Starting phenix.real_space_refine on Wed Mar 4 03:04:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6raf_4773/03_2026/6raf_4773.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raf_4773/03_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_4773/03_2026/6raf_4773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raf_4773/03_2026/6raf_4773.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6raf_4773/03_2026/6raf_4773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raf_4773/03_2026/6raf_4773.map" } 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-dev-5986/lib/python3.9/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: 2.44, per 1000 atoms: 0.24 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: 0.82 Conformation dependent library (CDL) restraints added in 562.2 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: 0.23 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: 1.29 Time building geometry restraints manager: 1.13 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: 5978 26.41 - 52.82: 153 52.82 - 79.23: 37 79.23 - 105.63: 11 105.63 - 132.04: 2 Dihedral angle restraints: 6181 sinusoidal: 2522 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 6178 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.160 Find NCS groups from input model: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 13.654 132.043 3833 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 covalent geometry : bond 0.00795 (10388) covalent geometry : angle 1.58368 (14094) SS BOND : bond 0.02179 ( 2) SS BOND : angle 2.02420 ( 4) hydrogen bonds : bond 0.16746 ( 667) hydrogen bonds : angle 6.57486 ( 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 : 0.402 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: 0.1277 time to fit residues: 38.9030 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 : 0.391 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 280 GLN B 531 HIS B 556 HIS C 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138182 restraints weight = 13752.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138642 restraints weight = 10044.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139133 restraints weight = 8520.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140259 restraints weight = 7063.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140361 restraints weight = 6735.204| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10390 Z= 0.147 Angle : 0.672 10.932 14098 Z= 0.348 Chirality : 0.042 0.202 1606 Planarity : 0.006 0.064 1782 Dihedral : 7.705 131.619 1481 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.02 % Favored : 98.90 % Rotamer: Outliers : 1.62 % Allowed : 9.35 % Favored : 89.03 % 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: 1.30 (0.23), residues: 1274 helix: 1.83 (0.18), residues: 789 sheet: 0.27 (0.42), residues: 125 loop : -1.10 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.017 0.001 TYR B 92 PHE 0.016 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 covalent geometry : bond 0.00301 (10388) covalent geometry : angle 0.67208 (14094) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.68921 ( 4) hydrogen bonds : bond 0.05483 ( 667) hydrogen bonds : angle 4.46854 ( 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 203 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8456 (m-40) cc_final: 0.8086 (m-40) REVERT: A 317 PHE cc_start: 0.6447 (m-10) cc_final: 0.5387 (t80) REVERT: A 338 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7366 (mttp) REVERT: A 512 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6841 (mm) REVERT: B 242 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 303 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7410 (tm-30) REVERT: C 45 ARG cc_start: 0.6287 (ttp-170) cc_final: 0.5851 (ttm-80) REVERT: C 60 TYR cc_start: 0.7236 (m-80) cc_final: 0.7027 (m-80) outliers start: 17 outliers final: 9 residues processed: 196 average time/residue: 0.1191 time to fit residues: 31.4088 Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 0.0270 chunk 102 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3980 r_free = 0.3980 target = 0.164460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136028 restraints weight = 13792.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137206 restraints weight = 9415.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137257 restraints weight = 7014.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138065 restraints weight = 6901.