Starting phenix.real_space_refine on Fri Sep 11 16:37:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6raf_4773/09_2026/6raf_4773.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 6563 2.51 5 N 1793 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10174 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4710 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 24, 'TRANS': 563} Chain: "B" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4508 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.24, per 1000 atoms: 0.22 Number of scatterers: 10174 At special positions: 0 Unit cell: (95.853, 92.622, 157.242, 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 25 16.00 P 5 15.00 Mg 1 11.99 O 1787 8.00 N 1793 7.00 C 6563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 626.6 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 66.6% alpha, 11.5% 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 11 through 21 removed outlier: 3.917A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.944A pdb=" N PHE A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.712A pdb=" N GLU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 120 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.817A pdb=" N TYR A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 138 through 173 removed outlier: 3.502A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.608A pdb=" N THR A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 222 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 231 through 285 removed outlier: 3.815A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 289 through 314 removed outlier: 3.761A pdb=" N GLN A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 4.058A pdb=" N ASP A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'A' and resid 398 through 407 removed outlier: 3.759A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.667A pdb=" N ARG A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.809A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 498 through 514 removed outlier: 4.279A pdb=" N SER A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.632A pdb=" N GLY A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'B' and resid 6 through 18 Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 54 removed outlier: 3.665A pdb=" N TYR B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 57 through 105 removed outlier: 4.132A pdb=" N TYR B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 4.056A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.690A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 207 removed outlier: 3.547A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 270 removed outlier: 3.896A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 3.956A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 317 removed outlier: 3.514A pdb=" N LEU B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.621A pdb=" N GLY B 294 " --> pdb=" O TRP B 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.563A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.586A pdb=" N THR B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.056A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 521 removed outlier: 3.843A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.826A pdb=" N ALA B 535 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 537 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 3.578A pdb=" N GLN B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 383 removed outlier: 6.786A pdb=" N VAL A 375 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA A 361 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS A 377 " --> pdb=" O TRP A 359 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP A 359 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL A 379 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 357 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.360A pdb=" N GLY A 437 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ASP A 522 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 439 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 388 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 565 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 448 through 449 removed outlier: 3.837A pdb=" N GLY A 448 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 361 removed outlier: 7.007A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.494A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.530A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1956 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: 1.83 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1611 1.31 - 1.44: 2811 1.44 - 1.57: 5912 1.57 - 1.70: 9 1.70 - 1.82: 45 Bond restraints: 10388 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" N PRO B 170 " pdb=" CD PRO B 170 