Starting phenix.real_space_refine on Wed Mar 4 13:36:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7omm_12990/03_2026/7omm_12990.cif Found real_map, /net/cci-nas-00/data/ceres_data/7omm_12990/03_2026/7omm_12990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7omm_12990/03_2026/7omm_12990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7omm_12990/03_2026/7omm_12990.map" model { file = "/net/cci-nas-00/data/ceres_data/7omm_12990/03_2026/7omm_12990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7omm_12990/03_2026/7omm_12990.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.048 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 31 5.16 5 C 8889 2.51 5 N 2392 2.21 5 O 2669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13981 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5462 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 25, 'TRANS': 672} Chain breaks: 1 Chain: "B" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "C" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3731 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 27, 'TRANS': 451} Chain: "D" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3768 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Time building chain proxies: 2.87, per 1000 atoms: 0.21 Number of scatterers: 13981 At special positions: 0 Unit cell: (186.329, 77.7108, 158.071, 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 31 16.00 O 2669 8.00 N 2392 7.00 C 8889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 737 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 585.8 milliseconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 33 sheets defined 25.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.715A pdb=" N GLU B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 155 removed outlier: 4.628A pdb=" N GLU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.762A pdb=" N THR C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 149 Processing helix chain 'C' and resid 159 through 168 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.738A pdb=" N TRP C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.582A pdb=" N GLU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.037A pdb=" N THR C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Proline residue: C 276 - end of helix removed outlier: 4.489A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 318 Processing helix chain 'C' and resid 326 through 336 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 348 through 355 removed outlier: 3.703A pdb=" N ILE C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 421 through 429 removed outlier: 3.715A pdb=" N GLU C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 444 Processing helix chain 'C' and resid 452 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 155 Processing helix chain 'D' and resid 165 through 173 Proline residue: D 171 - end of helix Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 186 through 197 removed outlier: 3.694A pdb=" N GLY D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 253 through 266 removed outlier: 4.078A pdb=" N ALA D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.818A pdb=" N ILE D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 324 removed outlier: 3.772A pdb=" N LYS D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'D' and resid 353 through 362 removed outlier: 4.108A pdb=" N ASN D 357 " --> pdb=" O TRP D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.953A pdb=" N LYS D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 420 Processing helix chain 'D' and resid 427 through 437 Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 456 through 476 Processing helix chain 'D' and resid 479 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.522A pdb=" N VAL A 118 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 169 removed outlier: 4.061A pdb=" N PHE A 200 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 211 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 213 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 238 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.098A pdb=" N VAL A 227 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277 removed outlier: 3.644A pdb=" N PHE A 288 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 307 removed outlier: 3.669A pdb=" N GLY A 313 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 317 through 320 removed outlier: 3.721A pdb=" N ARG A 331 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A 336 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AB2, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.772A pdb=" N ARG A 443 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 421 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 441 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 456 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 442 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 444 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=AB4, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.569A pdb=" N ASN A 504 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 511 through 513 removed outlier: 3.798A pdb=" N PHE A 594 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG A 593 " --> pdb=" O GLY A 632 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 627 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 629 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 639 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 511 through 513 removed outlier: 3.668A pdb=" N THR A 578 " --> pdb=" O GLN A 600 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 627 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 629 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 639 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 656 through 658 removed outlier: 3.671A pdb=" N VAL A 657 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 676 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 678 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP A 692 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 712 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 726 " --> pdb=" O ASN A 716 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 727 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 742 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 749 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 757 " --> pdb=" O TYR A 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.953A pdb=" N ILE B 88 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 82 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU B 90 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.739A pdb=" N LEU B 120 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.528A pdb=" N VAL C 82 " --> pdb=" O CYS C 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.722A pdb=" N GLY C 13 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 37 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 52 " --> pdb=" O TRP C 39 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG C 41 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TRP C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 62 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.722A pdb=" N GLY C 13 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 152 through 155 removed outlier: 5.791A pdb=" N LEU C 124 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 155 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE C 126 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 125 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE C 178 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP C 127 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA C 180 " --> pdb=" O TRP C 127 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY C 377 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL C 227 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 379 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 152 through 155 removed outlier: 5.791A pdb=" N LEU C 124 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 155 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE C 126 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 125 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE C 178 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP C 127 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA C 180 " --> pdb=" O TRP C 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AC7, first strand: chain 'C' and resid 262 through 264 removed outlier: 8.557A pdb=" N SER C 262 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR C 342 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU C 264 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N ASN C 344 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 340 " --> pdb=" O ASN C 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 284 through 287 removed outlier: 5.683A pdb=" N ALA C 285 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP C 297 " --> pdb=" O LYS C 287 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.597A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 85 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 39 through 42 removed outlier: 4.034A pdb=" N ALA D 95 " --> pdb=" O VAL D 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.192A pdb=" N LEU D 130 " --> pdb=" O THR D 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 184 through 185 removed outlier: 3.861A pdb=" N SER D 386 " --> pdb=" O TRP D 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AD5, first strand: chain 'D' and resid 347 through 350 removed outlier: 4.046A pdb=" N ASN D 350 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 372 through 373 502 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2735 1.33 - 1.45: 3684 1.45 - 1.57: 7846 1.57 - 1.70: 2 1.70 - 1.82: 55 Bond restraints: 14322 Sorted by residual: bond pdb=" N ILE D 182 " pdb=" CA ILE D 182 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.15e-02 7.56e+03 1.92e+01 bond pdb=" N VAL D 160 " pdb=" CA VAL D 160 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.08e-02 8.57e+03 1.79e+01 bond pdb=" N LYS D 90 " pdb=" CA LYS D 90 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.77e+01 bond pdb=" N ILE A 293 " pdb=" CA ILE A 293 " ideal model delta sigma weight residual 1.459 1.495 -0.036 9.10e-03 1.21e+04 1.58e+01 bond pdb=" N ILE D 34 " pdb=" CA ILE D 34 