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138579 restraints weight = 6086.164| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3068 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= 0.137 Angle : 0.640 10.681 14098 Z= 0.321 Chirality : 0.041 0.178 1606 Planarity : 0.005 0.050 1782 Dihedral : 7.318 116.759 1479 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 2.86 % Allowed : 11.93 % Favored : 85.21 % 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: 1.72 (0.23), residues: 1274 helix: 2.19 (0.18), residues: 794 sheet: 0.14 (0.43), residues: 130 loop : -0.93 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 482 TYR 0.018 0.001 TYR B 92 PHE 0.012 0.002 PHE B 251 TRP 0.017 0.001 TRP B 446 HIS 0.003 0.001 HIS B 400 Details of bonding type rmsd covalent geometry : bond 0.00290 (10388) covalent geometry : angle 0.63974 (14094) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.23396 ( 4) hydrogen bonds : bond 0.05029 ( 667) hydrogen bonds : angle 4.10697 ( 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 189 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.8064 (t0) cc_final: 0.7569 (t0) REVERT: A 317 PHE cc_start: 0.6473 (m-10) cc_final: 0.5295 (t80) REVERT: A 338 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7445 (mttp) REVERT: A 502 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7672 (mttp) REVERT: A 512 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6827 (mm) REVERT: B 242 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7194 (tm-30) REVERT: B 288 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8987 (tt) REVERT: B 304 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6934 (ttp80) REVERT: B 314 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 83 MET cc_start: 0.5171 (mpp) cc_final: 0.4672 (mpp) outliers start: 30 outliers final: 18 residues processed: 173 average time/residue: 0.1154 time to fit residues: 27.0335 Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER 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 468 GLU 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 C residue 3 GLN 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: 0.8980 chunk 39 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4053 r_free = 0.4053 target = 0.171624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142222 restraints weight = 13680.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145497 restraints weight = 8768.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147782 restraints weight = 6443.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149240 restraints weight = 5211.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150368 restraints weight = 4505.647| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10390 Z= 0.132 Angle : 0.608 8.310 14098 Z= 0.304 Chirality : 0.040 0.173 1606 Planarity : 0.004 0.050 1782 Dihedral : 6.787 100.441 1479 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.53 % Allowed : 12.60 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.23), residues: 1274 helix: 2.34 (0.18), residues: 793 sheet: 0.02 (0.46), residues: 121 loop : -0.71 (0.31), residues: 360 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 0.019 0.001 PHE A 257 TRP 0.013 0.001 TRP B 446 HIS 0.005 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00283 (10388) covalent geometry : angle 0.60855 (14094) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.29756 ( 4) hydrogen bonds : bond 0.04656 ( 667) hydrogen bonds : angle 3.97020 ( 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 192 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8333 (m-40) cc_final: 0.8054 (m-40) REVERT: A 145 ASN cc_start: 0.7965 (t0) cc_final: 0.7440 (t0) REVERT: A 317 PHE cc_start: 0.6499 (m-10) cc_final: 0.5487 (t80) REVERT: A 512 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6824 (mm) REVERT: A 535 ARG cc_start: 0.7161 (mtp85) cc_final: 0.6948 (ptp-170) REVERT: B 242 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7584 (tm-30) REVERT: B 304 ARG cc_start: 0.7140 (ttp80) cc_final: 0.6882 (ttp80) REVERT: C 34 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 82 GLN cc_start: 0.6183 (tp40) cc_final: 0.5961 (tp-100) outliers start: 37 outliers final: 22 residues processed: 174 average time/residue: 0.1104 time to fit residues: 26.3769 Evaluate side-chains 168 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 473 LEU Chi-restraints excluded: chain A residue 512 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 301 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 344 VAL 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 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3908 r_free = 0.3908 target = 0.161111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132583 restraints weight = 12964.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135011 restraints weight = 8850.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136968 restraints weight = 6742.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137996 restraints weight = 5598.