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.56e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.15e+01 ... (remaining 10383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 13759 4.51 - 9.01: 314 9.01 - 13.52: 18 13.52 - 18.02: 1 18.02 - 22.53: 2 Bond angle restraints: 14094 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 117.34 22.53 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 118.21 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" N PHE A 260 " pdb=" CA PHE A 260 " pdb=" C PHE A 260 " ideal model delta sigma weight residual 111.02 121.06 -10.04 1.22e+00 6.72e-01 6.78e+01 angle pdb=" C5 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 126.80 118.73 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" N ILE A 76 " pdb=" CA ILE A 76 " pdb=" CB ILE A 76 " ideal model delta sigma weight residual 110.57 120.13 -9.56 1.28e+00 6.10e-01 5.58e+01 ... (remaining 14089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.41: 5952 26.41 - 52.82: 149 52.82 - 79.23: 37 79.23 - 105.63: 10 105.63 - 132.04: 2 Dihedral angle restraints: 6150 sinusoidal: 2491 harmonic: 3659 Sorted by residual: dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 72.04 -132.04 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 56.75 -116.74 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" CA ASN A 315 " pdb=" C ASN A 315 " pdb=" N LEU A 316 " pdb=" CA LEU A 316 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1206 0.089 - 0.177: 310 0.177 - 0.266: 64 0.266 - 0.354: 19 0.354 - 0.443: 7 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1603 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 384 " 0.093 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 385 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 34 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C LEU A 34 " -0.093 2.00e-02 2.50e+03 pdb=" O LEU A 34 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE A 35 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 276 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C VAL A 276 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL A 276 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 277 " -0.026 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1662 2.79 - 3.31: 9715 3.31 - 3.84: 16603 3.84 - 4.37: 18229 4.37 - 4.90: 32336 Nonbonded interactions: 78545 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.258 2.170 nonbonded pdb=" OH TYR B 20 " pdb=" OD2 ASP B 93 " model vdw 2.366 3.040 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 602 " model vdw 2.382 2.170 nonbonded pdb=" NH1 ARG C 19 " pdb=" OE1 GLN C 82 " model vdw 2.421 3.120 nonbonded pdb=" O ILE A 438 " pdb=" OH TYR B 214 " model vdw 2.437 3.040 ... (remaining 78540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.670 Find NCS groups from input model: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.008 0.115 10390 Z= 0.467 Angle : 1.584 22.525 14098 Z= 0.996 Chirality : 0.089 0.443 1606 Planarity : 0.012 0.141 1782 Dihedral : 13.512 132.043 3802 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.45 % Favored : 96.23 % Rotamer: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Cbeta Deviations : 0.43 % 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: -0.14 (0.22), residues: 1274 helix: 0.59 (0.18), residues: 780 sheet: 0.33 (0.46), residues: 120 loop : -1.56 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG A 199 TYR 0.044 0.005 TYR B 92 PHE 0.034 0.003 PHE A 304 TRP 0.040 0.003 TRP A 374 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.47 (10388) covalent geometry : angle 1.58368 / 1.00 (14094) SS BOND : bond 0.02179 / 1.04 ( 2) SS BOND : angle 2.02420 / 1.12 ( 4) hydrogen bonds : bond 0.16746 / 11.58 ( 667) hydrogen bonds : angle 6.57486 / 4.79 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8465 (m-40) cc_final: 0.8094 (m-40) REVERT: A 440 LEU cc_start: 0.8892 (mt) cc_final: 0.8517 (mp) REVERT: A 453 ASN cc_start: 0.7109 (t0) cc_final: 0.6658 (t0) REVERT: A 542 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8332 (ttmm) REVERT: B 9 LEU cc_start: 0.7798 (mt) cc_final: 0.7545 (mp) REVERT: B 214 TYR cc_start: 0.8331 (m-80) cc_final: 0.7943 (m-80) REVERT: B 281 PHE cc_start: 0.8837 (m-80) cc_final: 0.8492 (m-80) REVERT: B 303 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7290 (tm-30) REVERT: B 355 ARG cc_start: 0.7675 (tpt-90) cc_final: 0.7170 (mmm-85) REVERT: C 39 GLN cc_start: 0.6922 (tt0) cc_final: 0.6585 (tp40) REVERT: C 45 ARG cc_start: 0.5997 (ttp-170) cc_final: 0.5761 (ttm170) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.1217 time to fit residues: 37.5300 Evaluate side-chains 141 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN B 280 GLN B 556 HIS C 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138158 restraints weight = 13725.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139003 restraints weight = 10071.