Starting phenix.real_space_refine on Thu Jul 2 15:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hf5_34713/07_2026/8hf5_34713.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5732 2.51 5 N 1462 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.40, per 1000 atoms: 0.16 Number of scatterers: 8918 At special positions: 0 Unit cell: (81.51, 80.652, 143.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 6 15.00 Mg 2 11.99 O 1686 8.00 N 1462 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 300.8 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 66.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.776A pdb=" N LEU A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 195 removed outlier: 3.561A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 250 removed outlier: 4.201A pdb=" N LEU A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 4.085A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.903A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.876A pdb=" N ILE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.773A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.522A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 417 removed outlier: 4.064A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 443 removed outlier: 3.870A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 464 removed outlier: 4.362A pdb=" N GLU A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.683A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.004A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 4.230A pdb=" N ALA A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.607A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 683' Processing helix chain 'A' and resid 700 through 706 removed outlier: 3.530A pdb=" N LEU A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 168 through 194 removed outlier: 3.628A pdb=" N TYR B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 196 No H-bonds generated for 'chain 'B' and resid 195 through 196' Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 200 through 250 removed outlier: 3.569A pdb=" N ALA B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.820A pdb=" N ILE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 304 removed outlier: 5.630A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 325 removed outlier: 4.096A pdb=" N VAL B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.159A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.676A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 387 removed outlier: 3.970A pdb=" N TYR B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 416 Processing helix chain 'B' and resid 420 through 431 removed outlier: 3.572A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 463 removed outlier: 4.272A pdb=" N VAL B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.545A pdb=" N MET B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 587 through 598 removed outlier: 3.552A pdb=" N ILE B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.683A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.595A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 removed outlier: 4.216A pdb=" N ALA B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.828A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.803A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 489 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN A 538 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.608A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP A 646 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU A 563 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 643 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE A 674 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 645 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 697 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 500 through 506 removed outlier: 6.937A pdb=" N SER B 501 " --> pdb=" O HIS B 490 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS B 490 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 503 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 505 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 