Starting phenix.real_space_refine on Fri Jul 3 06:40:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqh_43443/07_2026/8vqh_43443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqh_43443/07_2026/8vqh_43443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vqh_43443/07_2026/8vqh_43443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqh_43443/07_2026/8vqh_43443.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqh_43443/07_2026/8vqh_43443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqh_43443/07_2026/8vqh_43443.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 Cu 2 5.60 5 S 74 5.16 5 C 8011 2.51 5 N 2249 2.21 5 O 2315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 12659 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3072 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 24, 'TRANS': 379} Chain: "B" Number of atoms: 3257 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 419, 3230 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 393} Conformer: "B" Number of residues, atoms: 419, 3230 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 393} bond proxies already assigned to first conformer: 3272 Chain: "C" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3061 Classifications: {'peptide': 403} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 378} Chain: "D" Number of atoms: 3249 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 419, 3230 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 393} Conformer: "B" Number of residues, atoms: 419, 3230 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 393} bond proxies already assigned to first conformer: 3281 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CU': 2} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 77 SG CYS A 29 48.531 58.923 93.357 1.00 35.70 S ATOM 276 SG CYS A 54 53.919 58.853 93.477 1.00 39.52 S ATOM 742 SG CYS A 115 52.101 57.698 97.688 1.00 39.41 S ATOM 6406 SG CYS C 29 41.814 53.354 25.767 1.00 30.06 S ATOM 6605 SG CYS C 54 36.373 53.132 25.531 1.00 39.06 S ATOM 7071 SG CYS C 115 38.225 51.653 21.415 1.00 33.08 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N MET B 408 " occ=0.50 ... (11 atoms not shown) pdb=" CE BMET B 408 " occ=0.50 residue: pdb=" N MET D 408 " occ=0.50 ... (11 atoms not shown) pdb=" CE BMET D 408 " occ=0.50 Time building chain proxies: 4.01, per 1000 atoms: 0.32 Number of scatterers: 12659 At special positions: 0 Unit cell: (87.74, 100.04, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 2 28.99 Fe 8 26.01 S 74 16.00 O 2315 8.00 N 2249 7.00 C 8011 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: 1.07 Conformation dependent library (CDL) restraints added in 904.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 501 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 115 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 54 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 29 " pdb=" SF4 C 501 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 115 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 54 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 29 " Number of angles added : 18 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3028 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 57.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.087A pdb=" N TRP A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.894A pdb=" N ALA A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 123 through 136 removed outlier: 3.627A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 183 through 198 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.885A pdb=" N GLY A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 292 removed outlier: 4.912A pdb=" N ALA A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 374 through 385 removed outlier: 4.316A pdb=" N ASN A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.823A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.564A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.655A pdb=" N GLY B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.771A pdb=" N LEU B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 84 removed outlier: 3.636A pdb=" N ALA B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.588A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 145 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 212 through 224 removed outlier: 6.440A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 254 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 273 through 279 removed outlier: 4.691A pdb=" N TYR B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.503A pdb=" N MET B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.574A pdb=" N VAL B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 367 Processing helix chain 'B' and resid 390 through 419 Proline residue: B 405 - end of helix Processing helix chain 'C' and resid 32 through 41 removed outlier: 4.189A pdb=" N TRP C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 84 through 103 Processing helix chain 'C' and resid 114 through 120 Processing helix chain 'C' and resid 123 through 135 removed outlier: 3.606A pdb=" N ALA C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 165 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.587A pdb=" N GLY C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.051A pdb=" N PHE C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 355 through 367 Processing helix chain 'C' and resid 374 through 385 removed outlier: 4.439A pdb=" N ASN