chirality restraints: 2322 Sorted by residual: chirality pdb=" C4' LMT D 302 " pdb=" C3' LMT D 302 " pdb=" C5' LMT D 302 " pdb=" O1B LMT D 302 " both_signs ideal model delta sigma weight residual False -2.55 -2.35 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL B 193 " pdb=" CA VAL B 193 " pdb=" CG1 VAL B 193 " pdb=" CG2 VAL B 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU E 19 " pdb=" CB LEU E 19 " pdb=" CD1 LEU E 19 " pdb=" CD2 LEU E 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2319 not shown) Planarity restraints: 2575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 226 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.53e+01 pdb=" C LEU C 226 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU C 226 " 0.025 2.00e-02 2.50e+03 pdb=" N THR C 227 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 48 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LYS C 48 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS C 48 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE C 49 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 159 " 0.024 2.00e-02 2.50e+03 1.58e-02 4.39e+00 pdb=" CG PHE B 159 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 159 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 159 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 159 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 159 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 159 " 0.010 2.00e-02 2.50e+03 ... (remaining 2572 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 252 2.69 - 3.24: 13828 3.24 - 3.79: 23045 3.79 - 4.35: 32706 4.35 - 4.90: 52536 Nonbonded interactions: 122367 Sorted by model distance: nonbonded pdb=" O2B LMT D 302 " pdb=" O6' LMT D 302 " model vdw 2.131 3.040 nonbonded pdb=" OE1 GLN C 110 " pdb=" NZ LYS C 112 " model vdw 2.196 3.120 nonbonded pdb=" OG1 THR B 236 " pdb=" O2P FMN B 501 " model vdw 2.196 3.040 nonbonded pdb=" O VAL C 52 " pdb=" OG SER C 163 " model vdw 2.200 3.040 nonbonded pdb=" NZ LYS C 192 " pdb=" O GLY C 217 " model vdw 2.215 3.120 ... (remaining 122362 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 : 0.009 0.859 15105 Z= 0.287 Angle : 0.746 20.425 20496 Z= 0.384 Chirality : 0.049 0.204 2322 Planarity : 0.006 0.063 2575 Dihedral : 15.493 89.068 5543 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 14.26 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.19), residues: 1888 helix: 1.00 (0.18), residues: 874 sheet: 0.01 (0.38), residues: 174 loop : -0.85 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 229 TYR 0.017 0.002 TYR D 141 PHE 0.032 0.003 PHE B 159 TRP 0.021 0.003 TRP B 103 HIS 0.005 0.001 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (15097) covalent geometry : angle 0.71279 / 0.38 (20484) hydrogen bonds : bond 0.14823 / 10.05 ( 734) hydrogen bonds : angle 6.20130 / 4.35 ( 2094) metal coordination : bond 0.30405 / 10.16 ( 8) metal coordination : angle 9.13309 / 5.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8228 (mptt) REVERT: A 27 LYS cc_start: 0.8695 (mttp) cc_final: 0.8439 (mttm) REVERT: A 46 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7153 (mtm-85) REVERT: A 98 ASP cc_start: 0.8499 (m-30) cc_final: 0.8276 (m-30) REVERT: A 172 GLU cc_start: 0.7769 (tt0) cc_final: 0.7211 (mp0) REVERT: A 284 GLU cc_start: 0.8031 (mt-10) cc_final: 0.6931 (mp0) REVERT: A 333 GLU cc_start: 0.7010 (tt0) cc_final: 0.6151 (pt0) REVERT: A 433 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 444 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7333 (tttt) REVERT: B 318 ASP cc_start: 0.7556 (m-30) cc_final: 0.7100 (p0) REVERT: C 1 MET cc_start: 0.1763 (mtt) cc_final: 0.0518 (tmt) REVERT: C 56 GLU cc_start: 0.7223 (tp30) cc_final: 0.6816 (tp30) REVERT: C 58 LYS cc_start: 0.7149 (ptpp) cc_final: 0.6915 (ptpp) REVERT: C 95 LYS cc_start: 0.7436 (ttmm) cc_final: 0.6757 (tmtt) REVERT: C 148 MET cc_start: 0.8240 (mmt) cc_final: 0.7815 (mpt) REVERT: C 198 ASN cc_start: 0.6879 (t0) cc_final: 0.6319 (t0) REVERT: D 8 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4008 (mtpm) REVERT: E 27 THR