489 " --> pdb=" O GLN B 538 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN B 538 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 562 removed outlier: 6.577A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 512 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1524 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: 1.16 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1952 1.33 - 1.47: 2924 1.47 - 1.61: 4116 1.61 - 1.76: 0 1.76 - 1.90: 58 Bond restraints: 9050 Sorted by residual: bond pdb=" CA GLN A 226 " pdb=" C GLN A 226 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU B 645 " pdb=" C LEU B 645 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.23e-02 6.61e+03 2.61e+01 bond pdb=" CA GLN A 612 " pdb=" C GLN A 612 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.50e+01 bond pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 bond pdb=" CA GLN A 235 " pdb=" C GLN A 235 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 11678 2.88 - 5.76: 496 5.76 - 8.64: 72 8.64 - 11.52: 23 11.52 - 14.40: 9 Bond angle restraints: 12278 Sorted by residual: angle pdb=" N ARG A 202 " pdb=" CA ARG A 202 " pdb=" C ARG A 202 " ideal model delta sigma weight residual 113.28 99.73 13.55 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N ALA B 169 " pdb=" CA ALA B 169 " pdb=" C ALA B 169 " ideal model delta sigma weight residual 111.28 121.97 -10.69 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N PRO A 608 " pdb=" CA PRO A 608 " pdb=" C PRO A 608 " ideal model delta sigma weight residual 114.18 100.76 13.42 1.39e+00 5.18e-01 9.32e+01 angle pdb=" N TYR A 196 " pdb=" CA TYR A 196 " pdb=" C TYR A 196 " ideal model delta sigma weight residual 112.58 124.06 -11.48 1.22e+00 6.72e-01 8.86e+01 angle pdb=" N LYS B 163 " pdb=" CA LYS B 163 " pdb=" C LYS B 163 " ideal model delta sigma weight residual 114.12 101.16 12.96 1.39e+00 5.18e-01 8.69e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 5082 22.53 - 45.05: 333 45.05 - 67.58: 45 67.58 - 90.11: 6 90.11 - 112.63: 2 Dihedral angle restraints: 5468 sinusoidal: 2174 harmonic: 3294 Sorted by residual: dihedral pdb=" CA GLU A 469 " pdb=" C GLU A 469 " pdb=" N GLU A 470 " pdb=" CA GLU A 470 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C TYR A 216 " pdb=" N TYR A 216 " pdb=" CA TYR A 216 " pdb=" CB TYR A 216 " ideal model delta harmonic sigma weight residual -122.60 -135.72 13.12 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C GLN A 200 " pdb=" N GLN A 200 " pdb=" CA GLN A 200 " pdb=" CB GLN A 200 " ideal model delta harmonic sigma weight residual -122.60 -135.31 12.71 0 2.50e+00 1.60e-01 2.58e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1355 0.142 - 0.285: 108 0.285 - 0.427: 26 0.427 - 0.569: 9 0.569 - 0.711: 4 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CB ILE A 600 " pdb=" CA ILE A 600 " pdb=" CG1 ILE A 600 " pdb=" CG2 ILE A 600 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA TYR A 216 " pdb=" N TYR A 216 " pdb=" C TYR A 216 " pdb=" CB TYR A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" CA GLN A 200 " pdb=" N GLN A 200 " pdb=" C GLN A 200 " pdb=" CB GLN A 200 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 ... (remaining 1499 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 239 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE B 239 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE B 239 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B 240 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 610 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ASN B 610 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B 610 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 611 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 286 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE B 286 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 286 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 287 " -0.014 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 158 2.63 - 3.20: 7833 3.20 - 3.77: 13204 3.77 - 4.33: 17427 4.33 - 4.90: 28304 Nonbonded interactions: 66926 Sorted by model distance: nonbonded pdb=" O2B AGS A 801 " pdb="MG MG A 802 " model vdw 2.063 2.170 nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 2.064 2.170 nonbonded pdb=" OG1 THR A 524 " pdb="MG MG A 802 " model vdw 2.145 2.170 nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 2.170 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.171 2.170 ... (remaining 66921 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 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:5.