Starting phenix.real_space_refine on Wed Jan 22 11:01:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9emm_19820/01_2025/9emm_19820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9emm_19820/01_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_19820/01_2025/9emm_19820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9emm_19820/01_2025/9emm_19820.map" model { file = "/net/cci-nas-00/data/ceres_data/9emm_19820/01_2025/9emm_19820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9emm_19820/01_2025/9emm_19820.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.03, per 1000 atoms: 0.60 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: 4.74 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.36 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: 5.57 Time building geometry restraints manager: 5.48 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 41.540 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.460 ------------------------------------------------------------------------------- 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 18835 Z= 0.322 Angle : 0.654 11.474 25541 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.001 TRP E 238 HIS 0.005 0.001 HIS C 69 PHE 0.019 0.001 PHE B 336 TYR 0.019 0.001 TYR A 111 ARG 0.008 0.000 ARG B 162 *********************** 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 : 2.554 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: 0.3006 time to fit residues: 88.9641 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 : 2.134 ------------------------------------------------------------------------------- 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 193 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 179 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.155637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111979 restraints weight = 28833.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110430 restraints weight = 20568.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111253 restraints weight = 18340.123| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18835 Z= 0.272 Angle : 0.630 15.898 25541 Z= 0.325 Chirality : 0.044 0.212 2735 Planarity : 0.005 0.065 3365 Dihedral : 4.723 59.444 2551 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.79 % Favored : 90.12 % Rotamer: Outliers : 3.46 % Allowed : 32.69 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2287 helix: 0.64 (0.20), residues: 754 sheet: -1.38 (0.28), residues: 403 loop : -2.30 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 348 HIS 0.005 0.001 HIS A 228 PHE 0.016 0.001 PHE B 336 TYR 0.017 0.001 TYR A 111 ARG 0.006 0.000 ARG B 162 *********************** 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 265 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: E 70 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8169 (tt) REVERT: E 238 TRP cc_start: 0.7530 (t-100) cc_final: 0.7151 (t-100) REVERT: E 358 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: C 154 MET cc_start: 0.7726 (mpp) cc_final: 0.7295 (mpp) REVERT: C 184 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7843 (tm-30) REVERT: D 22 LEU cc_start: 0.9063 (pt) cc_final: 0.8800 (pt) REVERT: D 68 ASP cc_start: 0.7958 (t0) cc_final: 0.7646 (t0) REVERT: D 504 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8338 (mtt90) REVERT: B 240 GLU cc_start: 0.5938 (tm-30) cc_final: 0.5327 (pt0) REVERT: B 332 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8238 (m) outliers start: 68 outliers final: 26 residues processed: 256 average time/residue: 0.3047 time to fit residues: 120.9579 Evaluate side-chains 216 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 394 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 391 VAL 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 222 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.0060 chunk 183 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 255 HIS D 397 GLN ** 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 = 0.4036 r_free = 0.4036 target = 0.155036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106386 restraints weight = 28744.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108678 restraints weight = 20551.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110936 restraints weight = 15029.075| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18835 Z= 0.293 Angle : 0.617 9.983 25541 Z= 0.320 Chirality : 0.044 0.208 2735 Planarity : 0.005 0.052 3365 Dihedral : 4.683 58.129 2547 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.06 % Favored : 89.81 % Rotamer: Outliers : 4.53 % Allowed : 31.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 2287 helix: 0.60 (0.20), residues: 765 sheet: -1.40 (0.27), residues: 400 loop : -2.32 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 348 HIS 0.006 0.001 HIS A 228 PHE 0.018 0.001 PHE B 336 TYR 0.018 0.001 TYR A 111 ARG 0.005 0.000 ARG A 36 *********************** 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 286 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 197 time to evaluate : 2.052 Fit side-chains REVERT: A 188 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7910 (ptpp) REVERT: E 358 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: E 368 ASN cc_start: 0.8443 (t0) cc_final: 0.8196 (t0) REVERT: C 55 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7780 (pt) REVERT: C 99 PHE cc_start: 0.8585 (m-10) cc_final: 0.8232 (m-10) REVERT: C 184 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7850 (tm-30) REVERT: C 410 MET cc_start: 0.8340 (tpp) cc_final: 0.8079 (tpt) REVERT: D 22 LEU cc_start: 0.9044 (pt) cc_final: 0.8840 (pt) REVERT: D 68 ASP cc_start: 0.8075 (t0) cc_final: 0.7744 (t0) REVERT: D 76 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: D 149 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8318 (mm) REVERT: B 104 ASN cc_start: 0.7434 (t0) cc_final: 0.6829 (t0) REVERT: B 240 GLU cc_start: 0.5920 (tm-30) cc_final: 0.5599 (pt0) outliers start: 89 outliers final: 54 residues processed: 272 average time/residue: 0.2833 time to fit residues: 121.1907 Evaluate side-chains 245 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 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 312 TRP Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 499 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 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 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 34 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 76 LYS 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 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 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 159 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 331 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 166 optimal weight: 6.9990 chunk 112 optimal weight: 0.0970 chunk 149 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 230 GLN D 397 GLN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116072 restraints weight = 28176.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116443 restraints weight = 19641.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116101 restraints weight = 16445.996| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18835 Z= 0.143 Angle : 0.564 11.358 25541 Z= 0.286 Chirality : 0.042 0.215 2735 Planarity : 0.004 0.054 3365 Dihedral : 4.448 57.088 2547 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.09 % Favored : 91.82 % Rotamer: Outliers : 3.26 % Allowed : 32.38 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2287 helix: 0.72 (0.20), residues: 767 sheet: -0.96 (0.28), residues: 371 loop : -2.28 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 221 HIS 0.009 0.001 HIS A 228 PHE 0.011 0.001 PHE A 141 TYR 0.020 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 *********************** 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 269 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 2.184 Fit side-chains REVERT: A 379 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8392 (mt) REVERT: E 70 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7940 (tt) REVERT: E 358 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: E 368 ASN cc_start: 0.8373 (t0) cc_final: 0.8153 (t0) REVERT: C 99 PHE cc_start: 0.8540 (m-10) cc_final: 0.8234 (m-10) REVERT: C 154 MET cc_start: 0.7577 (mpp) cc_final: 0.7276 (mpp) REVERT: C 184 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7716 (tm-30) REVERT: C 496 GLU cc_start: 0.7993 (tp30) cc_final: 0.7669 (tp30) REVERT: D 68 ASP cc_start: 0.8024 (t0) cc_final: 0.7713 (t0) REVERT: D 504 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8485 (mtt90) REVERT: B 104 ASN cc_start: 0.7295 (t0) cc_final: 0.6709 (t0) REVERT: B 240 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5615 (pt0) REVERT: B 332 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8107 (m) outliers start: 64 outliers final: 26 residues processed: 257 average time/residue: 0.3019 time to fit residues: 119.5765 Evaluate side-chains 214 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 466 VAL 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 123 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 VAL 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 192 VAL Chi-restraints excluded: chain D residue 198 TYR 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 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 331 SER Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 14 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 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 = 0.4042 r_free = 0.4042 target = 0.155424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106336 restraints weight = 28874.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109229 restraints weight = 20213.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110323 restraints weight = 15772.552| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18835 Z= 0.321 Angle : 0.623 12.326 25541 Z= 0.322 Chirality : 0.045 0.205 2735 Planarity : 0.004 0.053 3365 Dihedral : 4.596 56.675 2547 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.14 % Favored : 89.77 % Rotamer: Outliers : 4.33 % Allowed : 31.67 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2287 helix: 0.68 (0.20), residues: 771 sheet: -1.33 (0.27), residues: 413 loop : -2.33 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 348 HIS 0.004 0.001 HIS C 69 PHE 0.019 0.002 PHE B 336 TYR 0.018 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 *********************** 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 273 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 188 time to evaluate : 2.161 Fit side-chains REVERT: A 347 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8474 (ttm170) REVERT: E 70 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7886 (tt) REVERT: E 358 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: E 368 ASN cc_start: 0.8430 (t0) cc_final: 0.8198 (t0) REVERT: C 55 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7788 (pt) REVERT: C 184 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7882 (tm-30) REVERT: D 55 LEU cc_start: 0.8909 (mm) cc_final: 0.8671 (mm) REVERT: D 68 ASP cc_start: 0.8077 (t0) cc_final: 0.7756 (t0) REVERT: D 94 PHE cc_start: 0.7787 (t80) cc_final: 0.7585 (t80) REVERT: D 410 MET cc_start: 0.7774 (tpp) cc_final: 0.7364 (mmp) REVERT: D 504 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8420 (mtt90) REVERT: B 104 ASN cc_start: 0.7373 (t0) cc_final: 0.6743 (t0) REVERT: B 240 GLU cc_start: 0.6006 (tm-30) cc_final: 0.5745 (pt0) REVERT: B 332 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8273 (m) outliers start: 85 outliers final: 59 residues processed: 255 average time/residue: 0.3137 time to fit residues: 124.2282 Evaluate side-chains 249 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 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 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 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 291 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 18 THR Chi-restraints excluded: chain D residue 24 LEU 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 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 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 118 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 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 95 optimal weight: 6.9990 chunk 117 optimal weight: 0.0770 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.154931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108083 restraints weight = 29060.