cc_start: 0.9002 (t) cc_final: 0.8660 (p) REVERT: E 95 GLU cc_start: 0.8205 (tt0) cc_final: 0.7815 (tt0) REVERT: E 100 ARG cc_start: 0.8315 (tpt-90) cc_final: 0.8114 (tpp80) REVERT: F 80 ARG cc_start: 0.7044 (mmt90) cc_final: 0.6639 (mmm-85) REVERT: F 107 GLU cc_start: 0.6022 (mm-30) cc_final: 0.5662 (mt-10) REVERT: F 118 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6307 (m-30) REVERT: F 212 TYR cc_start: 0.4498 (m-80) cc_final: 0.3684 (m-80) REVERT: F 214 MET cc_start: 0.6418 (mtm) cc_final: 0.6127 (mpt) REVERT: F 223 ILE cc_start: 0.5484 (mt) cc_final: 0.5236 (tt) REVERT: F 293 PHE cc_start: 0.6599 (m-80) cc_final: 0.6316 (m-80) REVERT: F 332 ASN cc_start: 0.6842 (p0) cc_final: 0.6640 (p0) REVERT: F 377 MET cc_start: 0.6570 (mmm) cc_final: 0.6345 (ttm) REVERT: F 399 GLU cc_start: 0.6792 (pt0) cc_final: 0.6150 (mp0) outliers start: 25 outliers final: 17 residues processed: 233 average time/residue: 0.6702 time to fit residues: 170.6649 Evaluate side-chains 231 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN C 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.188515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.124483 restraints weight = 11366.710| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.77 r_work: 0.2933 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15105 Z= 0.119 Angle : 0.553 14.840 20496 Z= 0.290 Chirality : 0.043 0.158 2322 Planarity : 0.004 0.037 2575 Dihedral : 7.893 65.478 2249 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 2.77 % Allowed : 13.35 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.53 (0.19), residues: 1888 helix: 1.43 (0.18), residues: 880 sheet: 0.22 (0.39), residues: 166 loop : -0.76 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 229 TYR 0.017 0.001 TYR D 141 PHE 0.019 0.001 PHE B 159 TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (15097) covalent geometry : angle 0.53981 / 0.29 (20484) hydrogen bonds : bond 0.05008 / 3.48 ( 734) hydrogen bonds : angle 5.07233 / 3.58 ( 2094) metal coordination : bond 0.00860 / 0.33 ( 8) metal coordination : angle 5.03557 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8334 (mptt) REVERT: A 46 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7147 (mtm-85) REVERT: A 98 ASP cc_start: 0.8486 (m-30) cc_final: 0.8219 (m-30) REVERT: A 106 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 172 GLU cc_start: 0.7824 (tt0) cc_final: 0.7180 (mp0) REVERT: A 284 GLU cc_start: 0.8026 (mt-10) cc_final: 0.6807 (mp0) REVERT: A 318 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7869 (tpt-90) REVERT: A 333 GLU cc_start: 0.7081 (tt0) cc_final: 0.6269 (pt0) REVERT: A 384 MET cc_start: 0.8643 (mmm) cc_final: 0.8354 (tmm) REVERT: A 433 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: A 444 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7227 (tttt) REVERT: B 318 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7204 (p0) REVERT: B 380 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: C 95 LYS cc_start: 0.7368 (ttmm) cc_final: 0.6683 (tmtt) REVERT: C 148 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7593 (mpt) REVERT: C 198 ASN cc_start: 0.6904 (t0) cc_final: 0.6318 (t0) REVERT: E 27 THR cc_start: 0.8892 (t) cc_final: 0.8647 (p) REVERT: E 95 GLU cc_start: 0.8159 (tt0) cc_final: 0.7849 (tt0) REVERT: F 82 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5744 (tmmm) REVERT: F 107 GLU cc_start: 0.5717 (mm-30) cc_final: 0.5287 (tp30) REVERT: F 118 ASP cc_start: 0.6652 (m-30) cc_final: 0.6163 (m-30) REVERT: F 223 ILE cc_start: 0.5005 (mt) cc_final: 0.4738 (tt) REVERT: F 245 MET cc_start: 0.3932 (tpt) cc_final: 0.1772 (pmm) REVERT: F 293 PHE cc_start: 0.6367 (m-80) cc_final: 0.6056 (m-80) REVERT: F 317 MET cc_start: 0.7205 (ptp) cc_final: 0.6275 (mtp) REVERT: F 399 GLU cc_start: 0.6851 (pt0) cc_final: 0.6232 (mp0) outliers start: 43 outliers final: 18 residues processed: 236 average time/residue: 0.6761 time to fit residues: 174.6100 Evaluate side-chains 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 93 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN C 116 GLN F 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.182996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116001 restraints weight = 11481.482| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.93 r_work: 0.2901 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15105 Z= 0.269 Angle : 0.755 14.530 20496 Z= 0.395 Chirality : 0.053 0.259 2322 Planarity : 0.006 0.072 2575 Dihedral : 8.336 73.645 2231 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 3.35 % Allowed : 14.32 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1888 helix: 0.86 (0.17), residues: 882 sheet: 0.22 (0.38), residues: 164 loop : -0.88 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 372 TYR 0.023 0.003 TYR F 248 PHE 0.034 0.003 PHE B 159 TRP 0.021 0.003 TRP B 70 HIS 0.007 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (15097) covalent geometry : angle 0.74381 / 0.39 (20484) hydrogen bonds : bond 0.07642 / 5.26 ( 734) hydrogen bonds : angle 5.29312 / 3.75 ( 2094) metal coordination : bond 0.01819 / 0.94 ( 8) metal coordination : angle 5.30606 / 2.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8283 (mptt) REVERT: A 46 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7149 (mtm-85) REVERT: A 98 ASP cc_start: 0.8510 (m-30) cc_final: 0.8268 (m-30) REVERT: A 106 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 172 GLU cc_start: 0.7797 (tt0) cc_final: 0.7188 (mp0) REVERT: A 188 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8524 (mttt) REVERT: A 279 MET cc_start: 0.8782 (mtm) cc_final: 0.8573 (mtt) REVERT: A 284 GLU cc_start: 0.8077 (mt-10) cc_final: 0.6917 (mp0) REVERT: A 318 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7995 (tpt170) REVERT: A 333 GLU cc_start: 0.7031 (tt0) cc_final: 0.6213 (pt0) REVERT: A 433 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: A 444 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7293 (tttt) REVERT: B 318 ASP cc_start: 0.7715 (m-30) cc_final: 0.7127 (p0) REVERT: B 380 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: C 56 GLU cc_start: 0.7210 (tp30) cc_final: 0.6786 (tp30) REVERT: C 95 LYS cc_start: 0.7426 (ttmm) cc_final: 0.6730 (tmtt) REVERT: C 148 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7727 (mpt) REVERT: C 198 ASN cc_start: 0.6984 (t0) cc_final: 0.6410 (t0) REVERT: E 1 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6582 (mmm) REVERT: E 27 THR cc_start: 0.8902 (t) cc_final: 0.8585 (p) REVERT: E 95 GLU cc_start: 0.8193 (tt0) cc_final: 0.7891 (tt0) REVERT: F 82 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.6265 (ttpt) REVERT: F 107 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5423 (mt-10) REVERT: F 118 ASP cc_start: 0.6705 (m-30) cc_final: 0.6270 (m-30) REVERT: F 293 PHE cc_start: 0.6503 (m-80) cc_final: 0.6216 (m-80) REVERT: F 317 MET cc_start: 0.7201 (ptp) cc_final: 0.6303 (mtp) REVERT: F 332 ASN cc_start: 0.6844 (p0) cc_final: 0.6622 (p0) REVERT: F 377 MET cc_start: 0.6435 (ttm) cc_final: 0.5905 (mmm) REVERT: F 390 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7320 (ttm) REVERT: F 398 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6448 (mm-30) REVERT: F 399 GLU cc_start: 0.6862 (pt0) cc_final: 0.6261 (mp0) REVERT: F 403 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6088 (tp) outliers start: 52 outliers final: 23 residues processed: 241 average time/residue: 0.6711 time to fit residues: 176.9183 Evaluate side-chains 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain F residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 20.0000 chunk 19 optimal weight: 0.0980 chunk 155 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 170 optimal weight: 40.0000 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN C 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.186607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122462 restraints weight = 11387.914| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.68 r_work: 0.2948 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15105 Z= 0.136 Angle : 0.573 12.980 20496 Z= 0.300 Chirality : 0.044 0.163 2322 Planarity : 0.005 0.044 2575 Dihedral : 7.888 70.764 2231 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.12 % Favored : 96.77 % Rotamer: Outliers : 3.10 % Allowed : 14.58 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.36 (0.19), residues: 1888 helix: 1.25 (0.18), residues: 884 sheet: 0.20 (0.37), residues: 171 loop : -0.83 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.021 0.002 TYR D 141 PHE 0.022 0.002 PHE B 159 TRP 0.021 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (15097) covalent geometry : angle 0.56166 / 0.30 (20484) hydrogen bonds : bond 0.05340 / 3.70 ( 734) hydrogen bonds : angle 4.93924 / 3.49 ( 2094) metal coordination : bond 0.00756 / 0.39 ( 8) metal coordination : angle 4.68184 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8312 (mptt) REVERT: A 46 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7137 (mtm-85) REVERT: A 98 ASP cc_start: 0.8554 (m-30) cc_final: 0.8298 (m-30) REVERT: A 106 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 172 GLU cc_start: 0.7770 (tt0) cc_final: 0.7200 (mp0) REVERT: A 188 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8350 (mttt) REVERT: A 279 MET cc_start: 0.8767 (mtm) cc_final: 0.8556 (mtt) REVERT: A 284 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7422 (tt0) REVERT: A 318 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7922 (tpt170) REVERT: A 333 GLU cc_start: 0.7095 (tt0) cc_final: 0.6196 (pt0) REVERT: A 433 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: A 444 LYS cc_start: 0.7544 (ttmm) cc_final: 0.7216 (tttt) REVERT: B 43 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6078 (tmt170) REVERT: B 318 ASP cc_start: 0.7734 (m-30) cc_final: 0.7222 (p0) REVERT: B 380 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: C 95 LYS cc_start: 0.7411 (ttmm) cc_final: 0.6728 (tmtt) REVERT: C 148 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7665 (mpt) REVERT: C 198 ASN cc_start: 0.6938 (t0) cc_final: 0.6376 (t0) REVERT: E 27 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8620 (p) REVERT: E 95 GLU cc_start: 0.8138 (tt0) cc_final: 0.7825 (tt0) REVERT: F 80 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6815 (mmt90) REVERT: F 82 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6202 (ttpt) REVERT: F 107 GLU cc_start: 0.5864 (mm-30) cc_final: 0.5326 (mt-10) REVERT: F 223 ILE cc_start: 0.5046 (mt) cc_final: 0.4769 (tt) REVERT: F 293 PHE cc_start: 0.6411 (m-80) cc_final: 0.6119 (m-80) REVERT: F 317 MET cc_start: 0.7180 (ptp) cc_final: 0.6323 (mtp) REVERT: F 377 MET cc_start: 0.6383 (ttm) cc_final: 0.5997 (mmm) REVERT: F 398 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6438 (mm-30) REVERT: F 399 GLU cc_start: 0.6880 (pt0) cc_final: 0.6229 (mp0) REVERT: F 403 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6135 (tp) outliers start: 48 outliers final: 23 residues processed: 242 average time/residue: 0.6467 time to fit residues: 171.3613 Evaluate side-chains 237 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 403 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 160 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 91 GLN C 116 GLN F 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.184275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.118279 restraints weight = 11419.024| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.95 r_work: 0.2867 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15105 Z= 0.214 Angle : 0.678 12.332 20496 Z= 0.355 Chirality : 0.049 0.224 2322 Planarity : 0.005 0.062 2575 Dihedral : 8.208 74.328 2231 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 3.61 % Allowed : 14.71 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.14 (0.19), residues: 1888 helix: 1.01 (0.17), residues: 883 sheet: 0.21 (0.38), residues: 173 loop : -0.89 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 372 TYR 0.021 0.002 TYR D 141 PHE 0.030 0.002 PHE B 159 TRP 0.019 0.003 TRP B 103 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (15097) covalent geometry : angle 0.66740 / 0.35 (20484) hydrogen bonds : bond 0.06778 / 4.68 ( 734) hydrogen bonds : angle 5.09768 / 3.60 ( 2094) metal coordination : bond 0.01470 / 0.77 ( 8) metal coordination : angle 4.94420 / 2.