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.011 0.079 9050 Z= 0.740 Angle : 1.384 14.404 12278 Z= 0.848 Chirality : 0.099 0.711 1502 Planarity : 0.007 0.057 1522 Dihedral : 14.796 112.635 3344 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.44 % Favored : 93.94 % Rotamer: Outliers : 3.74 % Allowed : 3.13 % Favored : 93.13 % Cbeta Deviations : 0.66 % 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: -1.78 (0.23), residues: 1122 helix: -0.60 (0.18), residues: 694 sheet: -0.01 (0.67), residues: 70 loop : -2.43 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 386 TYR 0.021 0.002 TYR B 228 PHE 0.034 0.003 PHE A 468 TRP 0.014 0.003 TRP B 408 HIS 0.010 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01077 / 0.74 ( 9050) covalent geometry : angle 1.38351 / 0.85 (12278) hydrogen bonds : bond 0.21394 / 14.25 ( 513) hydrogen bonds : angle 6.50830 / 4.73 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.348 Fit side-chains REVERT: A 173 LEU cc_start: 0.8835 (tp) cc_final: 0.8594 (tm) REVERT: A 201 MET cc_start: 0.7964 (mmm) cc_final: 0.7688 (mpp) REVERT: A 663 ASN cc_start: 0.9070 (m-40) cc_final: 0.8623 (m-40) REVERT: A 677 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.7854 (mmp-170) REVERT: A 710 PHE cc_start: 0.8632 (t80) cc_final: 0.8177 (t80) REVERT: B 164 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: B 471 LYS cc_start: 0.8417 (mmpt) cc_final: 0.8193 (mmmt) REVERT: B 713 HIS cc_start: 0.8998 (t70) cc_final: 0.8788 (t70) outliers start: 37 outliers final: 14 residues processed: 152 average time/residue: 0.3363 time to fit residues: 55.8320 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN A 226 GLN B 164 GLN B 423 GLN B 490 HIS B 610 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075979 restraints weight = 17762.754| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.87 r_work: 0.3115 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.163 Angle : 0.663 8.307 12278 Z= 0.345 Chirality : 0.043 0.415 1502 Planarity : 0.004 0.045 1522 Dihedral : 8.926 129.324 1259 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 4.04 % Allowed : 12.22 % Favored : 83.74 % 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: -0.33 (0.25), residues: 1122 helix: 0.68 (0.19), residues: 706 sheet: -0.20 (0.65), residues: 70 loop : -2.09 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 386 TYR 0.022 0.001 TYR A 196 PHE 0.013 0.001 PHE A 382 TRP 0.019 0.003 TRP B 408 HIS 0.003 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 9050) covalent geometry : angle 0.66296 / 0.34 (12278) hydrogen bonds : bond 0.08473 / 5.72 ( 513) hydrogen bonds : angle 4.16928 / 2.98 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.309 Fit side-chains REVERT: A 201 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7621 (mpt) REVERT: A 203 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7540 (m) REVERT: A 239 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 610 ASN cc_start: 0.7901 (m-40) cc_final: 0.7100 (t0) REVERT: A 663 ASN cc_start: 0.9130 (m-40) cc_final: 0.8733 (m-40) REVERT: A 677 ARG cc_start: 0.8328 (mmp-170) cc_final: 0.8112 (mmt180) REVERT: A 710 PHE cc_start: 0.8552 (t80) cc_final: 0.8210 (t80) REVERT: B 207 ILE cc_start: 0.7388 (mm) cc_final: 0.7117 (mt) REVERT: B 326 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8005 (tpt) REVERT: B 337 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8594 (mtt) REVERT: B 471 LYS cc_start: 0.8175 (mmpt) cc_final: 0.7974 (mmmt) REVERT: B 485 THR cc_start: 0.8872 (m) cc_final: 0.8651 (p) REVERT: B 518 ILE cc_start: 0.8721 (tt) cc_final: 0.8408 (pp) outliers start: 40 outliers final: 13 residues processed: 129 average time/residue: 0.3019 time to fit residues: 43.3472 Evaluate