Starting phenix.real_space_refine on Thu Sep 18 16:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9emm_19820/09_2025/9emm_19820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9emm_19820/09_2025/9emm_19820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9emm_19820/09_2025/9emm_19820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9emm_19820/09_2025/9emm_19820.map" model { file = "/net/cci-nas-00/data/ceres_data/9emm_19820/09_2025/9emm_19820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9emm_19820/09_2025/9emm_19820.cif" } resolution = 3.7 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= 0.021 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 11670 2.51 5 N 3247 2.21 5 O 3394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18401 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3947 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 462} Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain breaks: 4 Chain: "C" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3947 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 462} Chain: "D" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3947 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 462} Chain: "B" Number of atoms: 4057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4057 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 474} Time building chain proxies: 4.63, per 1000 atoms: 0.25 Number of scatterers: 18401 At special positions: 0 Unit cell: (116.424, 125.664, 149.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3394 8.00 N 3247 7.00 C 11670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 416 " distance=2.03 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: 1.65 Conformation dependent library (CDL) restraints added in 749.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 40.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 Proline residue: A 40 - end of helix Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.864A pdb=" N ASN A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.544A pdb=" N TYR A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 124 No H-bonds generated for 'chain 'A' and resid 123 through 124' Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.977A pdb=" N ARG A 128 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.799A pdb=" N VAL A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.641A pdb=" N CYS A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.502A pdb=" N ILE A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.927A pdb=" N HIS A 385 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.593A pdb=" N SER A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 457 through 475 Proline residue: A 468 - end of helix removed outlier: 3.654A pdb=" N ALA A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.835A pdb=" N MET A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.687A pdb=" N GLU A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 51 removed outlier: 4.072A pdb=" N SER E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU E 45 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.517A pdb=" N ARG E 251 " --> pdb=" O GLY E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 282 removed outlier: 4.066A pdb=" N LEU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 293 Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.845A pdb=" N ALA E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 removed outlier: 4.666A pdb=" N SER E 312 " --> pdb=" O GLU E 309 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 314 " --> pdb=" O ARG E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 343 removed outlier: 3.561A pdb=" N TYR E 335 " --> pdb=" O GLN E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 440 through 451 removed outlier: 3.833A pdb=" N LEU E 444 " --> pdb=" O ASN E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 473 removed outlier: 3.602A pdb=" N ASP E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 107 through 126 removed outlier: 3.925A pdb=" N TYR C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.539A pdb=" N ALA C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 184 Processing helix chain 'C' and resid 200 through 213 removed outlier: 4.267A pdb=" N VAL C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 278 through 289 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.679A pdb=" N SER C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 456 through 474 Proline residue: C 468 - end of helix Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.736A pdb=" N GLU C 496 " --> pdb=" O PRO C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 48 Proline residue: D 40 - end of helix Processing helix chain 'D' and resid 66 through 81 Processing helix chain 'D' and resid 87 through 95 Processing helix chain 'D' and resid 107 through 126 Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.659A pdb=" N ALA D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.782A pdb=" N LYS D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 161' Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.536A pdb=" N SER D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.596A pdb=" N SER D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 268 removed outlier: 3.902A pdb=" N LEU D 263 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 removed outlier: 3.793A pdb=" N ILE D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.574A pdb=" N GLU D 324 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 436 through 448 Processing helix chain 'D' and resid 449 through 453 removed