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138909 restraints weight = 4969.125| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3746 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= 0.124 Angle : 0.581 7.958 14098 Z= 0.289 Chirality : 0.040 0.176 1606 Planarity : 0.004 0.047 1782 Dihedral : 6.227 84.579 1479 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.15 % Allowed : 13.84 % Favored : 83.02 % 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: 2.01 (0.23), residues: 1274 helix: 2.43 (0.18), residues: 791 sheet: -0.00 (0.47), residues: 115 loop : -0.67 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.018 0.001 TYR A 589 PHE 0.023 0.001 PHE A 257 TRP 0.011 0.001 TRP B 446 HIS 0.005 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00267 (10388) covalent geometry : angle 0.58132 (14094) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.14344 ( 4) hydrogen bonds : bond 0.04415 ( 667) hydrogen bonds : angle 3.88048 ( 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 192 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8276 (m-40) cc_final: 0.7977 (m-40) REVERT: A 145 ASN cc_start: 0.7925 (t0) cc_final: 0.7417 (t0) REVERT: A 317 PHE cc_start: 0.6693 (m-10) cc_final: 0.5605 (t80) REVERT: A 473 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 502 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7367 (mtmm) REVERT: A 512 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6820 (mm) REVERT: A 535 ARG cc_start: 0.7241 (mtp85) cc_final: 0.7024 (ptp-110) REVERT: B 304 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6967 (tmm-80) REVERT: C 34 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7918 (mt) outliers start: 33 outliers final: 22 residues processed: 175 average time/residue: 0.1093 time to fit residues: 26.4655 Evaluate side-chains 168 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 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 172 ILE 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: 0.9980 chunk 48 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3927 r_free = 0.3927 target = 0.159214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128714 restraints weight = 14073.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131790 restraints weight = 9198.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133878 restraints weight = 6880.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135177 restraints weight = 5653.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136267 restraints weight = 4945.980| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10390 Z= 0.172 Angle : 0.631 8.611 14098 Z= 0.314 Chirality : 0.041 0.169 1606 Planarity : 0.004 0.044 1782 Dihedral : 6.000 86.414 1479 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.63 % Allowed : 14.79 % Favored : 81.58 % 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: 1.73 (0.23), residues: 1274 helix: 2.19 (0.18), residues: 793 sheet: -0.15 (0.46), residues: 120 loop : -0.77 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 560 TYR 0.019 0.002 TYR B 92 PHE 0.023 0.002 PHE A 257 TRP 0.012 0.001 TRP B 14 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00395 (10388) covalent geometry : angle 0.63075 (14094) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.40914 ( 4) hydrogen bonds : bond 0.04903 ( 667) hydrogen bonds : angle 4.02706 ( 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 188 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8298 (m-40) cc_final: 0.7985 (m-40) REVERT: A 145 ASN cc_start: 0.8146 (t0) cc_final: 0.7561 (t0) REVERT: A 317 PHE cc_start: 0.6544 (m-10) cc_final: 0.5586 (t80) REVERT: A 473 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 556 LEU cc_start: 0.6595 (mm) cc_final: 0.6091 (mm) REVERT: B 288 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9025 (tt) REVERT: C 34 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.7972 (mt) outliers start: 38 outliers final: 29 residues processed: 165 average time/residue: 0.1102 time to fit residues: 25.0328 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 : 0.286 ------------------------------------------------------------------------------- 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 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 B residue 10 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 133 VAL 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 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 505 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4017 r_free = 0.4017 target = 0.168232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140326 restraints weight = 13593.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141252 restraints weight = 9502.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142049 restraints weight = 7983.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142816 restraints weight = 7188.