C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.508A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 423 removed outlier: 3.702A pdb=" N PHE C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 415 - end of helix Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.738A pdb=" N GLY D 15 " --> pdb=" O PRO D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.653A pdb=" N PHE D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 85 removed outlier: 4.382A pdb=" N ALA D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.520A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 212 through 226 removed outlier: 6.620A pdb=" N SER D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA D 219 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 254 Processing helix chain 'D' and resid 265 through 272 Processing helix chain 'D' and resid 273 through 279 removed outlier: 4.461A pdb=" N TYR D 277 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 304 removed outlier: 3.869A pdb=" N GLY D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.623A pdb=" N GLY D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.996A pdb=" N LYS D 364 " --> pdb=" O ARG D 360 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 365 " --> pdb=" O HIS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 419 Proline residue: D 405 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.185A pdb=" N LEU A 109 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 179 removed outlier: 6.059A pdb=" N LEU A 177 " --> pdb=" O ALA A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 352 removed outlier: 8.215A pdb=" N SER A 351 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 327 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A 300 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 327 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 302 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N THR A 329 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER A 299 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 372 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A 301 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR A 371 " --> pdb=" O LYS A 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 57 removed outlier: 8.166A pdb=" N SER B 56 " --> pdb=" O MET B 26 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 28 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 190 removed outlier: 5.676A pdb=" N CYS B 156 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 188 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER B 155 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 209 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN B 157 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 334 removed outlier: 8.432A pdb=" N LEU B 333 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 285 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 310 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 282 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 354 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE B 284 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 353 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 145 removed outlier: 6.589A pdb=" N PHE C 45 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 112 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 47 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY C 73 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE C 46 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA C 75 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 48 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 2 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 202 through 204 removed outlier: 6.404A pdb=" N LEU C 177 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 349 through 351 removed outlier: 8.706A pdb=" N VAL C 349 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 325 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N SER C 351 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 327 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL C 300 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 326 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER C 299 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL C 372 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE C 301 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR C 371 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.271A pdb=" N HIS D 27 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY D 92 " --> pdb=" O HIS D 27 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 29 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE D 89 " --> pdb=" O VAL D 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 185 through 190 removed outlier: 7.050A pdb=" N CYS D 156 " --> pdb=" O ASN D 187 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 189 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 158 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER D 155 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL D 209 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN D 157 " --> pdb=" O VAL D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 333 through 334 removed outlier: 8.639A pdb=" N LEU D 333 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET D 310 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 283 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N MET D 310 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 285 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS D 312 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG D 282 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU D 354 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE D 284 " --> pdb=" O LEU D 354 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1772 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: 2.24 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.28: 2117 1.28 - 1.53: 10158 1.53 - 1.79: 559 1.79 - 2.04: 94 2.04 - 2.29: 24 Bond restraints: 12952 Sorted by residual: bond pdb=" CG PRO A 214 " pdb=" CD PRO A 214 " ideal model delta sigma weight residual 1.503 1.023 0.480 3.40e-02 8.65e+02 1.99e+02 bond pdb=" CG PRO C 280 " pdb=" CD PRO C 280 " ideal model delta sigma weight residual 1.503 1.078 0.425 3.40e-02 8.65e+02 1.56e+02 bond pdb=" C MET D 408 " pdb=" CA BMET D 408 " ideal model delta sigma weight residual 1.523 1.620 -0.096 1.30e-02 5.92e+03 5.50e+01 bond pdb=" C MET B 408 " pdb=" O MET B 408 " ideal model delta sigma weight residual 1.236 1.320 -0.084 1.25e-02 6.40e+03 4.50e+01 bond pdb=" C MET D 408 " pdb=" O MET D 408 " ideal model delta sigma weight residual 1.237 1.307 -0.070 1.17e-02 7.31e+03 3.59e+01 ... (remaining 12947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 17583 5.41 - 10.82: 32 10.82 - 16.23: 3 16.23 - 21.64: 2 21.64 - 27.05: 3 Bond angle restraints: 17623 Sorted by residual: angle pdb=" N PRO C 280 " pdb=" CD PRO C 280 " pdb=" CG PRO C 280 " ideal model delta sigma weight residual 103.20 76.15 27.05 1.50e+00 4.44e-01 3.25e+02 angle pdb=" N PRO A 214 " pdb=" CD PRO A 214 " pdb=" CG PRO A 214 " ideal model delta sigma weight residual 103.20 78.19 25.01 1.50e+00 4.44e-01 2.78e+02 angle pdb=" CA PRO C 280 " pdb=" CB PRO C 280 " pdb=" CG PRO C 280 " ideal model delta sigma weight residual 104.50 82.36 22.14 1.90e+00 2.77e-01 1.36e+02 angle pdb=" O MET D 408 " pdb=" C MET D 408 " pdb=" CA AMET D 408 " ideal model delta sigma weight residual 120.55 132.51 -11.96 1.06e+00 8.90e-01 1.27e+02 angle pdb=" O MET D 408 " pdb=" C MET D 408 " pdb=" CA BMET D 408 " ideal model delta sigma weight residual 120.55 132.16 -11.61 1.06e+00 8.90e-01 1.20e+02 ... (remaining 17618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6515 17.96 - 35.91: 871 35.91 - 53.87: 293 53.87 - 71.82: 65 71.82 - 89.78: 23 Dihedral angle restraints: 7767 sinusoidal: 3054 harmonic: 4713 Sorted by residual: dihedral pdb=" CA PRO A 415 " pdb=" C PRO A 415 " pdb=" N VAL A 416 " pdb=" CA VAL A 416 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" N PRO C 280 " pdb=" CG PRO C 280 " pdb=" CD PRO C 280 " pdb=" CB PRO C 280 " ideal model delta sinusoidal sigma weight residual 30.00 85.30 -55.30 1 1.50e+01 4.44e-03 1.84e+01 dihedral pdb=" CA ARG A 417 " pdb=" C ARG A 417 " pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 7764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.216: 1978 4.216 - 8.433: 0 8.433 - 12.649: 0 12.649 - 16.866: 0 16.866 - 21.082: 8 Chirality restraints: 1986 Sorted by residual: chirality pdb="FE4 SF4 A 501 " pdb=" S1 SF4 A 501 " pdb=" S2 SF4 A 501 " pdb=" S3 SF4 A 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.53 21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 C 501 " pdb=" S1 SF4 C 501 " pdb=" S2 SF4 C 501 " pdb=" S3 SF4 C 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.52 21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4 A 501 " pdb=" S2 SF4 A 501 " pdb=" S3 SF4 A 501 " pdb=" S4 SF4 A 501 " both_signs ideal model delta sigma weight residual False -10.55 10.44 -21.00 2.00e-01 2.50e+01 1.10e+04 ... (remaining 1983 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 382 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 383 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 383 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 383 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 379 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO A 380 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 213 " 0.048 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO A 214 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.036 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 15 2.27 - 2.93: 5400 2.93 - 3.59: 19986 3.59 - 4.24: 33448 4.24 - 4.90: 55736 Nonbonded interactions: 114585 Sorted by model distance: nonbonded pdb=" OD1 ASP D 36 " pdb="FE2 SF4 C 501 " model vdw 1.618 3.000 nonbonded pdb=" OD1 ASP B 36 " pdb="FE2 SF4 A 501 " model vdw 1.883 3.000 nonbonded pdb=" O GLY D 132 " pdb=" OG SER D 136 " model vdw 2.158 3.040 nonbonded pdb=" NH1 ARG B 167 " pdb=" O ASP B 381 " model vdw 2.161 3.120 nonbonded pdb=" OG1 THR B 7 " pdb=" O GLU B 9 " model vdw 2.178 3.040 ... (remaining 114580 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 423 or resid 501)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 12 or resid 14 through 26 or resid 28 through 35 \ 9 or resid 361 through 407 or resid 409 through 419)) selection = (chain 'D' and (resid 1 through 12 or resid 14 through 26 or resid 28 through 35 \ 9 or resid 361 through 407 or resid 409 through 419)) } 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=0.09 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: 0.010 Normalize map: mean=0, sd=1: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.290 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.018 0.965 12958 Z= 0.555 Angle : 0.925 27.050 17641 Z= 0.510 Chirality : 1.329 21.082 1986 Planarity : 0.006 0.083 2318 Dihedral : 19.036 89.778 4739 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 4.06 % Allowed : 31.90 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -0.15 (0.20), residues: 1644 helix: 0.76 (0.18), residues: 836 sheet: -0.19 (0.41), residues: 169 loop : -1.17 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 423 TYR 0.022 0.002 TYR D 38 PHE 0.028 0.002 PHE B 73 TRP 0.025 0.002 TRP C 258 HIS 0.011 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.28 (12952) covalent geometry : angle 0.86512 / 0.51 (17623) hydrogen bonds : bond 0.13768 / 9.25 ( 605) hydrogen bonds : angle 6.74532 / 4.68 ( 1772) metal coordination : bond 0.75749 / 36.51 ( 6) metal coordination : angle 10.30882 / 5.