side-chains 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071244 restraints weight = 18110.069| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.87 r_work: 0.3026 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9050 Z= 0.219 Angle : 0.661 7.682 12278 Z= 0.348 Chirality : 0.044 0.359 1502 Planarity : 0.004 0.043 1522 Dihedral : 8.305 136.609 1246 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 4.24 % Allowed : 15.66 % Favored : 80.10 % 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: 0.26 (0.25), residues: 1122 helix: 1.22 (0.20), residues: 702 sheet: -0.39 (0.64), residues: 70 loop : -1.87 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.011 0.001 TYR A 433 PHE 0.016 0.002 PHE A 382 TRP 0.012 0.002 TRP B 408 HIS 0.003 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 9050) covalent geometry : angle 0.66140 / 0.35 (12278) hydrogen bonds : bond 0.08339 / 5.62 ( 513) hydrogen bonds : angle 4.07055 / 2.91 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.359 Fit side-chains REVERT: A 201 MET cc_start: 0.7785 (mmm) cc_final: 0.7546 (mpt) REVERT: A 203 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 239 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8724 (tt) REVERT: A 610 ASN cc_start: 0.7957 (m-40) cc_final: 0.7228 (t0) REVERT: A 663 ASN cc_start: 0.9173 (m-40) cc_final: 0.8785 (m-40) REVERT: A 677 ARG cc_start: 0.8410 (mmp-170) cc_final: 0.8175 (mmt180) REVERT: A 710 PHE cc_start: 0.8690 (t80) cc_final: 0.8388 (t80) REVERT: B 207 ILE cc_start: 0.7173 (mm) cc_final: 0.6941 (mp) REVERT: B 409 MET cc_start: 0.8340 (tmm) cc_final: 0.8055 (tmm) REVERT: B 471 LYS cc_start: 0.8223 (mmpt) cc_final: 0.7961 (mmmt) REVERT: B 518 ILE cc_start: 0.8922 (tt) cc_final: 0.8632 (pp) outliers start: 42 outliers final: 22 residues processed: 117 average time/residue: 0.3093 time to fit residues: 40.0228 Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074691 restraints weight = 18005.286| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.88 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.132 Angle : 0.562 7.529 12278 Z= 0.291 Chirality : 0.040 0.301 1502 Planarity : 0.003 0.040 1522 Dihedral : 8.108 138.992 1243 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.33 % Allowed : 18.38 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1122 helix: 1.62 (0.20), residues: 702 sheet: -0.20 (0.66), residues: 70 loop : -1.80 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 386 TYR 0.006 0.001 TYR B 491 PHE 0.014 0.001 PHE A 308 TRP 0.006 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 9050) covalent geometry : angle 0.56189 / 0.29 (12278) hydrogen bonds : bond 0.06745 / 4.53 ( 513) hydrogen bonds : angle 3.71466 / 2.64 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.222 Fit side-chains REVERT: A 201 MET cc_start: 0.7733 (mmm) cc_final: 0.7292 (mpp) REVERT: A 227 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8162 (tt0) REVERT: A 239 ILE cc_start: 0.8688 (tt) cc_final: 0.8486 (tt) REVERT: A 309 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: A 480 MET cc_start: 0.8327 (mmt) cc_final: 0.8043 (pmm) REVERT: A 663 ASN cc_start: 0.9163 (m-40) cc_final: 0.8772 (m-40) REVERT: A 677 ARG cc_start: 0.8457 (mmp-170) cc_final: 0.8222 (mmt180) REVERT: A 710 PHE cc_start: 0.8735 (t80) cc_final: 0.8405 (t80) REVERT: B 157 PHE cc_start: 0.4934 (m-10) cc_final: 0.4605 (m-10) REVERT: B 227 GLU cc_start: 0.8305 (tt0) cc_final: 0.8005 (tt0) REVERT: B 240 ASP cc_start: 0.8250 (t0) cc_final: 0.7959 (t0) REVERT: B 409 MET cc_start: 0.8263 (tmm) cc_final: 0.7999 (tmm) REVERT: B 471 LYS cc_start: 0.8311 (mmpt) cc_final: 0.8065 (mmmt) REVERT: B 518 ILE cc_start: 0.8816 (tt) cc_final: 0.8473 (pp) outliers start: 33 outliers final: 21 residues processed: 118 average time/residue: 0.2984 time to fit residues: 38.9834 Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074525 restraints weight = 18037.909| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.89 r_work: 0.3090 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.137 Angle : 0.568 8.153 12278 Z= 0.290 Chirality : 0.040 0.245 1502 Planarity : 0.003 0.042 1522 Dihedral : 8.009 139.766 1240 