outlier: 4.458A pdb=" N LEU D 452 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 475 removed outlier: 3.603A pdb=" N VAL D 459 " --> pdb=" O ARG D 455 " (cutoff:3.500A) Proline residue: D 468 - end of helix removed outlier: 3.571A pdb=" N ALA D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.902A pdb=" N GLU D 496 " --> pdb=" O PRO D 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 5.132A pdb=" N VAL B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Proline residue: B 40 - end of helix removed outlier: 3.910A pdb=" N GLU B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.525A pdb=" N ILE B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 153 removed outlier: 3.526A pdb=" N LEU B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.672A pdb=" N VAL B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 4.045A pdb=" N GLN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 3.808A pdb=" N SER B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 4.122A pdb=" N ARG B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.879A pdb=" N LEU B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.881A pdb=" N ARG B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.865A pdb=" N ARG B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 removed outlier: 3.985A pdb=" N VAL B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 475 removed outlier: 3.707A pdb=" N ALA B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 removed outlier: 4.082A pdb=" N MET B 482 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.695A pdb=" N GLU B 496 " --> pdb=" O PRO B 492 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.599A pdb=" N VAL A 58 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 134 removed outlier: 3.507A pdb=" N ARG A 162 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.868A pdb=" N GLY A 358 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 228 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 232 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER A 366 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.868A pdb=" N GLY A 358 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 228 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 232 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 391 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.522A pdb=" N PHE A 336 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 485 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 71 removed outlier: 3.874A pdb=" N ILE E 172 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL E 71 " --> pdb=" O ILE E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 235 through 237 removed outlier: 6.616A pdb=" N VAL E 236 " --> pdb=" O ILE E 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 347 through 353 removed outlier: 6.836A pdb=" N GLN E 363 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR E 350 " --> pdb=" O LYS E 361 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS E 361 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR E 352 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE E 359 " --> pdb=" O TYR E 352 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU E 376 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 364 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE E 372 " --> pdb=" O PHE E 364 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 320 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN E 319 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU E 396 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER E 321 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU E 394 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP E 323 " --> pdb=" O ILE E 392 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E 394 " --> pdb=" O LEU E 409 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL E 408 " --> pdb=" O GLN E 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 60 removed outlier: 6.543A pdb=" N LEU C 24 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N PHE C 60 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 26 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 23 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TYR C 134 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR C 25 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N VAL C 164 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE C 133 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 163 " --> pdb=" O TYR C 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 291 through 293 removed outlier: 3.532A pdb=" N ARG C 292 " --> pdb=" O MET C 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 355 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 229 " --> pdb=" O TYR C 354 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ARG C 356 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE C 231 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS C 228 " --> pdb=" O GLN C 371 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 232 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 365 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 391 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 404 " --> pdb=" O MET C 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 307 through 309 removed outlier: 6.590A pdb=" N GLN C 307 " --> pdb=" O TYR C 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.120A pdb=" N VAL D 57 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE D 23 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR D 134 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR D 25 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N VAL D 164 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE D 133 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 163 " --> pdb=" O TYR D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 291 through 292 removed outlier: 7.152A pdb=" N GLN D 371 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL D 229 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA D 369 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE D 231 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU D 367 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 391 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB7, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AB8, first strand: chain 'D' and resid 401 through 402 Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 25 removed outlier: 3.544A pdb=" N VAL B 132 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 131 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 164 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 133 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TYR B 193 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 163 " --> pdb=" O TYR B 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.154A pdb=" N GLY B 59 " --> pdb=" O PHE B 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 291 through 293 removed outlier: 3.520A pdb=" N LEU B 339 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 355 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N TYR B 354 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 229 " --> pdb=" O TYR B 354 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG B 356 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 231 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLN B 371 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 229 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 369 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 231 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU B 367 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL B 233 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 365 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 368 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 391 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY B 401 " --> pdb=" O ARG B 395 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 408 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 307 through 309 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 312 619 hydrogen bonds defined for protein. 1722 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: 2.82 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6160 1.34 - 1.46: 3809 1.46 - 1.58: 8708 1.58 - 1.70: 2 1.70 - 1.82: 156 Bond restraints: 18835 Sorted by residual: bond pdb=" N ILE D 396 " pdb=" CA ILE D 396 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.06e-02 8.90e+03 1.37e+01 bond pdb=" N ILE B 396 " pdb=" CA ILE B 396 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" N ARG B 395 " pdb=" CA ARG B 395 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.20e-02 6.94e+03 7.59e+00 bond pdb=" CA ALA C 251 " pdb=" C ALA C 251 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" N GLN D 397 " pdb=" CA GLN D 397 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.40e+00 ... (remaining 18830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 25178 2.29 - 4.59: 316 4.59 - 6.88: 35 6.88 - 9.18: 10 9.18 - 11.47: 2 Bond angle restraints: 25541 Sorted by residual: angle pdb=" CA PRO E 74 " pdb=" N PRO E 74 " pdb=" CD PRO E 74 " ideal model delta sigma weight residual 112.00 103.89 8.11 1.40e+00 5.10e-01 3.35e+01 angle pdb=" CA PRO D 158 " pdb=" N PRO D 158 " pdb=" CD PRO D 158 " ideal model delta sigma weight residual 112.00 104.44 7.56 1.40e+00 5.10e-01 2.92e+01 angle pdb=" C GLU C 240 " pdb=" CA GLU C 240 " pdb=" CB GLU C 240 " ideal model delta sigma weight residual 115.89 110.34 5.55 1.32e+00 5.74e-01 1.77e+01 angle pdb=" N ILE D 396 " pdb=" CA ILE D 396 " pdb=" C ILE D 396 " ideal model delta sigma weight residual 112.12 109.13 2.99 8.40e-01 1.42e+00 1.26e+01 angle pdb=" N ASN D 399 " pdb=" CA ASN D 399 " pdb=" C ASN D 399 " ideal model delta sigma weight residual 111.92 107.40 4.52 1.34e+00 5.57e-01 1.14e+01 ... (remaining 25536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9500 17.75 - 35.50: 1367 35.50 - 53.25: 400 53.25 - 70.99: 72 70.99 - 88.74: 23 Dihedral angle restraints: 11362 sinusoidal: 4704 harmonic: 6658 Sorted by residual: dihedral pdb=" CB CYS E 410 " pdb=" SG CYS E 410 " pdb=" SG CYS E 416 " pdb=" CB CYS E 416 " ideal model delta sinusoidal sigma weight residual 93.00 147.61 -54.61 1 1.00e+01 1.00e-02 4.04e+01 dihedral pdb=" SG CYS E 410 " pdb=" CB CYS E 416 " pdb=" SG CYS E 416 " pdb=" CA CYS E 416 " ideal model delta sinusoidal sigma weight residual -73.00 2.55 -75.55 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" CA ASP B 196 " pdb=" C ASP B 196 " pdb=" N HIS B 197 " pdb=" CA HIS B 197 " ideal model delta harmonic sigma weight residual -180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 11359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1967 0.043 - 0.087: 572 0.087 - 0.130: 172 0.130 - 0.174: 19 0.174 - 0.217: 5 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CA PRO D 158 " pdb=" N PRO D 158 " pdb=" C PRO D 158 " pdb=" CB PRO D 158 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE B 396 " pdb=" N ILE B 396 " pdb=" C ILE B 396 " pdb=" CB ILE B 396 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA THR A 467 " pdb=" N THR A 467 " pdb=" C THR A 467 " pdb=" CB THR A 467 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 2732 not shown) Planarity restraints: 3365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 157 " -0.084 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO D 158 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO D 158 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 158 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 73 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO E 74 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 456 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ALA C 456 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA C 456 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP C 457 " 0.011 2.00e-02 2.50e+03 ... (remaining 3362 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 285 2.65 - 3.21: 16680 3.21 - 3.77: 26264 3.77 - 4.34: 33196 4.34 - 4.90: 55895 Nonbonded interactions: 132320 Sorted by model distance: nonbonded pdb=" NE2 GLN D 397 " pdb=" CD PRO D 398 " model vdw 2.087 3.520 nonbonded pdb=" CG GLN D 397 " pdb=" CD PRO D 398 " model vdw 2.189 3.840 nonbonded pdb=" O ARG A 63 " pdb=" OH TYR A 100 " model vdw 2.197 3.040 nonbonded pdb=" OG SER D 87 " pdb=" OD2 ASP D 89 " model vdw 2.205 3.040 nonbonded pdb=" O SER B 248 " pdb=" OG SER B 248 " model vdw 2.220 3.040 ... (remaining 132315 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' selection = (chain 'B' and resid 17 through 509) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.005 0.107 18836 Z= 0.209 Angle : 0.654 11.474 25543 Z= 0.344 Chirality : 0.045 0.217 2735 Planarity : 0.005 0.123 3365 Dihedral : 18.074 88.743 7065 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.63 % Favored : 89.29 % Rotamer: Outliers : 0.25 % Allowed : 35.69 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.18), residues: 2287 helix: 0.72 (0.21), residues: 720 sheet: -1.45 (0.28), residues: 379 loop : -2.24 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 162 TYR 0.019 0.001 TYR A 111 PHE 0.019 0.001 PHE B 336 TRP 0.024 0.001 TRP E 238 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00486 (18835) covalent geometry : angle 0.65377 (25541) SS BOND : bond 0.00175 ( 1) SS BOND : angle 1.15415 ( 2) hydrogen bonds : bond 0.24715 ( 607) hydrogen bonds : angle 7.07024 ( 1722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: C 184 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7823 (tm-30) outliers start: 5 outliers final: 5 residues processed: 188 average time/residue: 0.1293 time to fit residues: 38.4976 Evaluate side-chains 186 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 181 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 198 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 0.0870 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 390 ASN D 397 GLN B 126 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113093 restraints weight = 28552.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111922 restraints weight = 19047.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112720 restraints weight = 17818.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113029 restraints weight = 16250.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113162 restraints weight = 15717.794| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18836 Z= 0.155 Angle : 0.614 15.982 25543 Z= 0.315 Chirality : 0.044 0.211 2735 Planarity : 0.005 0.065 3365 Dihedral : 4.667 59.380 2551 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.44 % Favored : 90.47 % Rotamer: Outliers : 3.41 % Allowed : 32.43 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.18), residues: 2287 helix: 0.65 (0.20), residues: 755 sheet: -1.33 (0.28), residues: 403 loop : -2.27 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.017 0.001 TYR A 111 PHE 0.014 0.001 PHE B 336 TRP 0.013 0.001 TRP E 238 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00359 (18835) covalent geometry : angle 0.61413 (25541) SS BOND : bond 0.00347 ( 1) SS BOND : angle 0.91096 ( 2) hydrogen bonds : bond 0.05265 ( 607) hydrogen bonds : angle 5.27259 ( 1722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: E 70 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8059 (tt) REVERT: E 238 TRP cc_start: 0.7539 (t-100) cc_final: 0.7122 (t-100) REVERT: E 358 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: C 154 MET cc_start: 0.7727 (mpp) cc_final: 0.7293 (mpp) REVERT: C 184 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7795 (tm-30) REVERT: D 22 LEU cc_start: 0.9045 (pt) cc_final: 0.8789 (pt) REVERT: D 68 ASP cc_start: 0.8041 (t0) cc_final: 0.7728 (t0) REVERT: D 504 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8274 (mtt90) REVERT: B 240 GLU cc_start: 0.5917 (tm-30) cc_final: 0.5295 (pt0) REVERT: B 332 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8211 (m) outliers start: 67 outliers final: 24 residues processed: 257 average time/residue: 0.1328 time to fit residues: 53.7687 Evaluate side-chains 215 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 404 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 219 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.157759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110373 restraints weight = 28834.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112921 restraints weight = 21830.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113543 restraints weight = 16267.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113909 restraints weight = 14330.