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8305 (mptt) REVERT: A 46 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7234 (mtm-85) REVERT: A 106 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 172 GLU cc_start: 0.7807 (tt0) cc_final: 0.7180 (mp0) REVERT: A 188 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8494 (mttt) REVERT: A 284 GLU cc_start: 0.8128 (mt-10) cc_final: 0.6966 (mp0) REVERT: A 318 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7969 (tpt170) REVERT: A 333 GLU cc_start: 0.7204 (tt0) cc_final: 0.6345 (pt0) REVERT: A 433 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 444 LYS cc_start: 0.7609 (ttmm) cc_final: 0.7272 (tttt) REVERT: B 43 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6567 (ptm-80) REVERT: B 149 MET cc_start: 0.8651 (mtp) cc_final: 0.8426 (mtm) REVERT: B 318 ASP cc_start: 0.7677 (m-30) cc_final: 0.7182 (p0) REVERT: B 380 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: C 56 GLU cc_start: 0.7196 (tp30) cc_final: 0.6741 (tp30) REVERT: C 95 LYS cc_start: 0.7462 (ttmm) cc_final: 0.6675 (tmtt) REVERT: C 148 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7776 (mpt) REVERT: C 196 ASP cc_start: 0.6744 (p0) cc_final: 0.6528 (p0) REVERT: C 198 ASN cc_start: 0.7011 (t0) cc_final: 0.6269 (t0) REVERT: E 1 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6647 (mmm) REVERT: E 27 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8578 (p) REVERT: E 95 GLU cc_start: 0.8197 (tt0) cc_final: 0.7908 (tt0) REVERT: F 80 ARG cc_start: 0.7230 (mmt90) cc_final: 0.6897 (mmt90) REVERT: F 82 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6255 (ttpt) REVERT: F 107 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5499 (mt-10) REVERT: F 223 ILE cc_start: 0.5132 (mt) cc_final: 0.4863 (tt) REVERT: F 293 PHE cc_start: 0.6497 (m-80) cc_final: 0.6184 (m-80) REVERT: F 317 MET cc_start: 0.7103 (ptp) cc_final: 0.6230 (mtp) REVERT: F 377 MET cc_start: 0.6291 (ttm) cc_final: 0.5932 (mmm) REVERT: F 383 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5481 (ttp) REVERT: F 390 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7255 (ttm) REVERT: F 398 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6389 (mm-30) REVERT: F 399 GLU cc_start: 0.6855 (pt0) cc_final: 0.6259 (mp0) REVERT: F 403 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6149 (tp) outliers start: 56 outliers final: 28 residues processed: 254 average time/residue: 0.6592 time to fit residues: 183.7458 Evaluate side-chains 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 390 MET Chi-restraints excluded: chain F residue 403 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 91 GLN C 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.186181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.146298 restraints weight = 11339.774| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.34 r_work: 0.3252 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15105 Z= 0.152 Angle : 0.596 11.330 20496 Z= 0.312 Chirality : 0.045 0.166 2322 Planarity : 0.005 0.049 2575 Dihedral : 7.983 73.346 2231 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 3.29 % Allowed : 15.42 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.32 (0.19), residues: 1888 helix: 1.23 (0.18), residues: 883 sheet: 0.22 (0.38), residues: 171 loop : -0.88 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 199 TYR 0.021 0.002 TYR D 141 PHE 0.024 0.002 PHE B 159 TRP 0.019 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (15097) covalent geometry : angle 0.58602 / 0.31 (20484) hydrogen bonds : bond 0.05628 / 3.90 ( 734) hydrogen bonds : angle 4.93036 / 3.48 ( 2094) metal coordination : bond 0.00949 / 0.50 ( 8) metal coordination : angle 4.48566 / 2.