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142889 restraints weight = 6122.512| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10390 Z= 0.137 Angle : 0.599 8.177 14098 Z= 0.297 Chirality : 0.040 0.175 1606 Planarity : 0.004 0.042 1782 Dihedral : 5.830 88.507 1479 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.63 % Allowed : 15.94 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.23), residues: 1274 helix: 2.27 (0.18), residues: 790 sheet: -0.16 (0.47), residues: 114 loop : -0.72 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.016 0.001 TYR B 92 PHE 0.024 0.001 PHE A 257 TRP 0.009 0.001 TRP A 193 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00306 (10388) covalent geometry : angle 0.59921 (14094) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.16954 ( 4) hydrogen bonds : bond 0.04519 ( 667) hydrogen bonds : angle 3.88668 ( 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 185 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8360 (m-40) cc_final: 0.8072 (m-40) REVERT: A 145 ASN cc_start: 0.8091 (t0) cc_final: 0.7479 (t0) REVERT: A 168 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: A 317 PHE cc_start: 0.6823 (m-10) cc_final: 0.5480 (t80) REVERT: A 512 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6765 (mm) REVERT: B 288 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9026 (tt) REVERT: C 34 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8061 (mt) REVERT: C 83 MET cc_start: 0.5823 (mpp) cc_final: 0.5518 (mpp) outliers start: 38 outliers final: 25 residues processed: 167 average time/residue: 0.1053 time to fit residues: 24.4072 Evaluate side-chains 171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 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 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 111 HIS 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 Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 0.0030 chunk 75 optimal weight: 4.9990 chunk 35 optimal weight: 0.0670 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3984 r_free = 0.3984 target = 0.164414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134901 restraints weight = 13799.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138030 restraints weight = 8971.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140187 restraints weight = 6685.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141671 restraints weight = 5456.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142362 restraints weight = 4747.416| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10390 Z= 0.118 Angle : 0.594 7.810 14098 Z= 0.293 Chirality : 0.039 0.172 1606 Planarity : 0.004 0.041 1782 Dihedral : 5.640 87.970 1479 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.48 % Allowed : 17.18 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.24), residues: 1274 helix: 2.41 (0.18), residues: 798 sheet: -0.04 (0.48), residues: 110 loop : -0.62 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 188 TYR 0.012 0.001 TYR B 92 PHE 0.032 0.001 PHE C 68 TRP 0.008 0.001 TRP A 193 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00250 (10388) covalent geometry : angle 0.59443 (14094) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.21722 ( 4) hydrogen bonds : bond 0.04052 ( 667) hydrogen bonds : angle 3.75092 ( 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: 26 poor density : 158 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8289 (m-40) cc_final: 0.7980 (m-40) REVERT: A 145 ASN cc_start: 0.7998 (t0) cc_final: 0.7403 (t0) REVERT: A 317 PHE cc_start: 0.6764 (m-10) cc_final: 0.5620 (t80) REVERT: A 473 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8086 (tp) REVERT: A 512 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6841 (mm) REVERT: B 184 ASP cc_start: 0.7396 (t0) cc_final: 0.7178 (m-30) REVERT: B 277 GLU cc_start: 0.7514 (pp20) cc_final: 0.6847 (pp20) REVERT: B 281 PHE cc_start: 0.8832 (m-80) cc_final: 0.8053 (m-80) REVERT: B 288 LEU cc_start: 0.9347 (tp) cc_final: 0.9050 (tt) REVERT: B 416 VAL cc_start: 0.8983 (t) cc_final: 0.8668 (p) REVERT: C 34 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.7980 (mt) outliers start: 26 outliers final: 21 residues processed: 168 average time/residue: 0.1101 time to fit residues: 25.3093 Evaluate side-chains 168 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 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 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 505 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 3 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4055 r_free = 0.4055 target = 0.171459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141577 restraints weight = 13685.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145061 restraints weight = 8636.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147411 restraints weight = 6291.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149040 restraints weight = 5064.