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114046 restraints weight = 14676.022| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18836 Z= 0.122 Angle : 0.569 9.882 25543 Z= 0.292 Chirality : 0.042 0.211 2735 Planarity : 0.004 0.048 3365 Dihedral : 4.476 57.813 2547 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.79 % Favored : 91.12 % Rotamer: Outliers : 3.21 % Allowed : 32.38 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.18), residues: 2287 helix: 0.73 (0.20), residues: 760 sheet: -1.02 (0.29), residues: 373 loop : -2.31 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 36 TYR 0.019 0.001 TYR A 111 PHE 0.011 0.001 PHE C 264 TRP 0.011 0.001 TRP C 91 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00273 (18835) covalent geometry : angle 0.56925 (25541) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.51538 ( 2) hydrogen bonds : bond 0.04308 ( 607) hydrogen bonds : angle 4.94253 ( 1722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.752 Fit side-chains REVERT: E 70 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8049 (tt) REVERT: E 299 GLU cc_start: 0.9064 (tp30) cc_final: 0.8863 (tm-30) REVERT: E 358 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: C 184 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7709 (tm-30) REVERT: D 22 LEU cc_start: 0.9042 (pt) cc_final: 0.8786 (pt) REVERT: D 68 ASP cc_start: 0.7903 (t0) cc_final: 0.7615 (t0) REVERT: D 504 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8354 (mtt90) REVERT: B 104 ASN cc_start: 0.7285 (t0) cc_final: 0.6783 (t0) REVERT: B 240 GLU cc_start: 0.5858 (tm-30) cc_final: 0.5406 (pt0) outliers start: 63 outliers final: 33 residues processed: 247 average time/residue: 0.1328 time to fit residues: 51.2091 Evaluate side-chains 218 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 97 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 255 HIS ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.155617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107848 restraints weight = 28898.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109420 restraints weight = 20263.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109932 restraints weight = 16516.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110203 restraints weight = 14189.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110500 restraints weight = 14267.017| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18836 Z= 0.182 Angle : 0.604 11.842 25543 Z= 0.312 Chirality : 0.044 0.206 2735 Planarity : 0.004 0.053 3365 Dihedral : 4.590 57.034 2547 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.97 % Favored : 89.90 % Rotamer: Outliers : 4.33 % Allowed : 31.42 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.18), residues: 2287 helix: 0.68 (0.20), residues: 767 sheet: -1.29 (0.28), residues: 400 loop : -2.30 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.018 0.001 TYR A 111 PHE 0.018 0.001 PHE B 336 TRP 0.013 0.001 TRP C 348 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00434 (18835) covalent geometry : angle 0.60383 (25541) SS BOND : bond 0.00289 ( 1) SS BOND : angle 0.76768 ( 2) hydrogen bonds : bond 0.04765 ( 607) hydrogen bonds : angle 4.89753 ( 1722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 191 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: E 70 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7911 (tt) REVERT: E 358 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: C 55 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7761 (pt) REVERT: C 99 PHE cc_start: 0.8610 (m-10) cc_final: 0.8289 (m-10) REVERT: C 154 MET cc_start: 0.7678 (mpp) cc_final: 0.7234 (mpp) REVERT: C 184 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7862 (tm-30) REVERT: C 496 GLU cc_start: 0.8295 (tp30) cc_final: 0.7883 (tp30) REVERT: D 22 LEU cc_start: 0.9048 (pt) cc_final: 0.8839 (pt) REVERT: D 68 ASP cc_start: 0.8087 (t0) cc_final: 0.7772 (t0) REVERT: D 504 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8354 (mtt90) REVERT: B 104 ASN cc_start: 0.7401 (t0) cc_final: 0.6824 (t0) REVERT: B 199 LEU cc_start: 0.7735 (tp) cc_final: 0.7450 (tt) REVERT: B 240 GLU cc_start: 0.6009 (tm-30) cc_final: 0.5761 (pt0) REVERT: B 332 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8332 (m) outliers start: 85 outliers final: 53 residues processed: 260 average time/residue: 0.1218 time to fit residues: 50.4121 Evaluate side-chains 242 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 139 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.153796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104574 restraints weight = 28974.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107340 restraints weight = 19754.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108531 restraints weight = 15853.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109606 restraints weight = 13036.