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8449 (mptt) REVERT: A 46 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7705 (mtm-85) REVERT: A 188 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8549 (mttt) REVERT: A 284 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7369 (mp0) REVERT: A 318 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7934 (tpt170) REVERT: A 333 GLU cc_start: 0.7586 (tt0) cc_final: 0.7289 (pt0) REVERT: A 433 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: B 39 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8625 (mt) REVERT: B 43 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7043 (ptm-80) REVERT: B 380 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: C 198 ASN cc_start: 0.7259 (t0) cc_final: 0.6907 (t0) REVERT: D 207 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8100 (mt-10) REVERT: E 1 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7079 (mmm) REVERT: E 27 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8468 (p) REVERT: F 317 MET cc_start: 0.6550 (ptp) cc_final: 0.6131 (mtp) outliers start: 51 outliers final: 27 residues processed: 238 average time/residue: 0.6653 time to fit residues: 173.4681 Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 109 GLN B 91 GLN B 256 GLN C 79 ASN C 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.179897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113238 restraints weight = 11456.508| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.85 r_work: 0.2841 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15105 Z= 0.226 Angle : 0.701 11.827 20496 Z= 0.366 Chirality : 0.050 0.224 2322 Planarity : 0.006 0.063 2575 Dihedral : 8.341 82.072 2231 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 3.35 % Allowed : 15.55 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.08 (0.19), residues: 1888 helix: 0.94 (0.17), residues: 883 sheet: 0.03 (0.37), residues: 184 loop : -0.89 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.021 0.002 TYR D 141 PHE 0.030 0.003 PHE B 159 TRP 0.019 0.003 TRP B 70 HIS 0.007 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (15097) covalent geometry : angle 0.69244 / 0.37 (20484) hydrogen bonds : bond 0.06937 / 4.79 ( 734) hydrogen bonds : angle 5.09354 / 3.60 ( 2094) metal coordination : bond 0.01705 / 0.87 ( 8) metal coordination : angle 4.68886 / 2.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8283 (mptt) REVERT: A 46 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7190 (mtm-85) REVERT: A 188 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8495 (mttt) REVERT: A 284 GLU cc_start: 0.8169 (mt-10) cc_final: 0.6976 (mp0) REVERT: A 318 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8003 (tpt170) REVERT: A 433 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: B 39 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8361 (mt) REVERT: B 43 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.6508 (ptm-80) REVERT: B 380 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: B 382 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8588 (tpt) REVERT: C 198 ASN cc_start: 0.6957 (t0) cc_final: 0.6410 (t0) REVERT: E 1 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6674 (mmm) REVERT: E 27 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8533 (p) REVERT: F 107 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6096 (mt-10) REVERT: F 293 PHE cc_start: 0.6450 (m-80) cc_final: 0.6208 (m-80) REVERT: F 317 MET cc_start: 0.7038 (ptp) cc_final: 0.6242 (mtm) REVERT: F 377 MET cc_start: 0.6331 (mmm) cc_final: 0.6037 (ttm) REVERT: F 390 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7214 (ttm) outliers start: 52 outliers final: 28 residues processed: 239 average time/residue: 0.6512 time to fit residues: 170.2208 Evaluate side-chains 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 109 GLN B 91 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.183977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117584 restraints weight = 11478.639| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.07 r_work: 0.2934 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 0.044 15105 Z= 0.122 Angle : 0.548 10.292 20496 Z= 0.288 Chirality : 0.043 0.160 2322 Planarity : 0.005 0.045 2575 Dihedral : 7.679 80.962 2227 