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150024 restraints weight = 4354.706| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4473 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= 0.125 Angle : 0.606 9.239 14098 Z= 0.297 Chirality : 0.039 0.166 1606 Planarity : 0.004 0.040 1782 Dihedral : 5.532 86.628 1479 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.10 % Allowed : 18.42 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.24), residues: 1274 helix: 2.45 (0.18), residues: 790 sheet: -0.06 (0.48), residues: 110 loop : -0.60 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 304 TYR 0.014 0.001 TYR B 92 PHE 0.031 0.001 PHE A 257 TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00275 (10388) covalent geometry : angle 0.60575 (14094) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.12586 ( 4) hydrogen bonds : bond 0.04132 ( 667) hydrogen bonds : angle 3.74075 ( 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 174 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8299 (m-40) cc_final: 0.7994 (m-40) REVERT: A 145 ASN cc_start: 0.8024 (t0) cc_final: 0.7433 (t0) REVERT: A 317 PHE cc_start: 0.6715 (m-10) cc_final: 0.5595 (t80) REVERT: A 473 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8181 (tp) REVERT: A 512 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6844 (mm) REVERT: B 184 ASP cc_start: 0.7484 (t0) cc_final: 0.7096 (m-30) REVERT: B 277 GLU cc_start: 0.7258 (pp20) cc_final: 0.6485 (pp20) REVERT: B 281 PHE cc_start: 0.8833 (m-80) cc_final: 0.8083 (m-80) REVERT: B 288 LEU cc_start: 0.9360 (tp) cc_final: 0.9064 (tt) REVERT: B 416 VAL cc_start: 0.8957 (t) cc_final: 0.8648 (p) REVERT: C 34 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.7975 (mt) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.1087 time to fit residues: 24.1256 Evaluate side-chains 165 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 507 LEU Chi-restraints excluded: chain A residue 512 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 373 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 0.0070 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3999 r_free = 0.3999 target = 0.165602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138185 restraints weight = 13688.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138722 restraints weight = 9090.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139221 restraints weight = 7655.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139702 restraints weight = 7162.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140050 restraints weight = 6548.560| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10390 Z= 0.119 Angle : 0.614 9.439 14098 Z= 0.298 Chirality : 0.039 0.168 1606 Planarity : 0.004 0.057 1782 Dihedral : 5.461 85.250 1479 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.19 % Allowed : 18.51 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.24), residues: 1274 helix: 2.54 (0.18), residues: 785 sheet: -0.00 (0.48), residues: 110 loop : -0.58 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 188 TYR 0.016 0.001 TYR A 589 PHE 0.032 0.001 PHE A 257 TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00260 (10388) covalent geometry : angle 0.61365 (14094) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.17525 ( 4) hydrogen bonds : bond 0.03950 ( 667) hydrogen bonds : angle 3.69421 ( 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 176 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8353 (m-40) cc_final: 0.8089 (m-40) REVERT: A 145 ASN cc_start: 0.8052 (t0) cc_final: 0.7455 (t0) REVERT: A 317 PHE cc_start: 0.6758 (m-10) cc_final: 0.5421 (t80) REVERT: A 473 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8064 (tp) REVERT: B 277 GLU cc_start: 0.7128 (pp20) cc_final: 0.6657 (pp20) REVERT: B 281 PHE cc_start: 0.8804 (m-80) cc_final: 0.8110 (m-80) REVERT: B 288 LEU cc_start: 0.9341 (tp) cc_final: 0.9074 (tt) REVERT: B 416 VAL cc_start: 0.8939 (t) cc_final: 0.8659 (p) REVERT: C 34 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8038 (mt) outliers start: 23 outliers final: 19 residues processed: 162 average time/residue: 0.1043 time to fit residues: 23.4946 Evaluate side-chains 166 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 507 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3913 r_free = 0.3913 target = 0.158311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127474 restraints weight = 14086.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130363 restraints weight = 9235.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132387 restraints weight = 6953.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133798 restraints weight = 5751.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134775 restraints weight = 5043.061| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10390 Z= 0.203 Angle : 0.692 9.739 14098 Z= 0.340 Chirality : 0.043 0.180 1606 Planarity : 0.004 0.046 1782 Dihedral : 5.615 87.474 1479 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.29 % Allowed : 18.51 % 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: 1.64 (0.23), residues: 1274 helix: 2.10 (0.18), residues: 787 sheet: -0.25 (0.47), residues: 116 loop : -0.64 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 64 TYR 0.023 0.002 TYR B 92 PHE 0.030 0.002 PHE A 257 TRP 0.013 0.002 TRP B 446 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00482 (10388) covalent geometry : angle 0.69168 (14094) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.55689 ( 4) hydrogen bonds : bond 0.04914 ( 667) hydrogen bonds : angle 4.00263 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1646.76 seconds wall clock time: 28 minutes 59.93 seconds (1739.93 seconds total)