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109926 restraints weight = 12428.591| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18836 Z= 0.227 Angle : 0.647 12.389 25543 Z= 0.336 Chirality : 0.045 0.208 2735 Planarity : 0.005 0.057 3365 Dihedral : 4.748 56.379 2547 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.32 % Favored : 89.55 % Rotamer: Outliers : 5.50 % Allowed : 30.30 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.18), residues: 2287 helix: 0.60 (0.20), residues: 765 sheet: -1.44 (0.27), residues: 416 loop : -2.40 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.018 0.001 TYR A 111 PHE 0.021 0.002 PHE B 336 TRP 0.016 0.001 TRP C 348 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00547 (18835) covalent geometry : angle 0.64655 (25541) SS BOND : bond 0.00259 ( 1) SS BOND : angle 0.77710 ( 2) hydrogen bonds : bond 0.05157 ( 607) hydrogen bonds : angle 4.99297 ( 1722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 193 time to evaluate : 0.770 Fit side-chains REVERT: A 228 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6851 (t-170) REVERT: A 347 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8484 (ttm170) REVERT: E 70 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7840 (tt) REVERT: E 358 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: C 55 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7765 (pt) REVERT: C 99 PHE cc_start: 0.8623 (m-10) cc_final: 0.8269 (m-10) REVERT: C 184 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7872 (tm-30) REVERT: D 68 ASP cc_start: 0.8095 (t0) cc_final: 0.7788 (t0) REVERT: D 149 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8279 (mm) REVERT: D 223 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.9025 (ptt90) REVERT: D 397 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6616 (pp30) REVERT: D 410 MET cc_start: 0.7656 (mmm) cc_final: 0.7334 (tpp) REVERT: B 104 ASN cc_start: 0.7405 (t0) cc_final: 0.6772 (t0) REVERT: B 240 GLU cc_start: 0.6169 (tm-30) cc_final: 0.5739 (tt0) REVERT: B 332 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8332 (m) outliers start: 108 outliers final: 71 residues processed: 284 average time/residue: 0.1359 time to fit residues: 61.1026 Evaluate side-chains 263 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 183 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 223 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 53 optimal weight: 40.0000 chunk 170 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.156138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108805 restraints weight = 28748.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110772 restraints weight = 19295.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111033 restraints weight = 15008.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111016 restraints weight = 14634.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111175 restraints weight = 14003.808| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18836 Z= 0.142 Angle : 0.597 12.946 25543 Z= 0.305 Chirality : 0.043 0.207 2735 Planarity : 0.004 0.059 3365 Dihedral : 4.612 55.672 2547 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.18 % Favored : 90.69 % Rotamer: Outliers : 4.38 % Allowed : 31.42 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.18), residues: 2287 helix: 0.69 (0.20), residues: 766 sheet: -1.31 (0.26), residues: 423 loop : -2.39 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.019 0.001 TYR A 111 PHE 0.013 0.001 PHE C 264 TRP 0.014 0.001 TRP E 238 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00333 (18835) covalent geometry : angle 0.59723 (25541) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.77414 ( 2) hydrogen bonds : bond 0.04120 ( 607) hydrogen bonds : angle 4.79397 ( 1722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 190 time to evaluate : 0.850 Fit side-chains REVERT: A 242 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8136 (mtm-85) REVERT: E 70 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7862 (tt) REVERT: E 358 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: C 55 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7733 (pt) REVERT: C 99 PHE cc_start: 0.8627 (m-10) cc_final: 0.8262 (m-10) REVERT: C 184 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7863 (tm-30) REVERT: C 410 MET cc_start: 0.8345 (tpp) cc_final: 0.8038 (tpt) REVERT: D 68 ASP cc_start: 0.8136 (t0) cc_final: 0.7828 (t0) REVERT: D 81 PHE cc_start: 0.7502 (m-10) cc_final: 0.7241 (m-10) REVERT: D 207 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (tt) REVERT: D 397 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6757 (pp30) REVERT: D 410 MET cc_start: 0.7669 (mmm) cc_final: 0.7274 (tpp) REVERT: D 504 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8450 (mtt90) REVERT: B 104 ASN cc_start: 0.7426 (t0) cc_final: 0.6730 (t0) REVERT: B 240 GLU cc_start: 0.6179 (tm-30) cc_final: 0.5845 (tt0) REVERT: B 313 MET cc_start: 0.7391 (tpp) cc_final: 0.7183 (tpp) REVERT: B 332 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8327 (m) outliers start: 86 outliers final: 53 residues processed: 261 average time/residue: 0.1375 time to fit residues: 56.4740 Evaluate side-chains 244 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 404 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 92 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107341 restraints weight = 28747.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110551 restraints weight = 19175.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111400 restraints weight = 15332.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112494 restraints weight = 12749.