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 4.55 % Allowed : 18.79 % Favored : 76.67 % 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: 0.97 (0.26), residues: 1122 helix: 1.81 (0.20), residues: 700 sheet: -0.12 (0.67), residues: 70 loop : -1.68 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 386 TYR 0.006 0.001 TYR B 491 PHE 0.013 0.001 PHE A 308 TRP 0.005 0.001 TRP A 408 HIS 0.001 0.000 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 9050) covalent geometry : angle 0.56751 / 0.29 (12278) hydrogen bonds : bond 0.06497 / 4.36 ( 513) hydrogen bonds : angle 3.63144 / 2.57 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 0.255 Fit side-chains REVERT: A 201 MET cc_start: 0.7684 (mmm) cc_final: 0.7349 (mpm) REVERT: A 227 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8172 (tt0) REVERT: A 239 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 309 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: A 480 MET cc_start: 0.8265 (mmt) cc_final: 0.7962 (pmm) REVERT: A 663 ASN cc_start: 0.9186 (m-40) cc_final: 0.8807 (m-40) REVERT: A 677 ARG cc_start: 0.8449 (mmp-170) cc_final: 0.8184 (mmp-170) REVERT: A 710 PHE cc_start: 0.8771 (t80) cc_final: 0.8423 (t80) REVERT: B 205 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5560 (tt) REVERT: B 227 GLU cc_start: 0.8357 (tt0) cc_final: 0.8020 (tt0) REVERT: B 471 LYS cc_start: 0.8301 (mmpt) cc_final: 0.8039 (mmmt) REVERT: B 479 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6216 (OUTLIER) REVERT: B 518 ILE cc_start: 0.8815 (tt) cc_final: 0.8481 (pp) outliers start: 45 outliers final: 25 residues processed: 122 average time/residue: 0.3048 time to fit residues: 40.9739 Evaluate side-chains 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 GLN B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074931 restraints weight = 18109.199| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.92 r_work: 0.3092 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.129 Angle : 0.553 8.796 12278 Z= 0.282 Chirality : 0.040 0.244 1502 Planarity : 0.003 0.042 1522 Dihedral : 7.979 140.070 1240 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.94 % Allowed : 19.60 % Favored : 76.46 % 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: 1.14 (0.26), residues: 1122 helix: 1.96 (0.20), residues: 700 sheet: -0.08 (0.67), residues: 70 loop : -1.63 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.009 0.001 TYR A 711 PHE 0.016 0.001 PHE A 308 TRP 0.002 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9050) covalent geometry : angle 0.55341 / 0.28 (12278) hydrogen bonds : bond 0.06146 / 4.12 ( 513) hydrogen bonds : angle 3.55156 / 2.52 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.248 Fit side-chains REVERT: A 201 MET cc_start: 0.7601 (mmm) cc_final: 0.7099 (mpp) REVERT: A 227 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8107 (tt0) REVERT: A 309 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: A 480 MET cc_start: 0.8206 (mmt) cc_final: 0.8004 (pmm) REVERT: A 663 ASN cc_start: 0.9175 (m-40) cc_final: 0.8795 (m-40) REVERT: A 677 ARG cc_start: 0.8467 (mmp-170) cc_final: 0.8098 (mmp-170) REVERT: A 710 PHE cc_start: 0.8823 (t80) cc_final: 0.8453 (t80) REVERT: B 205 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5596 (tt) REVERT: B 518 ILE cc_start: 0.8827 (tt) cc_final: 0.8482 (pp) outliers start: 39 outliers final: 25 residues processed: 113 average time/residue: 0.3208 time to fit residues: 39.8996 Evaluate side-chains 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074318 restraints weight = 18167.638| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.93 r_work: 0.3079 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.141 Angle : 0.576 9.489 12278 Z= 0.291 Chirality : 0.040 0.221 1502 Planarity : 0.003 0.041 1522 Dihedral : 7.956 140.930 1238 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 3.23 % Allowed : 21.31 % Favored : 75.45 % 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: 1.17 (0.26), residues: 1122 helix: 1.99 (0.20), residues: 698 sheet: -0.04 (0.67), residues: 70 loop : -1.61 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.008 0.001 TYR A 433 PHE 0.012 0.001 PHE A 382 TRP 