Starting phenix.real_space_refine on Tue Mar 3 22:59:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf5_34713/03_2026/8hf5_34713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf5_34713/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2026/8hf5_34713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2026/8hf5_34713.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2026/8hf5_34713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_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-5986/lib/python3.9/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: 2.18, per 1000 atoms: 0.24 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: 0.62 Conformation dependent library (CDL) restraints added in 342.9 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: 0.29 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: 1.43 Time building geometry restraints manager: 0.89 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: 5094 22.53 - 45.05: 343 45.05 - 67.58: 45 67.58 - 90.11: 6 90.11 - 112.63: 2 Dihedral angle restraints: 5490 sinusoidal: 2196 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 5487 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: 0.02 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 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 : 14.892 112.635 3366 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 covalent geometry : bond 0.01077 ( 9050) covalent geometry : angle 1.38351 (12278) hydrogen bonds : bond 0.21394 ( 513) hydrogen bonds : angle 6.50830 ( 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 : 0.329 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: 0.4264 time to fit residues: 70.3711 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 : 0.280 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.101238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075947 restraints weight = 17758.333| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.87 r_work: 0.3116 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9050 Z= 0.161 Angle : 0.659 8.215 12278 Z= 0.342 Chirality : 0.043 0.415 1502 Planarity : 0.004 0.045 1522 Dihedral : 9.759 131.863 1281 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 4.14 % Allowed : 12.02 % Favored : 83.84 % 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: -0.36 (0.25), residues: 1122 helix: 0.65 (0.19), residues: 706 sheet: -0.20 (0.65), residues: 70 loop : -2.07 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 386 TYR 0.020 0.001 TYR A 196 PHE 0.012 0.001 PHE A 382 TRP 0.019 0.003 TRP B 408 HIS 0.002 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9050) covalent geometry : angle 0.65906 (12278) hydrogen bonds : bond 0.08412 ( 513) hydrogen bonds : angle 4.15265 ( 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 142 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.272 Fit side-chains REVERT: A 203 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7493 (m) REVERT: A 239 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 610 ASN cc_start: 0.7871 (m-40) cc_final: 0.7072 (t0) REVERT: A 663 ASN cc_start: 0.9130 (m-40) cc_final: 0.8736 (m-40) REVERT: A 677 ARG cc_start: 0.8332 (mmp-170) cc_final: 0.7932 (mmp-170) REVERT: A 710 PHE cc_start: 0.8536 (t80) cc_final: 0.8199 (t80) REVERT: B 207 ILE cc_start: 0.7385 (mm) cc_final: 0.7111 (mt) REVERT: B 326 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8015 (tpt) REVERT: B 337 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8603 (mtt) REVERT: B 485 THR cc_start: 0.8871 (m) cc_final: 0.8648 (p) REVERT: B 518 ILE cc_start: 0.8711 (tt) cc_final: 0.8395 (pp) outliers start: 41 outliers final: 13 residues processed: 131 average time/residue: 0.3548 time to fit residues: 51.3850 Evaluate side-chains 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072538 restraints weight = 17992.746| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.86 r_work: 0.3048 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9050 Z= 0.188 Angle : 0.632 7.964 12278 Z= 0.332 Chirality : 0.043 0.359 1502 Planarity : 0.003 0.041 1522 Dihedral : 9.000 133.504 1268 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer: Outliers : 4.44 % Allowed : 15.15 % Favored : 80.40 % 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: 0.31 (0.25), residues: 1122 helix: 1.26 (0.20), residues: 702 sheet: -0.28 (0.65), residues: 70 loop : -1.88 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 386 TYR 0.010 