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.461 Fit side-chains REVERT: A 305 ASP cc_start: 0.5893 (m-30) cc_final: 0.5572 (m-30) REVERT: A 358 ARG cc_start: 0.5659 (mpp-170) cc_final: 0.5204 (mpp-170) REVERT: C 140 ARG cc_start: 0.7448 (mtm180) cc_final: 0.7228 (mtp180) REVERT: C 280 PRO cc_start: 0.7204 (Cg_exo) cc_final: 0.6685 (Cg_endo) REVERT: C 305 ASP cc_start: 0.7659 (m-30) cc_final: 0.7386 (m-30) REVERT: D 98 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: D 417 MET cc_start: 0.6329 (mtp) cc_final: 0.5903 (mpp) outliers start: 44 outliers final: 32 residues processed: 210 average time/residue: 0.5912 time to fit residues: 135.1399 Evaluate side-chains 196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.179145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147065 restraints weight = 23654.296| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.99 r_work: 0.3577 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.255 12958 Z= 0.371 Angle : 2.271 51.140 17641 Z= 1.337 Chirality : 0.404 6.520 1986 Planarity : 0.006 0.064 2318 Dihedral : 6.963 62.586 1868 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 6.67 % Allowed : 27.91 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -0.04 (0.21), residues: 1644 helix: 0.89 (0.18), residues: 848 sheet: -0.42 (0.39), residues: 176 loop : -1.13 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 423 TYR 0.017 0.002 TYR D 38 PHE 0.030 0.002 PHE B 73 TRP 0.016 0.002 TRP B 269 HIS 0.010 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01060 / 0.37 (12952) covalent geometry : angle 2.05015 / 1.34 (17623) hydrogen bonds : bond 0.04289 / 2.89 ( 605) hydrogen bonds : angle 5.58177 / 3.85 ( 1772) metal coordination : bond 0.03531 / 1.81 ( 6) metal coordination : angle 30.68363 / 16.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.520 Fit side-chains REVERT: A 43 ASP cc_start: 0.7162 (t70) cc_final: 0.6938 (t70) REVERT: A 80 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6071 (ptpt) REVERT: A 107 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.5807 (mmt-90) REVERT: A 293 GLU cc_start: 0.4846 (OUTLIER) cc_final: 0.4456 (tm-30) REVERT: A 358 ARG cc_start: 0.5868 (mpp-170) cc_final: 0.5214 (mpp-170) REVERT: B 120 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7579 (mt) REVERT: C 32 THR cc_start: 0.8247 (m) cc_final: 0.7800 (p) REVERT: C 85 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5685 (mt) REVERT: C 107 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7221 (mmm-85) REVERT: C 140 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7540 (mtp180) REVERT: C 149 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7215 (tp) REVERT: C 274 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: C 280 PRO cc_start: 0.7310 (Cg_exo) cc_final: 0.6865 (Cg_endo) REVERT: D 142 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7705 (mtp180) outliers start: 78 outliers final: 29 residues processed: 238 average time/residue: 0.6137 time to fit residues: 158.9170 Evaluate side-chains 202 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 9 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 63 optimal weight: 0.0170 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.176186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141877 restraints weight = 26749.256| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.08 r_work: 0.3531 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 12958 Z= 0.376 Angle : 2.266 50.879 17641 Z= 1.334 Chirality : 0.403 6.432 1986 Planarity : 0.006 0.059 2318 Dihedral : 5.768 49.730 1836 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 6.37 % Allowed : 27.45 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -0.07 (0.21), residues: 1644 helix: 0.89 (0.18), residues: 856 sheet: -0.44 (0.40), residues: 176 loop : -1.21 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 48 TYR 0.018 0.002 TYR D 38 PHE 0.034 0.002 PHE B 73 TRP 0.010 0.002 TRP B 269 HIS 0.011 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01082 / 0.38 (12952) covalent geometry : angle 2.04349 / 1.33 (17623) hydrogen bonds : bond 0.03946 / 2.66 ( 605) hydrogen bonds : angle 5.42511 / 3.76 ( 1772) metal coordination : bond 0.03338 / 1.74 ( 6) metal coordination : angle 30.70217 / 16.