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.09e-02 8.42e+03 1.34e+01 ... (remaining 14317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 17382 2.41 - 4.82: 1848 4.82 - 7.23: 188 7.23 - 9.64: 17 9.64 - 12.06: 2 Bond angle restraints: 19437 Sorted by residual: angle pdb=" N ASP D 181 " pdb=" CA ASP D 181 " pdb=" C ASP D 181 " ideal model delta sigma weight residual 111.07 121.03 -9.96 1.07e+00 8.73e-01 8.66e+01 angle pdb=" N ASP D 137 " pdb=" CA ASP D 137 " pdb=" C ASP D 137 " ideal model delta sigma weight residual 111.28 101.78 9.50 1.09e+00 8.42e-01 7.60e+01 angle pdb=" C ARG A 662 " pdb=" CA ARG A 662 " pdb=" CB ARG A 662 " ideal model delta sigma weight residual 110.44 103.83 6.61 9.00e-01 1.23e+00 5.39e+01 angle pdb=" CA ARG A 473 " pdb=" C ARG A 473 " pdb=" N PRO A 474 " ideal model delta sigma weight residual 117.67 123.91 -6.24 8.80e-01 1.29e+00 5.03e+01 angle pdb=" CA PHE D 402 " pdb=" CB PHE D 402 " pdb=" CG PHE D 402 " ideal model delta sigma weight residual 113.80 120.79 -6.99 1.00e+00 1.00e+00 4.89e+01 ... (remaining 19432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7232 17.81 - 35.62: 757 35.62 - 53.44: 311 53.44 - 71.25: 108 71.25 - 89.06: 23 Dihedral angle restraints: 8431 sinusoidal: 3300 harmonic: 5131 Sorted by residual: dihedral pdb=" CB CYS A 203 " pdb=" SG CYS A 203 " pdb=" SG CYS A 737 " pdb=" CB CYS A 737 " ideal model delta sinusoidal sigma weight residual 93.00 34.67 58.33 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CA MET A 780 " pdb=" C MET A 780 " pdb=" N ASP A 781 " pdb=" CA ASP A 781 " ideal model delta harmonic sigma weight residual 180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" N TYR D 36 " pdb=" C TYR D 36 " pdb=" CA TYR D 36 " pdb=" CB TYR D 36 " ideal model delta harmonic sigma weight residual 122.80 135.75 -12.95 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 8428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1503 0.095 - 0.190: 407 0.190 - 0.285: 116 0.285 - 0.380: 22 0.380 - 0.475: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA TYR D 36 " pdb=" N TYR D 36 " pdb=" C TYR D 36 " pdb=" CB TYR D 36 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB THR C 170 " pdb=" CA THR C 170 " pdb=" OG1 THR C 170 " pdb=" CG2 THR C 170 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA ILE D 389 " pdb=" N ILE D 389 " pdb=" C ILE D 389 " pdb=" CB ILE D 389 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 2049 not shown) Planarity restraints: 2546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 202 " 0.096 2.00e-02 2.50e+03 5.87e-02 6.03e+01 pdb=" CG PHE C 202 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE C 202 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE C 202 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE C 202 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE C 202 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 202 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 327 " -0.079 2.00e-02 2.50e+03 4.63e-02 4.29e+01 pdb=" CG TYR C 327 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 327 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR C 327 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 327 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 327 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR C 327 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 327 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 311 " -0.079 2.00e-02 2.50e+03 4.89e-02 4.18e+01 pdb=" CG PHE C 311 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE C 311 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE C 311 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE C 311 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE C 311 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 311 " -0.046 2.00e-02 2.50e+03 ... (remaining 2543 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 38 2.43 - 3.05: 8104 3.05 - 3.67: 21078 3.67 - 4.28: 31312 4.28 - 4.90: 52250 Nonbonded interactions: 112782 Sorted by model distance: nonbonded pdb=" O GLU D 401 " pdb=" OE1 GLU D 401 " model vdw 1.818 3.040 nonbonded pdb=" OD1 ASN D 296 " pdb=" N GLY D 297 " model vdw 2.224 3.120 nonbonded pdb=" OE1 GLN A 765 " pdb=" OG SER A 770 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR A 751 " pdb=" OG1 THR A 755 " model vdw 2.268 3.040 nonbonded pdb=" O TYR D 333 " pdb=" CD1 TYR D 333 " model vdw 2.276 3.340 ... (remaining 112777 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 'C' and (resid 5 through 13 or resid 15 through 16 or resid 18 through 29 \ or resid 39 or resid 41 through 49 or resid 51 through 53 or resid 61 or resid \ 63 through 72 or resid 74 or resid 76 through 95 or resid 97 through 99 or resid \ 105 or resid 107 through 108 or resid 110 or resid 112 through 483)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 16 or resid 18 through 29 \ or resid 39 or resid 41 through 49 or resid 51 through 53 or resid 61 or resid \ 63 through 72 or resid 74 or resid 76 through 95 or resid 97 through 99 or resid \ 105 or resid 107 or resid 114 or resid 116 or resid 118 through 489)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4596 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 : 0.010 0.053 14325 Z= 