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140495 restraints weight = 7500.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141128 restraints weight = 6659.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141243 restraints weight = 5921.219| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10390 Z= 0.145 Angle : 0.673 10.963 14098 Z= 0.349 Chirality : 0.042 0.201 1606 Planarity : 0.006 0.065 1782 Dihedral : 6.986 131.641 1450 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.02 % Favored : 98.90 % Rotamer: Outliers : 1.62 % Allowed : 9.54 % Favored : 88.84 % 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: 1.29 (0.23), residues: 1274 helix: 1.85 (0.18), residues: 788 sheet: 0.18 (0.42), residues: 131 loop : -1.16 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 304 TYR 0.018 0.001 TYR B 92 PHE 0.018 0.002 PHE A 296 TRP 0.025 0.002 TRP B 446 HIS 0.006 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (10388) covalent geometry : angle 0.67257 / 0.35 (14094) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 0.71362 / 0.33 ( 4) hydrogen bonds : bond 0.05476 / 3.63 ( 667) hydrogen bonds : angle 4.47366 / 3.26 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 PHE cc_start: 0.6425 (m-10) cc_final: 0.5427 (t80) REVERT: A 338 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7406 (mttp) REVERT: A 512 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6830 (mm) REVERT: B 242 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 303 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7414 (tm-30) REVERT: C 45 ARG cc_start: 0.6300 (ttp-170) cc_final: 0.5855 (ttm-80) REVERT: C 60 TYR cc_start: 0.7235 (m-80) cc_final: 0.7000 (m-80) outliers start: 17 outliers final: 9 residues processed: 198 average time/residue: 0.1070 time to fit residues: 28.9632 Evaluate side-chains 160 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132740 restraints weight = 13875.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134073 restraints weight = 9968.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134174 restraints weight = 7305.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134959 restraints weight = 7264.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135552 restraints weight = 6460.103| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10390 Z= 0.158 Angle : 0.657 10.487 14098 Z= 0.331 Chirality : 0.042 0.174 1606 Planarity : 0.005 0.053 1782 Dihedral : 6.339 117.205 1448 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.81 % Favored : 98.12 % Rotamer: Outliers : 3.15 % Allowed : 11.83 % Favored : 85.02 % 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: 1.59 (0.23), residues: 1274 helix: 2.08 (0.18), residues: 794 sheet: 0.14 (0.43), residues: 130 loop : -1.01 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 67 TYR 0.023 0.001 TYR A 589 PHE 0.015 0.002 PHE A 168 TRP 0.017 0.002 TRP A 193 HIS 0.005 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10388) covalent geometry : angle 0.65686 / 0.33 (14094) SS BOND : bond 0.00127 / 0.06 ( 2) SS BOND : angle 0.30123 / 0.16 ( 4) hydrogen bonds : bond 0.05242 / 3.47 ( 667) hydrogen bonds : angle 4.18780 / 3.05 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8364 (m-40) cc_final: 0.8050 (m-40) REVERT: A 145 ASN cc_start: 0.8116 (t0) cc_final: 0.7609 (t0) REVERT: A 317 PHE cc_start: 0.6564 (m-10) cc_final: 0.5355 (t80) REVERT: A 338 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7489 (mttp) REVERT: A 502 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7641 (mttp) REVERT: A 512 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6642 (mm) REVERT: B 242 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7255 (tm-30) REVERT: B 288 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8999 (tt) REVERT: B 304 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6993 (ttp80) REVERT: B 314 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 83 MET cc_start: 0.5094 (mpp) cc_final: 0.4594 (mpp) outliers start: 33 outliers final: 19 residues processed: 176 average time/residue: 0.1053 time to fit residues: 25.2078 Evaluate side-chains 166 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 91 optimal weight: 0.0670 chunk 84 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132971 restraints weight = 13023.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135503 restraints weight = 8830.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137402 restraints weight = 6698.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138385 restraints weight = 5551.