0.001 0.000 TRP A 408 HIS 0.005 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9050) covalent geometry : angle 0.57640 / 0.29 (12278) hydrogen bonds : bond 0.06220 / 4.17 ( 513) hydrogen bonds : angle 3.56476 / 2.53 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.210 Fit side-chains REVERT: A 201 MET cc_start: 0.7488 (mmm) cc_final: 0.6982 (mpp) REVERT: A 227 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8146 (tt0) REVERT: A 309 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 480 MET cc_start: 0.8345 (mmt) cc_final: 0.7906 (pmm) REVERT: A 663 ASN cc_start: 0.9186 (m-40) cc_final: 0.8811 (m-40) REVERT: A 677 ARG cc_start: 0.8470 (mmp-170) cc_final: 0.8265 (mmp-170) REVERT: A 710 PHE cc_start: 0.8834 (t80) cc_final: 0.8453 (t80) REVERT: B 205 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5522 (tt) REVERT: B 227 GLU cc_start: 0.8414 (tt0) cc_final: 0.8060 (tt0) REVERT: B 471 LYS cc_start: 0.8264 (mmpt) cc_final: 0.8051 (mmmt) REVERT: B 518 ILE cc_start: 0.8869 (tt) cc_final: 0.8543 (pp) outliers start: 32 outliers final: 26 residues processed: 108 average time/residue: 0.3070 time to fit residues: 36.5958 Evaluate side-chains 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075725 restraints weight = 18044.438| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.92 r_work: 0.3104 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9050 Z= 0.120 Angle : 0.558 10.707 12278 Z= 0.279 Chirality : 0.039 0.217 1502 Planarity : 0.003 0.045 1522 Dihedral : 7.917 140.912 1238 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 3.74 % Allowed : 21.21 % Favored : 75.05 % 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: 1.27 (0.26), residues: 1122 helix: 2.05 (0.20), residues: 702 sheet: 0.01 (0.67), residues: 70 loop : -1.56 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 386 TYR 0.006 0.001 TYR B 491 PHE 0.011 0.001 PHE A 308 TRP 0.002 0.000 TRP A 408 HIS 0.005 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9050) covalent geometry : angle 0.55823 / 0.28 (12278) hydrogen bonds : bond 0.05755 / 3.85 ( 513) hydrogen bonds : angle 3.48367 / 2.46 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.242 Fit side-chains REVERT: A 201 MET cc_start: 0.7508 (mmm) cc_final: 0.6999 (mpp) REVERT: A 227 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8119 (tt0) REVERT: A 309 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: A 480 MET cc_start: 0.8340 (mmt) cc_final: 0.7918 (pmm) REVERT: A 663 ASN cc_start: 0.9169 (m-40) cc_final: 0.8788 (m-40) REVERT: A 677 ARG cc_start: 0.8481 (mmp-170) cc_final: 0.8121 (mmp-170) REVERT: A 710 PHE cc_start: 0.8811 (t80) cc_final: 0.8377 (t80) REVERT: B 205 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5450 (tt) REVERT: B 227 GLU cc_start: 0.8365 (tt0) cc_final: 0.8048 (tt0) REVERT: B 402 LEU cc_start: 0.8610 (tm) cc_final: 0.8340 (mt) REVERT: B 471 LYS cc_start: 0.8268 (mmpt) cc_final: 0.8031 (mmmt) REVERT: B 518 ILE cc_start: 0.8822 (tt) cc_final: 0.8471 (pp) REVERT: B 605 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7378 (mp0) outliers start: 37 outliers final: 23 residues processed: 116 average time/residue: 0.3308 time to fit residues: 42.1395 Evaluate side-chains 109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.101724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075811 restraints weight = 17971.650| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.92 r_work: 0.3105 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9050 Z= 0.122 Angle : 0.572 10.116 12278 Z= 0.283 Chirality : 0.040 0.208 1502 Planarity : 0.003 0.046 1522 Dihedral : 7.733 141.566 1234 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 2.83 % Allowed : 22.73 % Favored : 74.44 % 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: 1.32 (0.26), residues: 1122 helix: 2.10 (0.20), residues: 700 sheet: -0.02 (0.67), residues: 70 loop : -1.56 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.006 0.001 TYR A 433 PHE 0.019 0.001 PHE A 308 TRP 0.002 0.000 TRP A 408 HIS 0.005 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9050) covalent geometry : angle 0.57198 / 0.28 (12278) hydrogen bonds : bond 0.05618 / 3.76 ( 