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7379 (t70) cc_final: 0.6871 (t0) REVERT: A 80 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6066 (ptpt) REVERT: A 107 ARG cc_start: 0.6201 (mmp80) cc_final: 0.5879 (mmt-90) REVERT: A 130 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6624 (mtm-85) REVERT: A 177 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6968 (tp) REVERT: A 358 ARG cc_start: 0.5993 (mpp-170) cc_final: 0.5501 (mpp-170) REVERT: B 98 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: C 32 THR cc_start: 0.8249 (m) cc_final: 0.7758 (p) REVERT: C 69 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7234 (tt0) REVERT: C 85 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5695 (mt) REVERT: C 107 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: C 140 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7520 (mtp180) REVERT: C 274 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: C 280 PRO cc_start: 0.7418 (Cg_exo) cc_final: 0.6955 (Cg_endo) REVERT: C 305 ASP cc_start: 0.7683 (m-30) cc_final: 0.7315 (m-30) REVERT: C 337 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7754 (mp) REVERT: D 34 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: D 142 ARG cc_start: 0.8050 (mtp-110) cc_final: 0.7737 (mtp180) outliers start: 74 outliers final: 28 residues processed: 243 average time/residue: 0.6654 time to fit residues: 174.4634 Evaluate side-chains 201 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139746 restraints weight = 26446.025| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.01 r_work: 0.3510 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 12958 Z= 0.387 Angle : 2.268 50.613 17641 Z= 1.335 Chirality : 0.404 6.438 1986 Planarity : 0.006 0.061 2318 Dihedral : 5.717 57.294 1828 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 6.44 % Allowed : 27.53 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -0.06 (0.21), residues: 1644 helix: 0.93 (0.18), residues: 849 sheet: -0.46 (0.41), residues: 176 loop : -1.23 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 423 TYR 0.020 0.002 TYR D 38 PHE 0.040 0.002 PHE B 73 TRP 0.011 0.002 TRP B 268 HIS 0.011 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01106 / 0.39 (12952) covalent geometry : angle 2.04746 / 1.33 (17623) hydrogen bonds : bond 0.03884 / 2.61 ( 605) hydrogen bonds : angle 5.40339 / 3.74 ( 1772) metal coordination : bond 0.03302 / 1.70 ( 6) metal coordination : angle 30.61467 / 16.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7475 (t70) cc_final: 0.6992 (t0) REVERT: A 80 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6000 (ptpt) REVERT: A 107 ARG cc_start: 0.6350 (mmp80) cc_final: 0.5979 (mmt-90) REVERT: A 120 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7068 (pt) REVERT: A 203 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6758 (ttm110) REVERT: A 358 ARG cc_start: 0.6155 (mpp-170) cc_final: 0.5600 (mpp-170) REVERT: B 98 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: B 134 ASP cc_start: 0.8384 (t0) cc_final: 0.8129 (t0) REVERT: C 32 THR cc_start: 0.8281 (m) cc_final: 0.7819 (p) REVERT: C 69 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7311 (tt0) REVERT: C 85 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5827 (mt) REVERT: C 107 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7466 (mmm-85) REVERT: C 140 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7514 (mtp180) REVERT: C 274 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: C 280 PRO cc_start: 0.7438 (Cg_exo) cc_final: 0.6992 (Cg_endo) REVERT: C 305 ASP cc_start: 0.7650 (m-30) cc_final: 0.7294 (m-30) REVERT: C 423 ARG cc_start: 0.6381 (mtm110) cc_final: 0.6155 (mtm180) REVERT: D 142 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7853 (mtm110) REVERT: D 182 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7126 (mmt) REVERT: D 315 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7150 (mpt90) outliers start: 75 outliers final: 35 residues processed: 234 average time/residue: 0.6163 time to fit residues: 156.4682 Evaluate side-chains 211 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 19 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 48 optimal weight: 0.0020 chunk 6 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137616 restraints weight = 23927.136| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.33 r_work: 0.3489 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 12958 Z= 0.368 Angle : 2.257 50.616 17641 Z= 1.330 Chirality : 0.402 6.404 1986 Planarity : 0.005 0.063 2318 Dihedral : 5.579 55.356 1827 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 6.13 % Allowed : 28.07 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.06 (0.21), residues: 1644 helix: 1.09 (0.18), residues: 848 sheet: -0.48 (0.41), residues: 176 loop : -1.24 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.017 0.002 TYR D 38 PHE 0.028 0.002 PHE B 73 TRP 0.010 0.002 TRP A 258 HIS 0.010 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.01069 / 0.37 (12952) covalent geometry : angle 2.03485 / 1.33 (17623) hydrogen bonds : bond 0.03548 / 2.38 ( 605) hydrogen bonds : angle 5.27334 / 3.66 ( 1772) metal coordination : bond 0.02606 / 1.39 ( 6) metal coordination : angle 30.65423 / 16.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7480 (t70) cc_final: 0.6989 (t0) REVERT: A 78 GLU cc_start: 0.6632 (mp0) cc_final: 0.5524 (mm-30) REVERT: A 80 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5817 (ptpt) REVERT: A 107 ARG cc_start: 0.6353 (OUTLIER) cc_final: 0.5967 (mmt-90) REVERT: A 130 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6605 (mtm-85) REVERT: A 135 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.5006 (p90) REVERT: A 203 ARG cc_start: 0.6968 (ttp-110) cc_final: 0.6742 (ttm110) REVERT: A 358 ARG cc_start: 0.6008 (mpp-170) cc_final: 0.5631 (mpp-170) REVERT: B 98 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6525 (mt-10) REVERT: B 134 ASP cc_start: 0.8328 (t0) cc_final: 0.8058 (t0) REVERT: B 417 MET cc_start: 0.6987 (mtm) cc_final: 0.6607 (ptp) REVERT: C 32 THR cc_start: 0.8160 (m) cc_final: 0.7593 (p) REVERT: C 69 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7200 (tt0) REVERT: C 107 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7483 (mmm-85) REVERT: C 140 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7505 (mtp180) REVERT: C 274 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: C 280 PRO cc_start: 0.7413 (Cg_exo) cc_final: 0.6980 (Cg_endo) REVERT: C 305 ASP cc_start: 0.7511 (m-30) cc_final: 0.7178 (m-30) REVERT: D 34 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: D 142 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7849 (mtp-110) REVERT: D 182 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7018 (mmt) REVERT: D 315 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7132 (mpt90) outliers start: 71 outliers final: 29 residues processed: 234 average time/residue: 0.6375 time to fit residues: 161.4554 Evaluate side-chains 207 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 0.9990 chunk 157 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 105 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 135 HIS ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 379 ASN D 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140179 restraints weight = 30650.773| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.36 r_work: 0.3508 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 12958 Z= 0.364 Angle : 2.251 50.635 17641 Z= 1.328 Chirality : 0.402 6.366 1986 Planarity : 0.005 0.065 2318 Dihedral : 5.315 59.400 1824 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 5.37 % Allowed : 28.60 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.15 (0.21), residues: 1644 helix: 1.18 (0.18), residues: 848 sheet: -0.48 (0.42), residues: 169 loop : -1.21 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 423 TYR 0.018 0.002 TYR D 38 PHE 0.022 0.002 PHE B 73 TRP 0.010 0.001 TRP A 258 HIS 0.013 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.01064 / 0.36 (12952) covalent geometry : angle 2.02860 / 1.33 (17623) hydrogen bonds : bond 0.03367 / 2.25 ( 605) hydrogen bonds : angle 5.16735 / 3.59 ( 1772) metal coordination : bond 0.03069 / 1.57 ( 6) metal coordination : angle 30.63327 / 16.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7356 (t70) cc_final: 0.6868 (t0) REVERT: A 78 GLU cc_start: 0.6535 (mp0) cc_final: 0.5409 (mm-30) REVERT: A 80 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.5841 (ptpt) REVERT: A 85 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.2782 (pp) REVERT: A 107 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5853 (mmt-90) REVERT: A 130 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6367 (mtm-85) REVERT: A 203 ARG cc_start: 0.6925 (ttp-110) cc_final: 0.6701 (ttm110) REVERT: A 238 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6252 (mtp180) REVERT: A 358 ARG cc_start: 0.5837 (mpp-170) cc_final: 0.5529 (mpp-170) REVERT: B 98 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: B 134 ASP cc_start: 0.8127 (t0) cc_final: 0.7911 (t0) REVERT: B 417 MET cc_start: 0.6912 (mtm) cc_final: 0.6656 (ptp) REVERT: C 32 THR cc_start: 0.7942 (m) cc_final: 0.7435 (p) REVERT: C 69 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7168 (tt0) REVERT: C 107 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: C 122 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8004 (tt) REVERT: C 140 ARG cc_start: 0.7807 (mtm180) cc_final: 0.7445 (mtp180) REVERT: C 177 LEU cc_start: 0.7479 (mt) cc_final: 0.7080 (mm) REVERT: C 274 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: C 280 PRO cc_start: 0.7105 (Cg_exo) cc_final: 0.6668 (Cg_endo) REVERT: C 337 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7652 (mp) REVERT: D 142 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7572 (mtm110) REVERT: D 315 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6907 (mpt90) outliers start: 61 outliers final: 29 residues processed: 223 average time/residue: 0.5744 time to fit residues: 139.2810 Evaluate side-chains 202 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 0.6980 chunk 136 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 56 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS D 34 GLN D 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140062 restraints weight = 28131.220| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.30 r_work: 0.3499 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 12958 Z= 0.369 Angle : 2.254 50.607 17641 Z= 1.329 Chirality : 0.402 6.397 1986 Planarity : 0.005 0.067 2318 Dihedral : 5.265 56.903 1824 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 5.21 % Allowed : 28.30 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.12 (0.21), residues: 1644 helix: 1.18 (0.18), residues: 849 sheet: -0.53 (0.41), residues: 169 loop : -1.26 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 365 TYR 0.019 0.002 TYR D 38 PHE 0.026 0.002 PHE B 73 TRP 0.009 0.002 TRP A 258 HIS 0.012 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.01073 / 0.37 (12952) covalent geometry : angle 2.03241 / 1.33 (17623) hydrogen bonds : bond 0.03443 / 2.30 ( 605) hydrogen bonds : angle 5.14406 / 3.58 ( 1772) metal coordination : bond 0.02788 / 1.43 ( 6) metal coordination : angle 30.59207 / 16.