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139476 restraints weight = 4928.968| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10390 Z= 0.123 Angle : 0.602 9.483 14098 Z= 0.299 Chirality : 0.040 0.177 1606 Planarity : 0.004 0.050 1782 Dihedral : 5.809 97.980 1448 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.24 % Allowed : 13.07 % Favored : 83.68 % 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: 1.92 (0.23), residues: 1274 helix: 2.35 (0.18), residues: 794 sheet: 0.05 (0.44), residues: 130 loop : -0.78 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.018 0.001 TYR A 589 PHE 0.018 0.001 PHE A 257 TRP 0.013 0.001 TRP B 446 HIS 0.006 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10388) covalent geometry : angle 0.60242 / 0.30 (14094) SS BOND : bond 0.00144 / 0.07 ( 2) SS BOND : angle 0.18282 / 0.16 ( 4) hydrogen bonds : bond 0.04560 / 3.02 ( 667) hydrogen bonds : angle 3.92621 / 2.86 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8298 (m-40) cc_final: 0.7981 (m-40) REVERT: A 145 ASN cc_start: 0.7917 (t0) cc_final: 0.7413 (t0) REVERT: A 317 PHE cc_start: 0.6538 (m-10) cc_final: 0.5534 (t80) REVERT: A 473 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8203 (tp) REVERT: A 502 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7401 (mtmm) REVERT: A 512 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6828 (mm) REVERT: B 9 LEU cc_start: 0.7734 (mp) cc_final: 0.7534 (mp) REVERT: B 304 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6881 (ttp80) REVERT: C 34 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7900 (mt) outliers start: 34 outliers final: 20 residues processed: 179 average time/residue: 0.1047 time to fit residues: 26.0888 Evaluate side-chains 171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 0.0010 chunk 94 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.160054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131839 restraints weight = 13007.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134372 restraints weight = 8877.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136170 restraints weight = 6802.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137147 restraints weight = 5622.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138204 restraints weight = 4994.021| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10390 Z= 0.130 Angle : 0.585 8.455 14098 Z= 0.290 Chirality : 0.040 0.169 1606 Planarity : 0.004 0.046 1782 Dihedral : 5.362 82.559 1448 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.96 % Allowed : 14.12 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.23), residues: 1274 helix: 2.44 (0.18), residues: 792 sheet: -0.10 (0.46), residues: 121 loop : -0.79 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 188 TYR 0.018 0.001 TYR A 589 PHE 0.025 0.001 PHE A 257 TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10388) covalent geometry : angle 0.58556 / 0.29 (14094) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 0.15241 / 0.11 ( 4) hydrogen bonds : bond 0.04499 / 2.99 ( 667) hydrogen bonds : angle 3.86769 / 2.82 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8279 (m-40) cc_final: 0.7935 (m-40) REVERT: A 145 ASN cc_start: 0.7926 (t0) cc_final: 0.7416 (t0) REVERT: A 317 PHE cc_start: 0.6731 (m-10) cc_final: 0.5652 (t80) REVERT: A 502 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7417 (mtmm) REVERT: A 512 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6877 (mm) REVERT: C 3 GLN cc_start: 0.6197 (mp10) cc_final: 0.5979 (mp10) REVERT: C 34 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7922 (mt) outliers start: 31 outliers final: 22 residues processed: 171 average time/residue: 0.1111 time to fit residues: 26.1307 Evaluate side-chains 166 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129079 restraints weight = 14043.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130866 restraints weight = 10292.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131355 restraints weight = 7700.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131896 restraints weight = 7460.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132335 restraints weight = 6609.010| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10390 Z= 0.170 Angle : 0.635 7.830 14098 Z= 0.315 Chirality : 0.042 0.171 1606 Planarity : 0.004 0.043 1782 Dihedral : 5.101 81.587 1448 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.34 % Allowed : 15.65 % Favored : 81.01 % 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: 1.69 (0.23), residues: 1274 helix: 2.19 (0.18), residues: 790 sheet: -0.31 (0.45), residues: 125 loop : -0.79 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.021 0.002 TYR A 589 PHE 0.024 0.002 PHE A 257 TRP 0.012 0.001 TRP B 14 HIS 0.004 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (10388) covalent geometry : angle 0.63481 / 0.32 (14094) SS BOND : bond 0.00234 / 0.12 ( 2) SS BOND : angle 0.43593 / 0.27 ( 4) hydrogen bonds : bond 0.04945 / 3.28 ( 667) hydrogen bonds : angle 4.03963 / 2.95 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.8174 (t0) cc_final: 0.7557 (t0) REVERT: A 317 PHE cc_start: 0.6602 (m-10) cc_final: 0.5453 (t80) REVERT: C 3 GLN cc_start: 0.6527 (mp10) cc_final: 0.5107 (pp30) outliers start: 35 outliers final: 28 residues processed: 170 average time/residue: 0.1085 time to fit residues: 25.5143 Evaluate side-chains 174 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132246 restraints weight = 13935.