0.709 Angle : 1.466 12.055 19443 Z= 1.051 Chirality : 0.097 0.475 2052 Planarity : 0.007 0.059 2546 Dihedral : 18.842 89.060 5178 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.30 % Favored : 90.19 % Rotamer: Outliers : 16.45 % Allowed : 11.92 % Favored : 71.64 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.19), residues: 1784 helix: 0.36 (0.25), residues: 410 sheet: -2.61 (0.22), residues: 479 loop : -2.36 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 672 TYR 0.079 0.004 TYR C 327 PHE 0.096 0.007 PHE C 202 TRP 0.064 0.005 TRP C 457 HIS 0.006 0.002 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.01038 (14322) covalent geometry : angle 1.46562 (19437) SS BOND : bond 0.00271 ( 3) SS BOND : angle 1.27521 ( 6) hydrogen bonds : bond 0.23826 ( 474) hydrogen bonds : angle 9.33549 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 175 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.6917 (tm-30) cc_final: 0.6203 (tm-30) REVERT: A 211 TYR cc_start: 0.8566 (p90) cc_final: 0.8285 (p90) REVERT: A 312 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (m) REVERT: A 393 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 425 ASP cc_start: 0.7258 (t0) cc_final: 0.6494 (t0) REVERT: A 463 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7075 (m100) REVERT: A 473 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: A 524 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: A 565 TYR cc_start: 0.6753 (t80) cc_final: 0.6340 (t80) REVERT: A 669 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7914 (pt) REVERT: A 780 MET cc_start: 0.6148 (ppp) cc_final: 0.5371 (ppp) REVERT: B 32 TYR cc_start: 0.5960 (m-10) cc_final: 0.5743 (m-10) REVERT: B 131 GLN cc_start: 0.7886 (pp30) cc_final: 0.7652 (pp30) REVERT: C 50 TRP cc_start: 0.7684 (t60) cc_final: 0.7045 (t60) REVERT: C 55 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.7765 (m-40) REVERT: C 63 TYR cc_start: 0.6874 (m-80) cc_final: 0.6642 (m-80) REVERT: D 5 VAL cc_start: 0.3554 (OUTLIER) cc_final: 0.3243 (m) REVERT: D 22 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5861 (mmm160) REVERT: D 49 GLU cc_start: 0.2884 (OUTLIER) cc_final: 0.2657 (mp0) REVERT: D 133 TRP cc_start: 0.3770 (OUTLIER) cc_final: 0.2523 (t60) REVERT: D 149 LYS cc_start: 0.4135 (OUTLIER) cc_final: 0.3933 (mttt) REVERT: D 187 HIS cc_start: 0.1454 (OUTLIER) cc_final: 0.1153 (p90) REVERT: D 195 GLN cc_start: 0.1923 (OUTLIER) cc_final: 0.1702 (mp10) REVERT: D 467 ARG cc_start: -0.0799 (OUTLIER) cc_final: -0.1118 (ttm170) outliers start: 236 outliers final: 78 residues processed: 373 average time/residue: 0.1168 time to fit residues: 63.1062 Evaluate side-chains 219 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 126 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 600 GLN Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 293 LYS Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 333 TYR Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 482 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 581 GLN C 100 ASN C 318 ASN D 141 ASN D 350 ASN D 357 ASN D 472 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.285493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 144)---------------| | r_work = 0.4734 r_free = 0.4734 target = 0.231588 restraints weight = 23744.012| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.78 r_work: 0.4384 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4281 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14325 Z= 0.163 Angle : 0.694 10.312 19443 Z= 0.368 Chirality : 0.047 0.239 2052 Planarity : 0.005 0.080 2546 Dihedral : 11.566 77.589 2180 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.74 % Favored : 91.14 % Rotamer: Outliers : 7.67 % Allowed : 18.89 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.19), residues: 1784 helix: 0.55 (0.24), residues: 417 sheet: -2.32 (0.22), residues: 512 loop : -2.21 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 176 TYR 0.032 0.002 TYR D 62 PHE 0.023 0.002 PHE D 190 TRP 0.014 0.002 TRP C 179 HIS 0.008 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00352 (14322) covalent geometry : angle 0.69397 (19437) SS BOND : bond 0.00179 ( 3) SS BOND : angle 1.14083 ( 6) hydrogen bonds : bond 0.04784 ( 474) hydrogen bonds : angle 6.42755 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 140 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5517 (OUTLIER) cc_final: 0.4794 (pp30) REVERT: A 155 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 256 SER cc_start: 0.8103 (t) cc_final: 0.7646 (p) REVERT: A 463 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (m100) REVERT: A 526 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7699 (mt) REVERT: A 780 MET cc_start: 0.6029 (ppp) cc_final: 0.5313 (ppp) REVERT: C 375 PHE cc_start: 0.2627 (OUTLIER) cc_final: 0.2005 (t80) REVERT: D 22 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6541 (mtp180) REVERT: D 357 ASN cc_start: -0.2288 (OUTLIER) cc_final: -0.2492 (t0) outliers start: 110 outliers final: 61 residues processed: 234 average time/residue: 0.1082 time to fit residues: 38.0601 Evaluate side-chains 191 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 323 LYS Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 