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112836 restraints weight = 12021.796| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18836 Z= 0.153 Angle : 0.607 14.781 25543 Z= 0.309 Chirality : 0.043 0.204 2735 Planarity : 0.004 0.057 3365 Dihedral : 4.590 55.465 2547 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.44 % Favored : 90.42 % Rotamer: Outliers : 4.23 % Allowed : 31.67 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.18), residues: 2287 helix: 0.68 (0.20), residues: 770 sheet: -1.32 (0.26), residues: 422 loop : -2.38 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.019 0.001 TYR A 111 PHE 0.016 0.001 PHE D 94 TRP 0.015 0.001 TRP E 238 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00364 (18835) covalent geometry : angle 0.60746 (25541) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.78868 ( 2) hydrogen bonds : bond 0.04197 ( 607) hydrogen bonds : angle 4.76178 ( 1722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 187 time to evaluate : 0.790 Fit side-chains REVERT: A 242 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8028 (mtm-85) REVERT: A 347 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8500 (ttm170) REVERT: E 70 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7839 (tt) REVERT: E 358 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: C 55 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7804 (pt) REVERT: C 99 PHE cc_start: 0.8620 (m-10) cc_final: 0.8257 (m-10) REVERT: C 184 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7899 (tm-30) REVERT: C 410 MET cc_start: 0.8322 (tpp) cc_final: 0.8106 (tpt) REVERT: D 68 ASP cc_start: 0.8119 (t0) cc_final: 0.7814 (t0) REVERT: D 207 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (tt) REVERT: D 397 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6579 (pp30) REVERT: D 410 MET cc_start: 0.7604 (mmm) cc_final: 0.7206 (tpp) REVERT: D 504 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8458 (mtt90) REVERT: B 104 ASN cc_start: 0.7451 (t0) cc_final: 0.6862 (t0) REVERT: B 105 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7222 (tpt) REVERT: B 240 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5895 (tt0) REVERT: B 332 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8309 (m) outliers start: 83 outliers final: 61 residues processed: 255 average time/residue: 0.1382 time to fit residues: 55.0292 Evaluate side-chains 254 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 166 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 HIS E 368 ASN ** B 197 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115180 restraints weight = 28313.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114100 restraints weight = 20723.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114757 restraints weight = 18321.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115052 restraints weight = 17717.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115334 restraints weight = 15371.991| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18836 Z= 0.114 Angle : 0.585 13.988 25543 Z= 0.294 Chirality : 0.042 0.215 2735 Planarity : 0.004 0.057 3365 Dihedral : 4.452 54.406 2547 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.39 % Rotamer: Outliers : 3.36 % Allowed : 32.23 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.18), residues: 2287 helix: 0.95 (0.20), residues: 744 sheet: -0.91 (0.27), residues: 403 loop : -2.46 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.019 0.001 TYR A 111 PHE 0.011 0.001 PHE C 264 TRP 0.019 0.001 TRP E 238 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00261 (18835) covalent geometry : angle 0.58465 (25541) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.82660 ( 2) hydrogen bonds : bond 0.03439 ( 607) hydrogen bonds : angle 4.60356 ( 1722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 201 time to evaluate : 0.759 Fit side-chains REVERT: E 70 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8088 (tt) REVERT: E 358 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: C 55 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7910 (pt) REVERT: C 75 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.7967 (ttp-110) REVERT: C 99 PHE cc_start: 0.8421 (m-10) cc_final: 0.8199 (m-10) REVERT: C 184 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7734 (tm-30) REVERT: D 68 ASP cc_start: 0.7961 (t0) cc_final: 0.7676 (t0) REVERT: D 201 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8147 (mmmm) REVERT: D 207 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8475 (tt) REVERT: D 504 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8525 (mtt90) REVERT: B 104 ASN cc_start: 0.7418 (t0) cc_final: 0.6879 (t0) REVERT: B 105 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7075 (tpt) REVERT: B 240 GLU cc_start: 0.6323 (tm-30) cc_final: 0.5862 (tt0) REVERT: B 332 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8240 (m) outliers start: 66 outliers final: 43 residues processed: 256 average time/residue: 0.1340 time to fit residues: 53.3730 Evaluate side-chains 238 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 44 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113327 restraints weight = 28420.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112197 restraints weight = 21288.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112816 restraints weight = 19179.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113500 restraints weight = 19049.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113483 restraints weight = 16389.685| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18836 Z= 0.173 Angle : 0.631 9.626 25543 Z= 0.322 Chirality : 0.044 0.204 2735 Planarity : 0.004 0.058 3365 Dihedral : 4.563 54.019 2547 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.97 % Favored : 89.94 % Rotamer: Outliers : 3.87 % Allowed : 32.18 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.18), residues: 2287 helix: 0.92 (0.20), residues: 747 sheet: -1.21 (0.26), residues: 432 loop : -2.43 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.018 0.001 TYR A 111 PHE 0.017 0.001 PHE B 336 TRP 0.022 0.001 TRP D 312 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00417 (18835) covalent geometry : angle 0.63070 (25541) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.88190 ( 2) hydrogen