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132927 restraints weight = 9605.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133301 restraints weight = 8116.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133675 restraints weight = 7218.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133879 restraints weight = 6989.232| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10390 Z= 0.150 Angle : 0.612 8.336 14098 Z= 0.302 Chirality : 0.041 0.170 1606 Planarity : 0.004 0.042 1782 Dihedral : 4.931 85.510 1448 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.44 % Allowed : 16.41 % Favored : 80.15 % 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: 1.74 (0.23), residues: 1274 helix: 2.27 (0.18), residues: 785 sheet: -0.41 (0.46), residues: 122 loop : -0.77 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.024 0.001 TYR A 589 PHE 0.024 0.002 PHE A 257 TRP 0.009 0.001 TRP A 193 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10388) covalent geometry : angle 0.61188 / 0.30 (14094) SS BOND : bond 0.00108 / 0.05 ( 2) SS BOND : angle 0.17578 / 0.13 ( 4) hydrogen bonds : bond 0.04650 / 3.09 ( 667) hydrogen bonds : angle 3.93912 / 2.89 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8429 (m-40) cc_final: 0.8194 (m-40) REVERT: A 145 ASN cc_start: 0.8158 (t0) cc_final: 0.7543 (t0) REVERT: A 168 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: A 317 PHE cc_start: 0.6637 (m-10) cc_final: 0.5443 (t80) REVERT: A 473 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 512 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6745 (mm) REVERT: A 542 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8161 (ttmm) REVERT: B 288 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9083 (tt) outliers start: 36 outliers final: 27 residues processed: 170 average time/residue: 0.1086 time to fit residues: 25.6036 Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 75 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132795 restraints weight = 13901.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134012 restraints weight = 9294.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134140 restraints weight = 7107.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134708 restraints weight = 7080.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135120 restraints weight = 6437.914| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10390 Z= 0.133 Angle : 0.599 9.049 14098 Z= 0.295 Chirality : 0.040 0.170 1606 Planarity : 0.004 0.041 1782 Dihedral : 4.824 88.794 1448 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.15 % Allowed : 16.89 % Favored : 79.96 % 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: 1.83 (0.23), residues: 1274 helix: 2.36 (0.18), residues: 784 sheet: -0.58 (0.44), residues: 127 loop : -0.67 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 304 TYR 0.019 0.001 TYR A 589 PHE 0.025 0.001 PHE A 257 TRP 0.010 0.001 TRP A 193 HIS 0.003 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10388) covalent geometry : angle 0.59920 / 0.30 (14094) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.25282 / 0.15 ( 4) hydrogen bonds : bond 0.04423 / 2.94 ( 667) hydrogen bonds : angle 3.86758 / 2.84 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8366 (m-40) cc_final: 0.8083 (m-40) REVERT: A 145 ASN cc_start: 0.8115 (t0) cc_final: 0.7489 (t0) REVERT: A 168 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7615 (m-10) REVERT: A 317 PHE cc_start: 0.6895 (m-10) cc_final: 0.5488 (t80) REVERT: A 473 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8188 (tp) REVERT: A 512 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6696 (mm) REVERT: A 574 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8256 (m) REVERT: B 288 LEU cc_start: 0.9389 (tp) cc_final: 0.9093 (tt) outliers start: 33 outliers final: 28 residues processed: 165 average time/residue: 0.1020 time to fit residues: 23.5092 Evaluate side-chains 175 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134566 restraints weight = 13902.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135031 restraints weight = 9330.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135428 restraints weight = 7375.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136249 restraints weight = 7376.