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 2.45 % Allowed : 16.39 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.49 (0.19), residues: 1888 helix: 1.42 (0.18), residues: 874 sheet: 0.12 (0.38), residues: 181 loop : -0.79 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 80 TYR 0.021 0.001 TYR D 141 PHE 0.019 0.001 PHE B 159 TRP 0.019 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15097) covalent geometry : angle 0.54064 / 0.29 (20484) hydrogen bonds : bond 0.04853 / 3.37 ( 734) hydrogen bonds : angle 4.79434 / 3.38 ( 2094) metal coordination : bond 0.00675 / 0.35 ( 8) metal coordination : angle 3.85985 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8287 (mptt) REVERT: A 46 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7112 (mtm-85) REVERT: A 284 GLU cc_start: 0.7997 (mt-10) cc_final: 0.6923 (mp0) REVERT: A 318 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8032 (tpt170) REVERT: A 433 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: B 39 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 43 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6331 (ptm-80) REVERT: B 380 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: C 56 GLU cc_start: 0.7011 (tp30) cc_final: 0.6616 (tp30) REVERT: C 198 ASN cc_start: 0.6865 (t0) cc_final: 0.6295 (t0) REVERT: C 242 MET cc_start: 0.8467 (mmm) cc_final: 0.8144 (mmt) REVERT: E 27 THR cc_start: 0.8791 (t) cc_final: 0.8558 (p) REVERT: F 293 PHE cc_start: 0.6451 (m-80) cc_final: 0.6095 (m-80) REVERT: F 317 MET cc_start: 0.6949 (ptp) cc_final: 0.6224 (mtm) REVERT: F 390 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7056 (ttm) REVERT: F 398 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6294 (mm-30) outliers start: 38 outliers final: 25 residues processed: 227 average time/residue: 0.6662 time to fit residues: 165.7061 Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 17 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 52 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 109 GLN B 91 GLN B 256 GLN C 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.180522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133797 restraints weight = 11544.772| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.49 r_work: 0.2869 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15105 Z= 0.204 Angle : 0.664 11.252 20496 Z= 0.348 Chirality : 0.048 0.201 2322 Planarity : 0.005 0.059 2575 Dihedral : 8.011 83.733 2227 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.77 % Allowed : 15.87 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.21 (0.19), residues: 1888 helix: 1.09 (0.17), residues: 883 sheet: 0.25 (0.38), residues: 171 loop : -0.89 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.023 0.002 TYR C 150 PHE 0.029 0.002 PHE B 159 TRP 0.018 0.003 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (15097) covalent geometry : angle 0.65568 / 0.35 (20484) hydrogen bonds : bond 0.06519 / 4.50 ( 734) hydrogen bonds : angle 5.00195 / 3.53 ( 2094) metal coordination : bond 0.01463 / 0.74 ( 8) metal coordination : angle 4.33604 / 2.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8338 (mptt) REVERT: A 46 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7203 (mtm-85) REVERT: A 284 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7017 (mp0) REVERT: A 318 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8003 (tpt170) REVERT: A 433 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: B 39 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 43 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6529 (ptm-80) REVERT: B 380 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: B 382 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8561 (tpt) REVERT: C 1 MET cc_start: 0.2218 (mtt) cc_final: 0.1601 (mmm) REVERT: C 56 GLU cc_start: 0.7206 (tp30) cc_final: 0.6862 (tp30) REVERT: C 198 ASN cc_start: 0.6933 (t0) cc_final: 0.6358 (t0) REVERT: E 1 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6666 (mmm) REVERT: E 27 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8576 (p) REVERT: F 293 PHE cc_start: 