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 covalent geometry : bond 0.00427 ( 9050) covalent geometry : angle 0.63177 (12278) hydrogen bonds : bond 0.07943 ( 513) hydrogen bonds : angle 3.96745 ( 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 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.257 Fit side-chains REVERT: A 203 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7564 (m) REVERT: A 239 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 309 PHE cc_start: 0.7943 (t80) cc_final: 0.7659 (m-80) REVERT: A 480 MET cc_start: 0.8399 (mmt) cc_final: 0.8017 (pmm) REVERT: A 610 ASN cc_start: 0.7894 (m-40) cc_final: 0.7183 (t0) REVERT: A 663 ASN cc_start: 0.9175 (m-40) cc_final: 0.8783 (m-40) REVERT: A 677 ARG cc_start: 0.8396 (mmp-170) cc_final: 0.8172 (mmt180) REVERT: A 710 PHE cc_start: 0.8701 (t80) cc_final: 0.8393 (t80) REVERT: B 207 ILE cc_start: 0.7097 (mm) cc_final: 0.6867 (mp) REVERT: B 240 ASP cc_start: 0.8518 (t0) cc_final: 0.8151 (t0) REVERT: B 409 MET cc_start: 0.8319 (tmm) cc_final: 0.8025 (tmm) REVERT: B 518 ILE cc_start: 0.8836 (tt) cc_final: 0.8518 (pp) outliers start: 44 outliers final: 24 residues processed: 119 average time/residue: 0.3537 time to fit residues: 46.5417 Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain A residue 197 VAL 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 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 350 ASP Chi-restraints excluded: chain B residue 406 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: 5.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073866 restraints weight = 18021.130| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.88 r_work: 0.3073 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2426 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= 0.147 Angle : 0.577 7.537 12278 Z= 0.298 Chirality : 0.041 0.294 1502 Planarity : 0.003 0.038 1522 Dihedral : 8.427 128.913 1265 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 3.84 % Allowed : 17.88 % Favored : 78.28 % 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: 0.74 (0.26), residues: 1122 helix: 1.64 (0.20), residues: 700 sheet: -0.18 (0.66), residues: 70 loop : -1.77 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.007 0.001 TYR B 491 PHE 0.013 0.001 PHE A 308 TRP 0.006 0.001 TRP B 408 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9050) covalent geometry : angle 0.57747 (12278) hydrogen bonds : bond 0.06934 ( 513) hydrogen bonds : angle 3.75337 ( 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 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.304 Fit side-chains REVERT: A 227 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8173 (tt0) REVERT: A 239 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 309 PHE cc_start: 0.7974 (t80) cc_final: 0.7699 (m-80) REVERT: A 663 ASN cc_start: 0.9169 (m-40) cc_final: 0.8780 (m-40) REVERT: A 677 ARG cc_start: 0.8449 (mmp-170) cc_final: 0.8214 (mmt180) REVERT: A 710 PHE cc_start: 0.8723 (t80) cc_final: 0.8402 (t80) REVERT: B 157 PHE cc_start: 0.5013 (m-10) cc_final: 0.4683 (m-10) REVERT: B 240 ASP cc_start: 0.8344 (t0) cc_final: 0.8023 (t0) REVERT: B 409 MET cc_start: 0.8295 (tmm) cc_final: 0.7676 (tmm) REVERT: B 479 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6082 (pt) REVERT: B 518 ILE cc_start: 0.8819 (tt) cc_final: 0.8487 (pp) outliers start: 38 outliers final: 23 residues processed: 118 average time/residue: 0.3509 time to fit residues: 45.8417 Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 197 VAL 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 329 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 559 TYR 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 412 VAL 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 Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073458 restraints weight = 18069.630| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.88 r_work: 0.3069 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.152 Angle : 0.594 8.202 12278 Z= 0.303 Chirality : 0.041 0.253 1502 Planarity : 0.003 0.036 1522 Dihedral : 8.143 128.823 1260 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 4.44 % Allowed : 18.69 % Favored : 76.87 % 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: 0.94 (0.26), residues: 1122 helix: 1.79 (0.20), residues: 700 sheet: -0.13 (0.67), residues: 70 loop : -1.68 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.019 0.001 TYR A 196 PHE 0.016 0.001 PHE A 308 TRP 0.005 