0.0070 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 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 = 0.5110 r_free = 0.5110 target = 0.263349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.221836 restraints weight = 22639.520| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 1.95 r_work: 0.4437 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4267 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14325 Z= 0.161 Angle : 0.658 9.124 19443 Z= 0.348 Chirality : 0.045 0.201 2052 Planarity : 0.005 0.079 2546 Dihedral : 8.556 59.042 2066 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.02 % Favored : 90.86 % Rotamer: Outliers : 5.99 % Allowed : 21.18 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.20), residues: 1784 helix: 0.71 (0.25), residues: 415 sheet: -2.22 (0.22), residues: 521 loop : -2.05 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 48 TYR 0.024 0.002 TYR D 62 PHE 0.017 0.002 PHE A 284 TRP 0.024 0.002 TRP D 39 HIS 0.006 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00353 (14322) covalent geometry : angle 0.65784 (19437) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.76225 ( 6) hydrogen bonds : bond 0.04409 ( 474) hydrogen bonds : angle 6.07284 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 129 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5505 (OUTLIER) cc_final: 0.4814 (pp30) REVERT: A 155 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 173 GLN cc_start: 0.6774 (tm-30) cc_final: 0.5941 (tm-30) REVERT: A 256 SER cc_start: 0.8243 (t) cc_final: 0.7908 (p) REVERT: A 526 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 780 MET cc_start: 0.6063 (ppp) cc_final: 0.5362 (ppp) REVERT: B 51 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8070 (mm) REVERT: C 375 PHE cc_start: 0.3113 (OUTLIER) cc_final: 0.2367 (t80) REVERT: D 138 LYS cc_start: -0.3101 (OUTLIER) cc_final: -0.4181 (mttt) REVERT: D 165 LYS cc_start: 0.3654 (mttp) cc_final: 0.3087 (tppt) outliers start: 86 outliers final: 46 residues processed: 201 average time/residue: 0.1085 time to fit residues: 33.2239 Evaluate side-chains 168 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 56 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 155 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 322 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN D 135 ASN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.264059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.222098 restraints weight = 22657.705| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 1.94 r_work: 0.4449 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4280 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14325 Z= 0.135 Angle : 0.625 9.469 19443 Z= 0.326 Chirality : 0.044 0.192 2052 Planarity : 0.005 0.083 2546 Dihedral : 7.251 57.449 2028 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.30 % Favored : 91.59 % Rotamer: Outliers : 5.16 % Allowed : 21.32 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.20), residues: 1784 helix: 0.84 (0.25), residues: 410 sheet: -2.08 (0.23), residues: 516 loop : -1.85 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 183 TYR 0.021 0.001 TYR D 62 PHE 0.015 0.002 PHE A 278 TRP 0.017 0.001 TRP C 179 HIS 0.008 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00294 (14322) covalent geometry : angle 0.62470 (19437) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.68884 ( 6) hydrogen bonds : bond 0.03942 ( 474) hydrogen bonds : angle 5.79954 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 123 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.4768 (pp30) REVERT: A 155 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 173 GLN cc_start: 0.6701 (tm-30) cc_final: 0.5899 (tm-30) REVERT: A 256 SER cc_start: 0.8115 (t) cc_final: 0.7794 (p) REVERT: A 365 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6325 (t80) REVERT: A 473 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8157 (mtt-85) REVERT: B 51 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 147 GLU cc_start: 0.7969 (tp30) cc_final: 0.7609 (tt0) REVERT: C 375 PHE cc_start: 0.3334 (OUTLIER) cc_final: 0.2496 (t80) REVERT: C 438 MET cc_start: -0.0094 (mmp) cc_final: -0.1070 (mmt) REVERT: D 165 LYS cc_start: 0.3286 (mttp) cc_final: 0.2794 (tppt) REVERT: D 166 LEU cc_start: -0.1283 (OUTLIER) cc_final: -0.1544 (tp) outliers start: 74 outliers final: 48 residues processed: 181 average time/residue: 0.1006 time to fit residues: 27.8035 Evaluate side-chains 173 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 407 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 53 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 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 = 0.5102 r_free = 0.5102 target = 0.262224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.227377 restraints weight = 23418.552| |-----------------------------------------------------------------------------| r_work (start): 0.4789 rms_B_bonded: 2.22 r_work: 0.4542 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4370 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14325 Z= 0.254 Angle : 0.762 9.137 19443 Z= 0.405 Chirality : 0.049 0.231 2052 Planarity : 0.006 0.080 2546 Dihedral : 7.632 55.444 