0.6531 (m-80) cc_final: 0.6166 (m-80) REVERT: F 317 MET cc_start: 0.6974 (ptp) cc_final: 0.6255 (mtm) REVERT: F 390 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7249 (ttm) REVERT: F 398 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6390 (mm-30) outliers start: 43 outliers final: 26 residues processed: 226 average time/residue: 0.6654 time to fit residues: 164.9086 Evaluate side-chains 231 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 164 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 109 GLN B 91 GLN B 256 GLN C 116 GLN C 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.183032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.117285 restraints weight = 11503.406| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.78 r_work: 0.2897 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15105 Z= 0.136 Angle : 0.574 10.388 20496 Z= 0.301 Chirality : 0.044 0.162 2322 Planarity : 0.005 0.046 2575 Dihedral : 7.723 83.091 2227 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.52 % Allowed : 16.26 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1888 helix: 1.35 (0.18), residues: 878 sheet: 0.27 (0.39), residues: 168 loop : -0.81 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.021 0.002 TYR D 141 PHE 0.021 0.002 PHE B 159 TRP 0.018 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15097) covalent geometry : angle 0.56616 / 0.30 (20484) hydrogen bonds : bond 0.05275 / 3.66 ( 734) hydrogen bonds : angle 4.84267 / 3.41 ( 2094) metal coordination : bond 0.00830 / 0.42 ( 8) metal coordination : angle 3.92756 / 2.15 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: A 46 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7125 (mtm-85) REVERT: A 284 GLU cc_start: 0.8061 (mt-10) cc_final: 0.6956 (mp0) REVERT: A 318 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7921 (tpt-90) REVERT: A 433 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: B 39 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 43 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6399 (ptm-80) REVERT: B 380 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.6988 (tm-30) REVERT: C 1 MET cc_start: 0.2232 (mtt) cc_final: 0.1507 (tpt) REVERT: C 198 ASN cc_start: 0.6920 (t0) cc_final: 0.6350 (t0) REVERT: C 242 MET cc_start: 0.8485 (mmm) cc_final: 0.8160 (mmt) REVERT: E 27 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8596 (p) REVERT: F 293 PHE cc_start: 0.6461 (m-80) cc_final: 0.6090 (m-80) REVERT: F 317 MET cc_start: 0.6961 (ptp) cc_final: 0.6226 (mtm) REVERT: F 377 MET cc_start: 0.6235 (mmm) cc_final: 0.5929 (ttp) REVERT: F 398 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6427 (mm-30) outliers start: 39 outliers final: 28 residues processed: 222 average time/residue: 0.6289 time to fit residues: 152.7031 Evaluate side-chains 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN B 256 GLN C 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.184600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122519 restraints weight = 11534.086| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.45 r_work: 0.2948 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15105 Z= 0.116 Angle : 0.536 9.985 20496 Z= 0.282 Chirality : 0.043 0.153 2322 Planarity : 0.005 0.047 2575 Dihedral : 7.393 81.824 2227 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 2.45 % Allowed : 16.26 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.67 (0.19), residues: 1888 helix: 1.61 (0.18), residues: 868 sheet: 0.06 (0.38), residues: 180 loop : -0.69 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.021 0.001 TYR D 141 PHE 0.018 0.001 PHE B 159 TRP 0.019 0.002 TRP B 103 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (15097) covalent geometry : angle 0.52886 / 0.28 (20484) hydrogen bonds : bond 0.04633 / 3.21 ( 734) hydrogen bonds : angle 4.70244 / 3.31 ( 2094) metal coordination : bond 0.00686 / 0.35 ( 8) metal coordination : angle 3.75954 / 2.15 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6359.44 seconds wall clock time: 109 minutes 13.73 seconds (6553.73 seconds total)