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7444 (t70) cc_final: 0.7034 (t0) REVERT: A 78 GLU cc_start: 0.6612 (mp0) cc_final: 0.5427 (mm-30) REVERT: A 80 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5995 (ptpt) REVERT: A 85 LEU cc_start: 0.3982 (OUTLIER) cc_final: 0.2997 (pp) REVERT: A 107 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5963 (mmt-90) REVERT: A 130 ARG cc_start: 0.7149 (mtm-85) cc_final: 0.6391 (mtm-85) REVERT: A 135 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.5002 (p90) REVERT: A 203 ARG cc_start: 0.6917 (ttp-110) cc_final: 0.6681 (ttm110) REVERT: A 238 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6516 (mtp180) REVERT: A 358 ARG cc_start: 0.6051 (mpp-170) cc_final: 0.5727 (mpp-170) REVERT: B 134 ASP cc_start: 0.8330 (t0) cc_final: 0.8067 (t0) REVERT: B 414 LEU cc_start: 0.7824 (mt) cc_final: 0.7597 (mt) REVERT: B 417 MET cc_start: 0.6934 (mtm) cc_final: 0.6703 (ptp) REVERT: C 32 THR cc_start: 0.8157 (m) cc_final: 0.7566 (p) REVERT: C 69 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7246 (tt0) REVERT: C 107 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7489 (mmm-85) REVERT: C 140 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7577 (mtp180) REVERT: C 177 LEU cc_start: 0.7633 (mt) cc_final: 0.7234 (mm) REVERT: C 274 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: C 280 PRO cc_start: 0.7296 (Cg_exo) cc_final: 0.6870 (Cg_endo) REVERT: D 34 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: D 315 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7085 (mpt90) outliers start: 58 outliers final: 33 residues processed: 215 average time/residue: 0.5564 time to fit residues: 129.9844 Evaluate side-chains 203 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 0.0010 chunk 56 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS D 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.175411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140424 restraints weight = 27063.091| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.20 r_work: 0.3518 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 12958 Z= 0.366 Angle : 2.253 50.575 17641 Z= 1.328 Chirality : 0.402 6.389 1986 Planarity : 0.005 0.058 2318 Dihedral : 5.198 53.466 1824 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.81 % Favored : 97.07 % Rotamer: Outliers : 5.21 % Allowed : 28.14 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.15 (0.21), residues: 1644 helix: 1.21 (0.18), residues: 849 sheet: -0.52 (0.41), residues: 169 loop : -1.25 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 423 TYR 0.019 0.002 TYR D 38 PHE 0.023 0.002 PHE B 73 TRP 0.009 0.002 TRP A 258 HIS 0.012 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01068 / 0.37 (12952) covalent geometry : angle 2.03042 / 1.33 (17623) hydrogen bonds : bond 0.03361 / 2.24 ( 605) hydrogen bonds : angle 5.11110 / 3.55 ( 1772) metal coordination : bond 0.02579 / 1.34 ( 6) metal coordination : angle 30.60236 / 16.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7422 (t70) cc_final: 0.6946 (t0) REVERT: A 78 GLU cc_start: 0.6570 (mp0) cc_final: 0.5332 (mm-30) REVERT: A 80 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5654 (ptpt) REVERT: A 85 LEU cc_start: 0.3790 (OUTLIER) cc_final: 0.2863 (pp) REVERT: A 107 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5841 (mmt-90) REVERT: A 130 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6393 (mtm-85) REVERT: A 135 HIS cc_start: 0.6688 (OUTLIER) cc_final: 0.4998 (p90) REVERT: A 165 VAL cc_start: 0.8251 (t) cc_final: 0.7813 (m) REVERT: A 203 ARG cc_start: 0.6879 (ttp-110) cc_final: 0.6643 (ttm110) REVERT: A 358 ARG cc_start: 0.6002 (mpp-170) cc_final: 0.5324 (mpp-170) REVERT: B 98 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: B 134 ASP cc_start: 0.8245 (t0) cc_final: 0.8029 (t0) REVERT: B 417 MET cc_start: 0.6914 (mtm) cc_final: 0.6688 (ptp) REVERT: C 32 THR cc_start: 0.8117 (m) cc_final: 0.7521 (p) REVERT: C 69 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7223 (tt0) REVERT: C 107 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7457 (mmm-85) REVERT: C 140 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7564 (mtp180) REVERT: C 177 LEU cc_start: 0.7561 (mt) cc_final: 0.7168 (mm) REVERT: C 274 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: C 280 PRO cc_start: 0.7186 (Cg_exo) cc_final: 0.6761 (Cg_endo) REVERT: D 315 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7014 (mpt90) outliers start: 58 outliers final: 35 residues processed: 213 average time/residue: 0.5498 time to fit residues: 127.3846 Evaluate side-chains 210 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 127 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 136 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 379 ASN D 34 GLN D 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140809 restraints weight = 27622.991| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.40 r_work: 0.3457 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 12958 Z= 0.365 Angle : 2.251 50.583 17641 Z= 1.328 Chirality : 0.402 6.389 1986 Planarity : 0.005 0.058 2318 Dihedral : 5.119 46.763 1824 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.50 % Favored : 97.37 % Rotamer: Outliers : 4.45 % Allowed : 28.76 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.19 (0.21), residues: 1644 helix: 1.24 (0.18), residues: 850 sheet: -0.56 (0.42), residues: 169 loop : -1.21 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 48 TYR 0.018 0.002 TYR D 38 PHE 0.030 0.002 PHE B 73 TRP 0.010 0.002 TRP B 6 HIS 0.011 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01065 / 0.37 (12952) covalent geometry : angle 2.02829 / 1.33 (17623) hydrogen bonds : bond 0.03306 / 2.20 ( 605) hydrogen bonds : angle 5.08216 / 3.53 ( 1772) metal coordination : bond 0.02788 / 1.41 ( 6) metal coordination : angle 30.61978 / 16.