2018 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.61 % Favored : 87.33 % Rotamer: Outliers : 6.41 % Allowed : 21.60 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.20), residues: 1784 helix: 0.64 (0.25), residues: 408 sheet: -2.47 (0.22), residues: 523 loop : -2.08 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 183 TYR 0.029 0.002 TYR A 565 PHE 0.030 0.003 PHE C 209 TRP 0.035 0.002 TRP C 179 HIS 0.015 0.002 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00574 (14322) covalent geometry : angle 0.76248 (19437) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.82078 ( 6) hydrogen bonds : bond 0.04559 ( 474) hydrogen bonds : angle 6.43126 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 116 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 155 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7092 (t80) REVERT: A 365 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7017 (t80) REVERT: A 473 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8117 (mtt-85) REVERT: B 51 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8367 (mm) REVERT: C 375 PHE cc_start: 0.4133 (OUTLIER) cc_final: 0.3871 (m-80) REVERT: C 438 MET cc_start: 0.0736 (mmp) cc_final: -0.0614 (mmt) REVERT: D 37 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7411 (pp) REVERT: D 54 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7130 (mt) REVERT: D 113 TRP cc_start: 0.8305 (m-10) cc_final: 0.7902 (m-10) REVERT: D 138 LYS cc_start: -0.0690 (OUTLIER) cc_final: -0.2492 (mttt) REVERT: D 165 LYS cc_start: 0.4344 (mttp) cc_final: 0.4012 (mttp) REVERT: D 184 PHE cc_start: 0.3887 (OUTLIER) cc_final: 0.3569 (m-80) outliers start: 92 outliers final: 48 residues processed: 190 average time/residue: 0.1057 time to fit residues: 30.6118 Evaluate side-chains 163 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 105 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 386 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 112 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 571 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.259729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4695 r_free = 0.4695 target = 0.210688 restraints weight = 22858.553| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 2.87 r_work: 0.4389 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14325 Z= 0.141 Angle : 0.661 10.149 19443 Z= 0.342 Chirality : 0.045 0.197 2052 Planarity : 0.005 0.088 2546 Dihedral : 6.697 53.078 2004 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 5.23 % Allowed : 22.44 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.20), residues: 1784 helix: 0.84 (0.25), residues: 408 sheet: -2.30 (0.22), residues: 529 loop : -1.97 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 33 TYR 0.024 0.002 TYR A 211 PHE 0.018 0.002 PHE D 381 TRP 0.040 0.002 TRP B 138 HIS 0.004 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00310 (14322) covalent geometry : angle 0.66084 (19437) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.74289 ( 6) hydrogen bonds : bond 0.03866 ( 474) hydrogen bonds : angle 5.92342 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 109 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.4855 (pp30) REVERT: A 173 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6150 (tm-30) REVERT: A 365 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6649 (t80) REVERT: A 473 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8270 (mtm-85) REVERT: A 780 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5611 (ppp) REVERT: B 51 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8088 (mm) REVERT: B 147 GLU cc_start: 0.7953 (tp30) cc_final: 0.7601 (tt0) REVERT: C 438 MET cc_start: 0.0373 (mmp) cc_final: -0.0785 (mmt) REVERT: D 54 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7320 (mt) REVERT: D 113 TRP cc_start: 0.8403 (m-10) cc_final: 0.8023 (m-10) REVERT: D 166 LEU cc_start: -0.1605 (OUTLIER) cc_final: -0.2360 (tp) outliers start: 75 outliers final: 49 residues processed: 168 average time/residue: 0.1024 time to fit residues: 26.1629 Evaluate side-chains 156 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 173 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** 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 = 0.5165 r_free = 0.5165 target = 0.291940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.256618 restraints weight = 23594.507| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 2.55 r_work: 0.4527 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14325 Z= 0.121 Angle : 0.629 10.083 19443 Z= 0.323 Chirality : 0.044 0.188 2052 Planarity : 0.005 0.073 2546 Dihedral : 6.337 51.202 2002 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 4.25 % Allowed : 23.62 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.20), residues: 1784 helix: 1.12 (0.26), residues: 402 sheet: -2.14 (0.22), residues: 533 loop : -1.88 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 33 TYR 0.025 0.001 TYR A 565 PHE 0.019 0.002 PHE D 184 TRP 0.045 0.001 TRP B 138 HIS 0.004 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00264 (14322) covalent geometry : angle 0.62939 (19437) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.69756 ( 6) hydrogen bonds : bond 