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9050) covalent geometry : angle 0.59380 (12278) hydrogen bonds : bond 0.06806 ( 513) hydrogen bonds : angle 3.69071 ( 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 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.436 Fit side-chains REVERT: A 227 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8202 (tt0) REVERT: A 239 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 309 PHE cc_start: 0.7968 (t80) cc_final: 0.7704 (m-80) REVERT: A 480 MET cc_start: 0.8236 (mmt) cc_final: 0.7943 (pmm) REVERT: A 663 ASN cc_start: 0.9162 (m-40) cc_final: 0.8785 (m-40) REVERT: A 677 ARG cc_start: 0.8471 (mmp-170) cc_final: 0.8220 (mmp-170) REVERT: A 710 PHE cc_start: 0.8737 (t80) cc_final: 0.8391 (t80) REVERT: B 205 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5496 (tt) REVERT: B 227 GLU cc_start: 0.8413 (tt0) cc_final: 0.8084 (tt0) REVERT: B 240 ASP cc_start: 0.8395 (t0) cc_final: 0.8059 (t0) REVERT: B 518 ILE cc_start: 0.8848 (tt) cc_final: 0.8526 (pp) outliers start: 44 outliers final: 24 residues processed: 119 average time/residue: 0.3969 time to fit residues: 51.6887 Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 187 TYR Chi-restraints excluded: chain A residue 192 ILE 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 329 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 0.0270 chunk 98 optimal weight: 0.0010 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.9446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3649 r_free = 0.3649 target = 0.101189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075205 restraints weight = 18075.465| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.91 r_work: 0.3101 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9050 Z= 0.123 Angle : 0.561 8.692 12278 Z= 0.284 Chirality : 0.040 0.243 1502 Planarity : 0.003 0.034 1522 Dihedral : 8.039 126.928 1260 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 3.74 % Allowed : 20.10 % Favored : 76.16 % 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: 1.16 (0.26), residues: 1122 helix: 1.96 (0.20), residues: 700 sheet: -0.03 (0.67), residues: 70 loop : -1.61 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.008 0.001 TYR A 711 PHE 0.011 0.001 PHE A 308 TRP 0.002 0.000 TRP B 408 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9050) covalent geometry : angle 0.56146 (12278) hydrogen bonds : bond 0.06046 ( 513) hydrogen bonds : angle 3.52301 ( 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 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.321 Fit side-chains REVERT: A 227 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8110 (tt0) REVERT: A 309 PHE cc_start: 0.8007 (t80) cc_final: 0.7736 (m-80) REVERT: A 480 MET cc_start: 0.8235 (mmt) cc_final: 0.7976 (pmm) REVERT: A 663 ASN cc_start: 0.9163 (m-40) cc_final: 0.8784 (m-40) REVERT: A 677 ARG cc_start: 0.8484 (mmp-170) cc_final: 0.8113 (mmp-170) REVERT: A 710 PHE cc_start: 0.8817 (t80) cc_final: 0.8394 (t80) REVERT: B 205 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5635 (tt) REVERT: B 227 GLU cc_start: 0.8377 (tt0) cc_final: 0.8059 (tt0) REVERT: B 240 ASP cc_start: 0.8142 (t0) cc_final: 0.7881 (t0) REVERT: B 518 ILE cc_start: 0.8839 (tt) cc_final: 0.8493 (pp) outliers start: 37 outliers final: 22 residues processed: 117 average time/residue: 0.3650 time to fit residues: 47.0836 Evaluate side-chains 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 329 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 406 ILE 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 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 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: 0.7980 chunk 20 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074835 restraints weight = 18057.732| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.91 r_work: 0.3089 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9050 Z= 0.134 Angle : 0.580 9.934 12278 Z= 0.292 Chirality : 0.040 0.221 1502 Planarity : 0.003 0.032 1522 Dihedral : 8.014 127.255 1260 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 3.43 % Allowed : 21.11 % 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: 1.20 (0.26), residues: 1122 helix: 2.00 (0.20), residues: 702 sheet: -0.05 (0.66), residues: 70 loop : -1.60 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.008 0.001 TYR A 433 PHE 0.015 0.001 PHE A 308 TRP 0.002 0.000 TRP A 408 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9050) covalent