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136482 restraints weight = 6258.095| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.129 Angle : 0.603 9.078 14098 Z= 0.296 Chirality : 0.040 0.165 1606 Planarity : 0.004 0.041 1782 Dihedral : 4.794 89.022 1448 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.44 % Allowed : 17.37 % Favored : 79.20 % 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: 1.91 (0.24), residues: 1274 helix: 2.39 (0.18), residues: 785 sheet: -0.36 (0.46), residues: 120 loop : -0.66 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 304 TYR 0.023 0.001 TYR A 589 PHE 0.027 0.001 PHE A 257 TRP 0.009 0.001 TRP A 193 HIS 0.006 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10388) covalent geometry : angle 0.60357 / 0.30 (14094) SS BOND : bond 0.00090 / 0.04 ( 2) SS BOND : angle 0.17118 / 0.11 ( 4) hydrogen bonds : bond 0.04299 / 2.87 ( 667) hydrogen bonds : angle 3.82842 / 2.81 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8402 (m-40) cc_final: 0.8139 (m-40) REVERT: A 145 ASN cc_start: 0.8112 (t0) cc_final: 0.7501 (t0) REVERT: A 168 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: A 317 PHE cc_start: 0.6897 (m-10) cc_final: 0.5649 (t80) REVERT: A 473 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8165 (tp) REVERT: A 512 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6754 (mm) REVERT: B 122 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 288 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9070 (tt) REVERT: C 112 LYS cc_start: 0.7802 (ptmm) cc_final: 0.7392 (tmmt) outliers start: 36 outliers final: 27 residues processed: 177 average time/residue: 0.1117 time to fit residues: 27.5193 Evaluate side-chains 182 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140267 restraints weight = 13677.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141319 restraints weight = 10083.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141809 restraints weight = 7673.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141983 restraints weight = 7176.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142343 restraints weight = 6887.183| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.138 Angle : 0.620 9.320 14098 Z= 0.304 Chirality : 0.040 0.164 1606 Planarity : 0.004 0.040 1782 Dihedral : 4.778 87.087 1448 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.24 % Allowed : 17.56 % Favored : 79.20 % 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: 1.81 (0.23), residues: 1274 helix: 2.31 (0.18), residues: 789 sheet: -0.20 (0.45), residues: 120 loop : -0.81 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 304 TYR 0.018 0.001 TYR C 113 PHE 0.028 0.001 PHE A 257 TRP 0.010 0.001 TRP A 193 HIS 0.006 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10388) covalent geometry : angle 0.62052 / 0.30 (14094) SS BOND : bond 0.00099 / 0.05 ( 2) SS BOND : angle 0.19242 / 0.11 ( 4) hydrogen bonds : bond 0.04355 / 2.92 ( 667) hydrogen bonds : angle 3.85224 / 2.83 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8420 (m-40) cc_final: 0.8192 (m-40) REVERT: A 145 ASN cc_start: 0.8108 (t0) cc_final: 0.7499 (t0) REVERT: A 168 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7573 (m-10) REVERT: A 473 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 512 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6780 (mm) REVERT: B 122 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 277 GLU cc_start: 0.7485 (pp20) cc_final: 0.6844 (pp20) REVERT: B 288 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9079 (tt) REVERT: B 301 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7143 (tp) REVERT: C 3 GLN cc_start: 0.6566 (mp10) cc_final: 0.5148 (pp30) outliers start: 34 outliers final: 25 residues processed: 165 average time/residue: 0.1075 time to fit residues: 24.8731 Evaluate side-chains 177 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130383 restraints weight = 13995.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133609 restraints weight = 8981.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135751 restraints weight = 6655.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137306 restraints weight = 5424.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138196 restraints weight = 4716.321| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10390 Z= 0.138 Angle : 0.617 9.282 14098 Z= 0.303 Chirality : 0.040 0.165 1606 Planarity : 0.004 0.042 1782 Dihedral : 4.775 85.235 1448 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.15 % Allowed : 17.75 % Favored : 79.10 % 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: 1.81 (0.23), residues: 1274 helix: 2.30 (0.18), residues: 787 sheet: -0.31 (0.44), residues: 125 loop : -0.74 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 304 TYR 0.016 0.001 TYR B 92 PHE 0.029 0.001 PHE A 257 TRP 0.010 0.001 TRP A 193 HIS 0.006 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10388) covalent geometry : angle 0.61681 / 0.30 (14094) SS BOND : bond 0.00125 / 0.06 ( 2) SS BOND : angle 0.20969 / 0.12 ( 4) hydrogen bonds : bond 0.04351 / 2.90 ( 667) hydrogen bonds : angle 3.82692 / 2.82 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.56 seconds wall clock time: 29 minutes 2.30 seconds (1742.30 seconds total)