0.03521 ( 474) hydrogen bonds : angle 5.57916 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 111 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5355 (OUTLIER) cc_final: 0.4734 (pp30) REVERT: A 173 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6219 (tm-30) REVERT: A 197 GLU cc_start: 0.7437 (tp30) cc_final: 0.7201 (tm-30) REVERT: A 365 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6344 (t80) REVERT: A 473 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8005 (mtt-85) REVERT: A 780 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.5149 (ppp) REVERT: B 51 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7955 (mm) REVERT: B 112 MET cc_start: 0.8465 (ptp) cc_final: 0.8187 (ptt) REVERT: C 438 MET cc_start: 0.1816 (mmp) cc_final: 0.0149 (mmt) REVERT: C 453 MET cc_start: 0.1095 (mmt) cc_final: -0.0289 (ttt) REVERT: D 54 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7249 (mt) REVERT: D 113 TRP cc_start: 0.8146 (m-10) cc_final: 0.7897 (m-10) REVERT: D 165 LYS cc_start: 0.4145 (mttp) cc_final: 0.3895 (mttp) outliers start: 61 outliers final: 45 residues processed: 156 average time/residue: 0.1057 time to fit residues: 24.8556 Evaluate side-chains 154 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 9 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 146 optimal weight: 0.2980 chunk 114 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 111 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** 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 = 0.5107 r_free = 0.5107 target = 0.263584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.232263 restraints weight = 23096.122| |-----------------------------------------------------------------------------| r_work (start): 0.4859 rms_B_bonded: 2.20 r_work: 0.4602 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4460 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14325 Z= 0.184 Angle : 0.679 10.920 19443 Z= 0.353 Chirality : 0.046 0.180 2052 Planarity : 0.005 0.075 2546 Dihedral : 6.621 50.618 2002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.10 % Favored : 88.85 % Rotamer: Outliers : 5.02 % Allowed : 23.34 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.20), residues: 1784 helix: 1.07 (0.26), residues: 402 sheet: -2.16 (0.22), residues: 537 loop : -1.97 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 33 TYR 0.026 0.002 TYR A 565 PHE 0.025 0.002 PHE D 184 TRP 0.041 0.002 TRP B 138 HIS 0.006 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00412 (14322) covalent geometry : angle 0.67940 (19437) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.66674 ( 6) hydrogen bonds : bond 0.03836 ( 474) hydrogen bonds : angle 5.83218 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 104 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.4860 (pp30) REVERT: A 173 GLN cc_start: 0.6899 (tm-30) cc_final: 0.6249 (tm-30) REVERT: A 365 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6763 (t80) REVERT: A 473 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8096 (mtt-85) REVERT: A 780 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5517 (ppp) REVERT: B 51 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 138 TRP cc_start: 0.7841 (m-10) cc_final: 0.7636 (m-90) REVERT: C 134 TYR cc_start: 0.4531 (OUTLIER) cc_final: 0.3627 (p90) REVERT: C 453 MET cc_start: 0.1217 (mmt) cc_final: -0.0530 (tpp) REVERT: D 54 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7352 (mt) REVERT: D 113 TRP cc_start: 0.8247 (m-10) cc_final: 0.7948 (m-10) REVERT: D 165 LYS cc_start: 0.4660 (mttp) cc_final: 0.4388 (mttp) REVERT: D 184 PHE cc_start: 0.3779 (OUTLIER) cc_final: 0.3392 (m-80) outliers start: 72 outliers final: 45 residues processed: 159 average time/residue: 0.0994 time to fit residues: 24.5855 Evaluate side-chains 155 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 67 optimal weight: 0.0570 chunk 169 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 ASN ** D 135 ASN ** 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 = 0.5121 r_free = 0.5121 target = 0.264846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.231230 restraints weight = 23025.974| |-----------------------------------------------------------------------------| r_work (start): 0.4839 rms_B_bonded: 2.20 r_work: 0.4603 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4430 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14325 Z= 0.145 Angle : 0.659 10.317 19443 Z= 0.338 Chirality : 0.045 0.186 2052 Planarity : 0.005 0.078 2546 Dihedral : 6.473 51.169 2002 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.80 % Favored : 91.14 % Rotamer: Outliers : 3.97 % Allowed : 24.25 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.20), residues: 1784 helix: 1.14 (0.26), residues: 403 sheet: -2.12 (0.22), residues: 530 loop : -1.95 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 57 TYR 0.020 0.001 TYR A 565 PHE 0.024 0.002 PHE D 184 TRP 0.035 0.001 TRP B 138 HIS 0.003 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00322 (14322) covalent geometry : angle 0.65916 (19437) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.77546 ( 6) hydrogen bonds : bond 0.03609 ( 474) hydrogen bonds : angle 5.64491 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5528 (OUTLIER) cc_final: 0.4873 (pp30) REVERT: A 173 GLN cc_start: 0.6924 (tm-30) cc_final: 0.6241 (tm-30) REVERT: A 197 GLU cc_start: 0.7720 (tp30) cc_final: 0.7435 (tm-30) REVERT: A 365 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 473 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8136 (mtt-85) REVERT: A 780 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5424 (ppp) REVERT: B 51 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8139 (mm) REVERT: C 50 TRP cc_start: 0.7587 (t60) cc_final: 0.7079 (t60) REVERT: C 438 MET cc_start: 0.0358 (mmp) cc_final: -0.0941 (mmt) REVERT: D 54 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6734 (mt) REVERT: D 113 TRP cc_start: 0.8184 (m-10) cc_final: 0.7887 (m-10) REVERT: D 165 LYS cc_start: 0.4380 (mttp) cc_final: 0.4168 (mttp) REVERT: D 166 LEU cc_start: -0.0682 (OUTLIER) cc_final: -0.1432 (tp) REVERT: D 184 PHE cc_start: 0.3185 (OUTLIER) cc_final: 0.2819 (m-80) outliers start: 57 outliers final: 46 residues processed: 149 average time/residue: 0.1078 time to fit residues: 24.6346 Evaluate side-chains 156 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 184 PHE Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 31 optimal weight: 0.0980 chunk 109 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 130 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 562 ASN ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN C 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.261815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.230566 restraints weight = 22820.583| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 1.98 r_work: 0.4549 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4376 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14325 Z= 0.106 Angle : 0.622 10.379 19443 Z= 0.316 Chirality : 0.043 0.190 2052 Planarity : 0.005 0.074 2546 Dihedral : 6.178 48.441 2002 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.57 % Favored : 92.38 % Rotamer: Outliers : 3.41 % Allowed : 24.60 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1784 helix: 1.21 (0.26), residues: 406 sheet: -1.79 (0.23), residues: 526 loop : -1.92 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.017 0.001 TYR A 565 PHE 0.023 0.001 PHE D 184 TRP 0.056 0.001 TRP B 138 HIS 0.003 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00226 (14322) covalent geometry : angle 0.62181 (19437) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.70082 ( 6) hydrogen bonds : bond 0.03270 ( 474) hydrogen bonds : angle 5.31800 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.5467 (OUTLIER) cc_final: 0.4752 (pp30) REVERT: A 173 GLN cc_start: 0.6800 (tm-30) cc_final: 0.6106 (tm-30) REVERT: A 195 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7782 (pp) REVERT: A 197 GLU cc_start: 0.7791 (tp30) cc_final: 0.7527 (tm-30) REVERT: A 365 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6433 (t80) REVERT: A 473 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8198 (mtt-85) REVERT: A 661 TYR cc_start: 0.8048 (p90) cc_final: 0.7791 (p90) REVERT: B 51 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7805 (mm) REVERT: B 112 MET cc_start: 0.8533 (ptp) cc_final: 0.8230 (ptt) REVERT: C 438 MET cc_start: 0.0285 (mmp) cc_final: -0.0950 (mmt) REVERT: C 453 MET cc_start: 0.0441 (mmt) cc_final: -0.0976 (tpp) REVERT: D 54 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6769 (mt) REVERT: D 113 TRP cc_start: 0.8320 (m-10) cc_final: 0.8055 (m-10) REVERT: D 165 LYS cc_start: 0.4364 (mttp) cc_final: 0.4154 (mttp) outliers start: 49 outliers final: 38 residues processed: 145 average time/residue: 0.1062 time to fit residues: 23.7939 Evaluate side-chains 150 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 302 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 143 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** A 600 GLN ** 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 = 0.5134 r_free = 0.5134 target = 0.265745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.234441 restraints weight = 22960.366| |-----------------------------------------------------------------------------| r_work (start): 0.4860 rms_B_bonded: 2.19 r_work: 0.4608 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4425 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14325 Z= 0.156 Angle : 0.658 10.019 19443 Z= 0.337 Chirality : 0.044 0.182 2052 Planarity : 0.005 0.068 2546 Dihedral : 6.293 48.800 2000 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.92 % Favored : 90.02 % Rotamer: Outliers : 3.55 % Allowed : 24.81 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1784 helix: 1.19 (0.26), residues: 406 sheet: -1.90 (0.23), residues: 530 loop : -1.96 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.019 0.002 TYR A 565 PHE 0.024 0.002 PHE D 184 TRP 0.052 0.002 TRP B 138 HIS 0.004 0.001 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00350 (14322) covalent geometry : angle 0.65785 (19437) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.65398 ( 6) hydrogen bonds : bond 0.03522 ( 474) hydrogen bonds : angle 5.53538 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4787.87 seconds wall clock time: 82 minutes 10.46 seconds (4930.46 seconds total)