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110091 restraints weight = 19680.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109775 restraints weight = 14510.856| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18835 Z= 0.290 Angle : 0.623 12.659 25541 Z= 0.320 Chirality : 0.044 0.204 2735 Planarity : 0.004 0.057 3365 Dihedral : 4.665 56.268 2547 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.06 % Favored : 89.81 % Rotamer: Outliers : 4.99 % Allowed : 31.26 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 2287 helix: 0.68 (0.20), residues: 767 sheet: -1.39 (0.26), residues: 425 loop : -2.41 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 348 HIS 0.006 0.001 HIS A 228 PHE 0.017 0.001 PHE B 336 TYR 0.019 0.001 TYR A 111 ARG 0.006 0.000 ARG B 162 *********************** 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 287 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 2.234 Fit side-chains REVERT: A 228 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6729 (t-170) REVERT: E 70 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7940 (tt) REVERT: E 358 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: E 368 ASN cc_start: 0.8426 (t0) cc_final: 0.8184 (t0) REVERT: C 55 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7798 (pt) REVERT: C 99 PHE cc_start: 0.8533 (m-10) cc_final: 0.8312 (m-10) REVERT: C 184 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7871 (tm-30) REVERT: D 55 LEU cc_start: 0.8959 (mm) cc_final: 0.8702 (mm) REVERT: D 68 ASP cc_start: 0.8075 (t0) cc_final: 0.7760 (t0) REVERT: D 81 PHE cc_start: 0.7513 (m-10) cc_final: 0.7274 (m-10) REVERT: D 94 PHE cc_start: 0.7753 (t80) cc_final: 0.7550 (t80) REVERT: D 207 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8396 (tt) REVERT: D 223 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8999 (ptt90) REVERT: D 504 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8410 (mtt90) REVERT: B 104 ASN cc_start: 0.7396 (t0) cc_final: 0.6730 (t0) REVERT: B 240 GLU cc_start: 0.6167 (tm-30) cc_final: 0.5849 (tt0) REVERT: B 332 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8329 (m) outliers start: 98 outliers final: 68 residues processed: 270 average time/residue: 0.2982 time to fit residues: 127.4942 Evaluate side-chains 259 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 183 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 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 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 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 A residue 499 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 358 GLU Chi-restraints excluded: chain E residue 390 ASP 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 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 365 VAL Chi-restraints excluded: chain C residue 383 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 18 THR Chi-restraints excluded: chain D residue 24 LEU 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 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 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 293 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 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 84 optimal weight: 0.0060 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 230 GLN D 388 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112666 restraints weight = 28139.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114002 restraints weight = 20261.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114657 restraints weight = 15952.163| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18835 Z= 0.154 Angle : 0.580 14.912 25541 Z= 0.292 Chirality : 0.042 0.210 2735 Planarity : 0.004 0.057 3365 Dihedral : 4.482 55.489 2547 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.40 % Favored : 91.52 % Rotamer: Outliers : 3.11 % Allowed : 32.59 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2287 helix: 0.81 (0.20), residues: 762 sheet: -0.98 (0.27), residues: 394 loop : -2.40 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 238 HIS 0.009 0.001 HIS A 228 PHE 0.011 0.001 PHE C 264 TYR 0.019 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 *********************** 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 257 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 2.088 Fit side-chains REVERT: A 242 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8041 (mtm-85) REVERT: E 70 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7955 (tt) REVERT: E 358 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: E 368 ASN cc_start: 0.8402 (t0) cc_final: 0.8173 (t0) REVERT: C 75 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.7936 (ttp-110) REVERT: C 184 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7827 (tm-30) REVERT: D 55 LEU cc_start: 0.8908 (mm) cc_final: 0.8663 (mm) REVERT: D 68 ASP cc_start: 0.8058 (t0) cc_final: 0.7742 (t0) REVERT: D 201 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8100 (mmmm) REVERT: D 504 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8491 (mtt90) REVERT: B 104 ASN cc_start: 0.7413 (t0) cc_final: 0.6748 (t0) REVERT: B 240 GLU cc_start: 0.6130 (tm-30) cc_final: 0.5767 (tt0) REVERT: B 332 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8250 (m) outliers start: 61 outliers final: 36 residues processed: 245 average time/residue: 0.3127 time to fit residues: 119.0240 Evaluate side-chains 228 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 242 ARG 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 466 VAL 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 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 365 VAL Chi-restraints excluded: chain C residue 417 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 201 LYS 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 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 404 LEU Chi-restraints excluded: chain B residue 425 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 90 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 127 optimal weight: 0.0030 chunk 189 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS E 329 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.157334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110193 restraints weight = 28493.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111768 restraints weight = 20196.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112377 restraints weight = 16482.149| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18835 Z= 0.215 Angle : 0.599 13.998 25541 Z= 0.301 Chirality : 0.043 0.206 2735 Planarity : 0.004 0.058 3365 Dihedral : 4.490 54.990 2547 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.36 % Favored : 90.56 % Rotamer: Outliers : 3.46 % Allowed : 32.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2287 helix: 0.96 (0.20), residues: 744 sheet: -1.18 (0.26), residues: 432 loop : -2.38 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 65 HIS 0.005 0.001 HIS C 69 PHE 0.013 0.001 PHE A 141 TYR 0.018 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 *********************** 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: 68 poor density : 199 time to evaluate : 2.196 Fit side-chains REVERT: A 242 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8074 (mtm-85) REVERT: E 70 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7917 (tt) REVERT: E 228 MET cc_start: 0.6539 (tpt) cc_final: 0.6298 (tpt) REVERT: E 358 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: E 368 ASN cc_start: 0.8422 (t0) cc_final: 0.8185 (t0) REVERT: C 75 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: C 184 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7857 (tm-30) REVERT: C 496 GLU cc_start: 0.8185 (tp30) cc_final: 0.7891 (tp30) REVERT: D 55 LEU cc_start: 0.8930 (mm) cc_final: 0.8630 (mm) REVERT: D 68 ASP cc_start: 0.8105 (t0) cc_final: 0.7793 (t0) REVERT: D 201 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8107 (mmmm) REVERT: D 207 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8406 (tt) REVERT: D 504 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8487 (mtt90) REVERT: B 104 ASN cc_start: 0.7458 (t0) cc_final: 0.6803 (t0) REVERT: B 240 GLU cc_start: 0.6214 (tm-30) cc_final: 0.5919 (tt0) REVERT: B 332 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8306 (m) outliers start: 68 outliers final: 51 residues processed: 254 average time/residue: 0.3079 time to fit residues: 120.3530 Evaluate side-chains 250 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 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 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 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 107 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 267 THR 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 417 THR Chi-restraints excluded: chain C residue 499 ILE 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 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 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 404 LEU Chi-restraints excluded: chain B residue 425 SER 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 27 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS B 96 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.158111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115026 restraints weight = 28580.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113898 restraints weight = 20577.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114030 restraints weight = 19888.983| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18835 Z= 0.196 Angle : 0.612 14.513 25541 Z= 0.305 Chirality : 0.043 0.204 2735 Planarity : 0.004 0.058 3365 Dihedral : 4.468 54.644 2547 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.18 % Favored : 90.73 % Rotamer: Outliers : 3.36 % Allowed : 32.74 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2287 helix: 0.96 (0.20), residues: 745 sheet: -0.94 (0.27), residues: 405 loop : -2.46 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 238 HIS 0.005 0.001 HIS C 69 PHE 0.012 0.001 PHE C 264 TYR 0.018 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 *********************** 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: 66 poor density : 201 time to evaluate : 2.195 Fit side-chains REVERT: A 242 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8003 (mtm-85) REVERT: E 70 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8109 (tt) REVERT: E 358 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: E 368 ASN cc_start: 0.8382 (t0) cc_final: 0.8154 (t0) REVERT: C 75 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.7958 (ttp-110) REVERT: C 99 PHE cc_start: 0.8446 (m-80) cc_final: 0.8208 (m-10) REVERT: C 184 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7804 (tm-30) REVERT: D 55 LEU cc_start: 0.8886 (mm) cc_final: 0.8658 (mm) REVERT: D 68 ASP cc_start: 0.8040 (t0) cc_final: 0.7740 (t0) REVERT: D 80 GLU cc_start: 0.8411 (tt0) cc_final: 0.8130 (tt0) REVERT: D 81 PHE cc_start: 0.7361 (m-10) cc_final: 0.6697 (m-10) REVERT: D 201 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8110 (mmmm) REVERT: D 207 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8453 (tt) REVERT: D 410 MET cc_start: 0.7629 (tpp) cc_final: 0.7378 (mmm) REVERT: D 504 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8513 (mtt90) REVERT: B 17 ARG cc_start: 0.6936 (tpt170) cc_final: 0.6715 (tpt170) REVERT: B 104 ASN cc_start: 0.7419 (t0) cc_final: 0.6845 (t0) REVERT: B 240 GLU cc_start: 0.6254 (tm-30) cc_final: 0.6019 (tt0) REVERT: B 332 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8264 (m) outliers start: 66 outliers final: 51 residues processed: 255 average time/residue: 0.3039 time to fit residues: 120.5704 Evaluate side-chains 250 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 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 242 ARG Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 291 THR 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 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 114 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 267 THR 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 417 THR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 SER 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 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 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 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 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 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 215 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 220 optimal weight: 0.0970 chunk 191 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 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 = 0.4092 r_free = 0.4092 target = 0.159689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116464 restraints weight = 28694.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114894 restraints weight = 21372.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115613 restraints weight = 19232.716| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18835 Z= 0.154 Angle : 0.602 14.072 25541 Z= 0.298 Chirality : 0.043 0.215 2735 Planarity : 0.004 0.055 3365 Dihedral : 4.224 35.931 2545 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.22 % Favored : 91.69 % Rotamer: Outliers : 2.70 % Allowed : 33.55 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2287 helix: 1.06 (0.21), residues: 739 sheet: -0.85 (0.27), residues: 405 loop : -2.40 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 238 HIS 0.007 0.001 HIS A 228 PHE 0.014 0.001 PHE A 141 TYR 0.018 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 ********************** 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 263 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 2.249 Fit side-chains revert: symmetry clash REVERT: A 269 MET cc_start: 0.8862 (ptm) cc_final: 0.8570 (ttp) REVERT: E 70 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7979 (tt) REVERT: E 234 LYS cc_start: 0.4758 (OUTLIER) cc_final: 0.4325 (pttm) REVERT: E 358 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: C 75 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.7880 (ttp-110) REVERT: C 99 PHE cc_start: 0.8523 (m-80) cc_final: 0.8271 (m-10) REVERT: C 184 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7828 (tm-30) REVERT: C 496 GLU cc_start: 0.7920 (tp30) cc_final: 0.7603 (tp30) REVERT: D 55 LEU cc_start: 0.8915 (mm) cc_final: 0.8630 (mm) REVERT: D 68 ASP cc_start: 0.8129 (t0) cc_final: 0.7836 (t0) REVERT: D 81 PHE cc_start: 0.7214 (m-10) cc_final: 0.6527 (m-10) REVERT: D 201 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7930 (mtpt) REVERT: D 410 MET cc_start: 0.7610 (tpp) cc_final: 0.7263 (mmm) REVERT: B 17 ARG cc_start: 0.6891 (tpt170) cc_final: 0.6636 (tpt170) REVERT: B 104 ASN cc_start: 0.7442 (t0) cc_final: 0.6827 (t0) REVERT: B 240 GLU cc_start: 0.6332 (tm-30) cc_final: 0.6085 (tt0) REVERT: B 332 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8248 (m) outliers start: 53 outliers final: 40 residues processed: 256 average time/residue: 0.3117 time to fit residues: 124.6451 Evaluate side-chains 242 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU 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 267 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 458 GLU 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 191 TYR Chi-restraints excluded: chain E residue 234 LYS 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 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 267 THR 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 D residue 34 THR 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 229 VAL Chi-restraints excluded: chain D residue 275 ILE 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 467 THR Chi-restraints excluded: chain D residue 484 LEU 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 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 425 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 204 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 0.0170 chunk 169 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4083 r_free = 0.4083 target = 0.158909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113477 restraints weight = 28484.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114470 restraints weight = 21057.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114553 restraints weight = 16160.311| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18835 Z= 0.199 Angle : 0.628 13.536 25541 Z= 0.315 Chirality : 0.043 0.207 2735 Planarity : 0.004 0.055 3365 Dihedral : 4.243 35.485 2545 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.96 % Favored : 90.95 % Rotamer: Outliers : 3.00 % Allowed : 33.40 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2287 helix: 1.08 (0.21), residues: 738 sheet: -0.88 (0.27), residues: 405 loop : -2.41 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 238 HIS 0.005 0.001 HIS C 69 PHE 0.020 0.001 PHE C 141 TYR 0.018 0.001 TYR A 111 ARG 0.007 0.000 ARG B 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5198.77 seconds wall clock time: 97 minutes 44.67 seconds (5864.67 seconds total)