513) hydrogen bonds : angle 3.43809 / 2.43 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.254 Fit side-chains REVERT: A 201 MET cc_start: 0.7506 (mmm) cc_final: 0.6997 (mpp) REVERT: A 227 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8111 (tt0) REVERT: A 309 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 663 ASN cc_start: 0.9172 (m-40) cc_final: 0.8793 (m-40) REVERT: A 677 ARG cc_start: 0.8489 (mmp-170) cc_final: 0.8177 (mmp-170) REVERT: A 710 PHE cc_start: 0.8774 (t80) cc_final: 0.8389 (t80) REVERT: B 205 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5354 (tt) REVERT: B 227 GLU cc_start: 0.8391 (tt0) cc_final: 0.8101 (tt0) REVERT: B 402 LEU cc_start: 0.8595 (tm) cc_final: 0.8335 (mt) REVERT: B 471 LYS cc_start: 0.8282 (mmpt) cc_final: 0.8044 (mmmt) REVERT: B 518 ILE cc_start: 0.8834 (tt) cc_final: 0.8482 (pp) REVERT: B 605 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7351 (mp0) outliers start: 28 outliers final: 19 residues processed: 106 average time/residue: 0.3078 time to fit residues: 35.8673 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0980 chunk 31 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078168 restraints weight = 17787.011| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.89 r_work: 0.3145 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9050 Z= 0.114 Angle : 0.579 11.324 12278 Z= 0.284 Chirality : 0.039 0.208 1502 Planarity : 0.003 0.041 1522 Dihedral : 7.675 141.183 1234 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.12 % Allowed : 23.33 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.42 (0.27), residues: 1122 helix: 2.20 (0.21), residues: 700 sheet: 0.07 (0.68), residues: 70 loop : -1.57 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.006 0.001 TYR A 559 PHE 0.018 0.001 PHE A 308 TRP 0.005 0.001 TRP A 408 HIS 0.005 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9050) covalent geometry : angle 0.57897 / 0.28 (12278) hydrogen bonds : bond 0.04998 / 3.34 ( 513) hydrogen bonds : angle 3.34279 / 2.36 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.355 Fit side-chains REVERT: A 201 MET cc_start: 0.7521 (mmm) cc_final: 0.7006 (mpp) REVERT: A 227 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8054 (tt0) REVERT: A 309 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: A 480 MET cc_start: 0.8050 (mmm) cc_final: 0.7715 (pmm) REVERT: A 663 ASN cc_start: 0.9184 (m-40) cc_final: 0.8799 (m-40) REVERT: A 677 ARG cc_start: 0.8504 (mmp-170) cc_final: 0.8220 (mmp-170) REVERT: A 710 PHE cc_start: 0.8756 (t80) cc_final: 0.8349 (t80) REVERT: B 205 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5267 (tt) REVERT: B 227 GLU cc_start: 0.8354 (tt0) cc_final: 0.8089 (tt0) REVERT: B 402 LEU cc_start: 0.8588 (tm) cc_final: 0.8358 (mt) REVERT: B 471 LYS cc_start: 0.8285 (mmpt) cc_final: 0.8036 (mmmt) REVERT: B 518 ILE cc_start: 0.8788 (tt) cc_final: 0.8411 (pp) REVERT: B 605 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7369 (mp0) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.3167 time to fit residues: 35.5424 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 41 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076383 restraints weight = 17843.441| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.88 r_work: 0.3117 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9050 Z= 0.121 Angle : 0.576 11.172 12278 Z= 0.284 Chirality : 0.039 0.198 1502 Planarity : 0.003 0.043 1522 Dihedral : 7.665 142.345 1234 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 2.32 % Allowed : 23.64 % Favored : 74.04 % 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: 1.50 (0.27), residues: 1122 helix: 2.25 (0.21), residues: 700 sheet: 0.10 (0.68), residues: 70 loop : -1.53 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 386 TYR 0.007 0.001 TYR A 433 PHE 0.017 0.001 PHE A 308 TRP 0.004 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9050) covalent geometry : angle 0.57565 / 0.28 (12278) hydrogen bonds : bond 0.05329 / 3.55 ( 513) hydrogen bonds : angle 3.37766 / 2.38 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.46 seconds wall clock time: 32 minutes 26.97 seconds (1946.97 seconds total)