bonds : bond 0.04289 ( 607) hydrogen bonds : angle 4.68780 ( 1722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 191 time to evaluate : 0.715 Fit side-chains REVERT: E 70 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8140 (tt) REVERT: E 358 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: C 55 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7920 (pt) REVERT: C 75 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.7960 (ttp-110) REVERT: C 99 PHE cc_start: 0.8456 (m-10) cc_final: 0.8239 (m-10) REVERT: C 184 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7792 (tm-30) REVERT: D 68 ASP cc_start: 0.7962 (t0) cc_final: 0.7704 (t0) REVERT: D 149 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (mm) REVERT: D 201 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8190 (mmmm) REVERT: D 207 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8464 (tt) REVERT: D 504 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8512 (mtt90) REVERT: B 104 ASN cc_start: 0.7428 (t0) cc_final: 0.6904 (t0) REVERT: B 105 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7101 (tpt) REVERT: B 332 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8256 (m) outliers start: 76 outliers final: 58 residues processed: 252 average time/residue: 0.1305 time to fit residues: 51.6446 Evaluate side-chains 253 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 168 optimal weight: 0.0670 chunk 23 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108975 restraints weight = 28547.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110375 restraints weight = 19575.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110731 restraints weight = 15722.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110834 restraints weight = 14514.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111116 restraints weight = 14226.949| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18836 Z= 0.154 Angle : 0.631 15.130 25543 Z= 0.320 Chirality : 0.044 0.208 2735 Planarity : 0.004 0.058 3365 Dihedral : 4.447 35.415 2545 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.62 % Favored : 90.25 % Rotamer: Outliers : 3.67 % Allowed : 32.38 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.18), residues: 2287 helix: 0.93 (0.20), residues: 745 sheet: -1.21 (0.26), residues: 432 loop : -2.44 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.019 0.001 TYR A 111 PHE 0.013 0.001 PHE B 336 TRP 0.021 0.001 TRP E 238 HIS 0.016 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00368 (18835) covalent geometry : angle 0.63124 (25541) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.85431 ( 2) hydrogen bonds : bond 0.04044 ( 607) hydrogen bonds : angle 4.66678 ( 1722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 0.682 Fit side-chains REVERT: A 242 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8132 (mtm-85) REVERT: E 70 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7829 (tt) REVERT: E 228 MET cc_start: 0.6672 (tpt) cc_final: 0.6354 (tpt) REVERT: E 234 LYS cc_start: 0.4758 (OUTLIER) cc_final: 0.4390 (pttm) REVERT: E 358 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: C 55 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7792 (pt) REVERT: C 75 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.7860 (ttp-110) REVERT: C 99 PHE cc_start: 0.8631 (m-10) cc_final: 0.8295 (m-10) REVERT: D 68 ASP cc_start: 0.8041 (t0) cc_final: 0.7764 (t0) REVERT: D 201 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8142 (mmmm) REVERT: D 207 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8381 (tt) REVERT: D 410 MET cc_start: 0.7769 (mmm) cc_final: 0.7134 (tpp) REVERT: D 504 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8462 (mtt90) REVERT: B 104 ASN cc_start: 0.7509 (t0) cc_final: 0.6839 (t0) REVERT: B 105 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7257 (tpt) REVERT: B 332 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8380 (m) outliers start: 72 outliers final: 59 residues processed: 247 average time/residue: 0.1319 time to fit residues: 51.0007 Evaluate side-chains 253 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 ARG Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.156047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109181 restraints weight = 28590.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110620 restraints weight = 19461.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110827 restraints weight = 15422.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111094 restraints weight = 14681.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111214 restraints weight = 14247.377| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18836 Z= 0.158 Angle : 0.625 9.879 25543 Z= 0.319 Chirality : 0.044 0.208 2735 Planarity : 0.004 0.055 3365 Dihedral : 4.464 35.062 2545 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.10 % Favored : 89.77 % Rotamer: Outliers : 3.92 % Allowed : 32.13 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.18), residues: 2287 helix: 0.94 (0.20), residues: 744 sheet: -1.24 (0.26), residues: 432 loop : -2.45 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 162 TYR 0.019 0.001 TYR A 111 PHE 0.021 0.001 PHE A 141 TRP 0.018 0.001 TRP E 238 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00379 (18835) covalent geometry : angle 0.62547 (25541) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.90116 ( 2) hydrogen bonds : bond 0.04122 ( 607) hydrogen bonds : angle 4.67614 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.55 seconds wall clock time: 51 minutes 33.83 seconds (3093.83 seconds total)