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7356 (t70) cc_final: 0.6969 (t0) REVERT: A 78 GLU cc_start: 0.6639 (mp0) cc_final: 0.5456 (mm-30) REVERT: A 80 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5718 (ptpt) REVERT: A 85 LEU cc_start: 0.3601 (OUTLIER) cc_final: 0.2817 (pp) REVERT: A 107 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5878 (mmt-90) REVERT: A 130 ARG cc_start: 0.7068 (mtm-85) cc_final: 0.6438 (mtm-85) REVERT: A 135 HIS cc_start: 0.6617 (OUTLIER) cc_final: 0.4924 (p90) REVERT: A 165 VAL cc_start: 0.8238 (t) cc_final: 0.7815 (m) REVERT: A 203 ARG cc_start: 0.6816 (ttp-110) cc_final: 0.6590 (ttm110) REVERT: B 134 ASP cc_start: 0.8148 (t0) cc_final: 0.7945 (t0) REVERT: C 32 THR cc_start: 0.7970 (m) cc_final: 0.7453 (p) REVERT: C 69 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7228 (tt0) REVERT: C 107 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7379 (mmm-85) REVERT: C 140 ARG cc_start: 0.7822 (mtm180) cc_final: 0.7489 (mtp180) REVERT: C 177 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7192 (mm) REVERT: C 274 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: C 280 PRO cc_start: 0.7069 (Cg_exo) cc_final: 0.6642 (Cg_endo) REVERT: D 34 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: D 73 PHE cc_start: 0.8200 (t80) cc_final: 0.7989 (t80) outliers start: 48 outliers final: 32 residues processed: 205 average time/residue: 0.5673 time to fit residues: 126.7542 Evaluate side-chains 201 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 114 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 95 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 307 GLN D 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141102 restraints weight = 24862.848| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.20 r_work: 0.3513 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 12958 Z= 0.377 Angle : 2.334 59.033 17641 Z= 1.379 Chirality : 0.402 6.390 1986 Planarity : 0.005 0.058 2318 Dihedral : 5.124 46.725 1823 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.31 % Rotamer: Outliers : 4.06 % Allowed : 29.52 % Favored : 66.41 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.06 % 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: 0.19 (0.21), residues: 1644 helix: 1.23 (0.18), residues: 850 sheet: -0.56 (0.42), residues: 169 loop : -1.21 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 48 TYR 0.015 0.002 TYR D 38 PHE 0.029 0.002 PHE B 73 TRP 0.009 0.002 TRP A 258 HIS 0.011 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01083 / 0.38 (12952) covalent geometry : angle 2.12004 / 1.38 (17623) hydrogen bonds : bond 0.03310 / 2.21 ( 605) hydrogen bonds : angle 5.08371 / 3.53 ( 1772) metal coordination : bond 0.02687 / 1.36 ( 6) metal coordination : angle 30.61775 / 16.73 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7439 (t70) cc_final: 0.7043 (t0) REVERT: A 78 GLU cc_start: 0.6709 (mp0) cc_final: 0.5515 (mm-30) REVERT: A 80 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5723 (ptpt) REVERT: A 85 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.2870 (pp) REVERT: A 107 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5954 (mmt-90) REVERT: A 130 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6540 (mtm-85) REVERT: A 135 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.4946 (p90) REVERT: A 165 VAL cc_start: 0.8275 (t) cc_final: 0.7871 (m) REVERT: A 203 ARG cc_start: 0.6841 (ttp-110) cc_final: 0.6612 (ttm110) REVERT: B 134 ASP cc_start: 0.8292 (t0) cc_final: 0.8047 (t0) REVERT: C 32 THR cc_start: 0.8116 (m) cc_final: 0.7544 (p) REVERT: C 69 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7301 (tt0) REVERT: C 107 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7423 (mmm-85) REVERT: C 140 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7551 (mtp180) REVERT: C 177 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7293 (mm) REVERT: C 274 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: C 280 PRO cc_start: 0.7269 (Cg_exo) cc_final: 0.6854 (Cg_endo) REVERT: D 73 PHE cc_start: 0.8225 (t80) cc_final: 0.8009 (t80) outliers start: 43 outliers final: 33 residues processed: 195 average time/residue: 0.5365 time to fit residues: 114.0453 Evaluate side-chains 200 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.0060 chunk 157 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140906 restraints weight = 26079.258| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.22 r_work: 0.3510 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 12958 Z= 0.377 Angle : 2.334 59.032 17641 Z= 1.379 Chirality : 0.402 6.390 1986 Planarity : 0.005 0.058 2318 Dihedral : 5.124 46.725 1823 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.31 % Rotamer: Outliers : 3.91 % Allowed : 29.68 % Favored : 66.41 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.06 % 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: 0.19 (0.21), residues: 1644 helix: 1.23 (0.18), residues: 850 sheet: -0.56 (0.42), residues: 169 loop : -1.21 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 48 TYR 0.015 0.002 TYR D 38 PHE 0.029 0.002 PHE B 73 TRP 0.009 0.002 TRP A 258 HIS 0.011 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.01083 / 0.38 (12952) covalent geometry : angle 2.12004 / 1.38 (17623) hydrogen bonds : bond 0.03310 / 2.21 ( 605) hydrogen bonds : angle 5.08371 / 3.53 ( 1772) metal coordination : bond 0.02687 / 1.36 ( 6) metal coordination : angle 30.61775 / 16.73 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.41 seconds wall clock time: 85 minutes 56.50 seconds (5156.50 seconds total)