geometry : angle 0.57975 (12278) hydrogen bonds : bond 0.06034 ( 513) hydrogen bonds : angle 3.50907 ( 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 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.346 Fit side-chains REVERT: A 227 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8146 (tt0) REVERT: A 309 PHE cc_start: 0.8013 (t80) cc_final: 0.7755 (m-80) REVERT: A 663 ASN cc_start: 0.9191 (m-40) cc_final: 0.8824 (m-40) REVERT: A 677 ARG cc_start: 0.8487 (mmp-170) cc_final: 0.8135 (mmp-170) REVERT: A 710 PHE cc_start: 0.8760 (t80) cc_final: 0.8388 (t80) REVERT: B 205 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5545 (tt) REVERT: B 227 GLU cc_start: 0.8400 (tt0) cc_final: 0.8069 (tt0) REVERT: B 518 ILE cc_start: 0.8819 (tt) cc_final: 0.8480 (pp) outliers start: 34 outliers final: 26 residues processed: 112 average time/residue: 0.3815 time to fit residues: 46.8951 Evaluate side-chains 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 329 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 LEU 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 285 SER Chi-restraints excluded: chain B residue 307 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077431 restraints weight = 17788.290| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.90 r_work: 0.3141 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9050 Z= 0.117 Angle : 0.571 9.497 12278 Z= 0.285 Chirality : 0.039 0.215 1502 Planarity : 0.003 0.031 1522 Dihedral : 7.921 124.036 1260 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.23 % Allowed : 21.52 % Favored : 75.25 % 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: 1.36 (0.27), residues: 1122 helix: 2.13 (0.20), residues: 704 sheet: 0.08 (0.67), residues: 70 loop : -1.59 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 606 TYR 0.010 0.001 TYR A 196 PHE 0.013 0.001 PHE A 308 TRP 0.001 0.000 TRP A 408 HIS 0.005 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9050) covalent geometry : angle 0.57107 (12278) hydrogen bonds : bond 0.05214 ( 513) hydrogen bonds : angle 3.35341 ( 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 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.278 Fit side-chains REVERT: A 227 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8081 (tt0) REVERT: A 309 PHE cc_start: 0.8011 (t80) cc_final: 0.7762 (m-10) REVERT: A 480 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7805 (pmm) REVERT: A 663 ASN cc_start: 0.9179 (m-40) cc_final: 0.8796 (m-40) REVERT: A 677 ARG cc_start: 0.8498 (mmp-170) cc_final: 0.8185 (mmp-170) REVERT: A 710 PHE cc_start: 0.8751 (t80) cc_final: 0.8368 (t80) REVERT: B 205 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5367 (tt) REVERT: B 227 GLU cc_start: 0.8342 (tt0) cc_final: 0.8081 (tt0) REVERT: B 402 LEU cc_start: 0.8603 (tm) cc_final: 0.8337 (mt) REVERT: B 518 ILE cc_start: 0.8784 (tt) cc_final: 0.8407 (pp) REVERT: B 605 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7371 (mp0) outliers start: 32 outliers final: 15 residues processed: 116 average time/residue: 0.3821 time to fit residues: 48.8925 Evaluate side-chains 100 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 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 480 MET 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 406 ILE Chi-restraints excluded: chain B residue 407 LEU 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 605 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075773 restraints weight = 17806.621| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.87 r_work: 0.3111 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9050 Z= 0.130 Angle : 0.581 10.932 12278 Z= 0.290 Chirality : 0.040 0.203 1502 Planarity : 0.003 0.030 1522 Dihedral : 7.736 125.701 1256 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 2.53 % Allowed : 22.83 % Favored : 74.65 % 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: 1.43 (0.27), residues: 1122 helix: 2.19 (0.21), residues: 700 sheet: 0.05 (0.67), residues: 70 loop : -1.53 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.007 0.001 TYR A 433 PHE 0.021 0.001 PHE A 308 TRP 0.003 0.001 TRP A 408 HIS 0.005 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9050) covalent geometry : angle 0.58127 (12278) hydrogen bonds : bond 0.05583 ( 513) hydrogen bonds : angle 3.41788 ( 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 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.371 Fit side-chains REVERT: A 227 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8139 (tt0) REVERT: A 309 PHE cc_start: 0.8016 (t80) cc_final: 0.7784 (m-10) REVERT: A 480 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7730 (pmm) REVERT: A 663 ASN cc_start: 0.9202 (m-40) cc_final: 0.8822 (m-40) REVERT: A 677 ARG cc_start: 0.8497 (mmp-170) cc_final: 0.8023 (mmp-170) REVERT: A 710 PHE cc_start: 0.8782 (t80) cc_final: 0.8401 (t80) REVERT: B 205 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5345 (tt) REVERT: B 227 GLU cc_start: 0.8369 (tt0) cc_final: 0.8102 (tt0) REVERT: B 402 LEU cc_start: 0.8628 (tm) cc_final: 0.8362 (mt) REVERT: B 518 ILE cc_start: 0.8807 (tt) cc_final: 0.8444 (pp) REVERT: B 605 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7365 (mp0) outliers start: 25 outliers final: 18 residues processed: 100 average time/residue: 0.4070 time to fit residues: 44.8824 Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 161 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 329 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 480 MET 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 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: 3.9990 chunk 31 optimal weight: 8.9990 chunk 99 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.103625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077714 restraints weight = 17667.464| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.89 r_work: 0.3147 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9050 Z= 0.116 Angle : 0.575 11.368 12278 Z= 0.284 Chirality : 0.039 0.202 1502 Planarity : 0.003 0.030 1522 Dihedral : 7.675 123.290 1256 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 1.72 % Allowed : 23.64 % Favored : 74.65 % 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: 1.49 (0.27), residues: 1122 helix: 2.23 (0.21), residues: 702 sheet: 0.07 (0.67), residues: 70 loop : -1.51 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 165 TYR 0.009 0.001 TYR A 196 PHE 0.020 0.001 PHE A 308 TRP 0.003 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9050) covalent geometry : angle 0.57487 (12278) hydrogen bonds : bond 0.05035 ( 513) hydrogen bonds : angle 3.31426 ( 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 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.309 Fit side-chains REVERT: A 227 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8152 (tt0) REVERT: A 309 PHE cc_start: 0.8025 (t80) cc_final: 0.7764 (m-10) REVERT: A 480 MET cc_start: 0.8055 (mmt) cc_final: 0.7823 (pmm) REVERT: A 663 ASN cc_start: 0.9184 (m-40) cc_final: 0.8800 (m-40) REVERT: A 677 ARG cc_start: 0.8506 (mmp-170) cc_final: 0.8106 (mmp-170) REVERT: A 710 PHE cc_start: 0.8768 (t80) cc_final: 0.8355 (t80) REVERT: B 205 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5189 (tt) REVERT: B 227 GLU cc_start: 0.8356 (tt0) cc_final: 0.8094 (tt0) REVERT: B 402 LEU cc_start: 0.8600 (tm) cc_final: 0.8368 (mt) REVERT: B 518 ILE cc_start: 0.8790 (tt) cc_final: 0.8430 (pp) REVERT: B 605 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7335 (mp0) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.4066 time to fit residues: 42.9701 Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 402 LEU 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 406 ILE 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: 0.8980 chunk 109 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 17 optimal weight: 0.0010 chunk 111 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076442 restraints weight = 17782.692| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.89 r_work: 0.3123 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.125 Angle : 0.576 11.315 12278 Z= 0.286 Chirality : 0.040 0.203 1502 Planarity : 0.003 0.030 1522 Dihedral : 7.685 124.878 1256 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 2.02 % Allowed : 23.43 % Favored : 74.55 % 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: 1.52 (0.27), residues: 1122 helix: 2.27 (0.21), residues: 700 sheet: 0.08 (0.67), residues: 70 loop : -1.50 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 165 TYR 0.006 0.001 TYR B 491 PHE 0.019 0.001 PHE A 308 TRP 0.003 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9050) covalent geometry : angle 0.57601 (12278) hydrogen bonds : bond 0.05326 ( 513) hydrogen bonds : angle 3.36196 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.27 seconds wall clock time: 40 minutes 10.34 seconds (2410.34 seconds total)