Starting phenix.real_space_refine on Mon Jul 28 13:04:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6raf_4773/07_2025/6raf_4773.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raf_4773/07_2025/6raf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6raf_4773/07_2025/6raf_4773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raf_4773/07_2025/6raf_4773.map" model { file = "/net/cci-nas-00/data/ceres_data/6raf_4773/07_2025/6raf_4773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raf_4773/07_2025/6raf_4773.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.68, per 1000 atoms: 0.66 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.20 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: 3.42 Time building geometry restraints manager: 2.91 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: 1.110 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.890 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.003 TRP A 374 HIS 0.004 0.001 HIS B 454 PHE 0.034 0.003 PHE A 304 TYR 0.044 0.005 TYR B 92 ARG 0.033 0.004 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.16746 ( 667) hydrogen bonds : angle 6.57486 ( 1956) SS BOND : bond 0.02179 ( 2) SS BOND : angle 2.02420 ( 4) covalent geometry : bond 0.00795 (10388) covalent geometry : angle 1.58368 (14094) *********************** 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 : 1.233 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: 0.8516 (mp) REVERT: A 453 ASN cc_start: 0.7109 (t0) cc_final: 0.6657 (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: 0.7291 (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: 0.2898 time to fit residues: 90.4726 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 : 1.043 ------------------------------------------------------------------------------- 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 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.164812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136553 restraints weight = 13633.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137170 restraints weight = 9704.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137636 restraints weight = 7622.078| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2413 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= 0.157 Angle : 0.684 10.864 14098 Z= 0.355 Chirality : 0.043 0.199 1606 Planarity : 0.006 0.066 1782 Dihedral : 7.781 132.589 1481 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.10 % Favored : 98.82 % Rotamer: Outliers : 1.81 % Allowed : 9.64 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1274 helix: 1.78 (0.18), residues: 788 sheet: 0.26 (0.42), residues: 125 loop : -1.16 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 446 HIS 0.006 0.001 HIS A 561 PHE 0.018 0.002 PHE A 296 TYR 0.019 0.001 TYR B 92 ARG 0.005 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 667) hydrogen bonds : angle 4.54598 ( 1956) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.68760 ( 4) covalent geometry : bond 0.00331 (10388) covalent geometry : angle 0.68375 (14094) *********************** 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 207 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8506 (mmp) cc_final: 0.8291 (tpp) REVERT: A 314 PHE cc_start: 0.4969 (OUTLIER) cc_final: 0.4671 (p90) REVERT: A 317 PHE cc_start: 0.6527 (m-10) cc_final: 0.5434 (t80) REVERT: A 338 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7446 (mttp) REVERT: B 9 LEU cc_start: 0.8063 (mt) cc_final: 0.7847 (mp) REVERT: B 303 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7429 (tm-30) REVERT: C 45 ARG cc_start: 0.6301 (ttp-170) cc_final: 0.5757 (ttm-80) outliers start: 19 outliers final: 11 residues processed: 201 average time/residue: 0.3184 time to fit residues: 89.6152 Evaluate side-chains 160 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU 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 314 PHE 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 40 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 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134469 restraints weight = 13934.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135618 restraints weight = 9458.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135640 restraints weight = 7135.255| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3035 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= 0.148 Angle : 0.646 10.664 14098 Z= 0.327 Chirality : 0.041 0.179 1606 Planarity : 0.005 0.054 1782 Dihedral : 7.431 119.107 1479 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.73 % Favored : 98.19 % Rotamer: Outliers : 3.05 % Allowed : 12.21 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1274 helix: 2.09 (0.18), residues: 794 sheet: 0.13 (0.43), residues: 130 loop : -1.02 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 446 HIS 0.006 0.001 HIS A 561 PHE 0.012 0.002 PHE A 171 TYR 0.018 0.001 TYR B 92 ARG 0.006 0.000 ARG B 482 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 667) hydrogen bonds : angle 4.17266 ( 1956) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.23770 ( 4) covalent geometry : bond 0.00324 (10388) covalent geometry : angle 0.64583 (14094) *********************** 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 191 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8345 (m-40) cc_final: 0.8034 (m-40) REVERT: A 145 ASN cc_start: 0.8089 (t0) cc_final: 0.7597 (t0) REVERT: A 317 PHE cc_start: 0.6525 (m-10) cc_final: 0.5307 (t80) REVERT: A 338 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7449 (mttp) REVERT: A 502 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7645 (mttp) REVERT: A 512 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6800 (mm) REVERT: B 9 LEU cc_start: 0.8020 (mt) cc_final: 0.7689 (mp) REVERT: B 288 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8991 (tt) REVERT: B 304 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6956 (ttp80) REVERT: B 314 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 83 MET cc_start: 0.5239 (mpp) cc_final: 0.4731 (mpp) outliers start: 32 outliers final: 19 residues processed: 170 average time/residue: 0.2522 time to fit residues: 58.6487 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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 532 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 ILE 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 428 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.171149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141130 restraints weight = 13444.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144647 restraints weight = 8514.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146751 restraints weight = 6184.117| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3486 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= 0.132 Angle : 0.602 8.434 14098 Z= 0.303 Chirality : 0.040 0.173 1606 Planarity : 0.005 0.051 1782 Dihedral : 6.785 97.847 1479 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.24 % Allowed : 13.45 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.23), residues: 1274 helix: 2.32 (0.18), residues: 793 sheet: 0.17 (0.46), residues: 114 loop : -0.82 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 352 HIS 0.005 0.001 HIS B 454 PHE 0.016 0.001 PHE B 163 TYR 0.016 0.001 TYR B 92 ARG 0.007 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 667) hydrogen bonds : angle 3.93453 ( 1956) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.40761 ( 4) covalent geometry : bond 0.00283 (10388) covalent geometry : angle 0.60197 (14094) *********************** 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 196 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8287 (m-40) cc_final: 0.7970 (m-40) REVERT: A 145 ASN cc_start: 0.8027 (t0) cc_final: 0.7490 (t0) REVERT: A 317 PHE cc_start: 0.6626 (m-10) cc_final: 0.5491 (t80) REVERT: A 502 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7506 (mtmm) REVERT: A 512 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6899 (mm) REVERT: A 535 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7094 (ptp-110) REVERT: B 304 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6915 (ttp80) REVERT: C 82 GLN cc_start: 0.6109 (tp40) cc_final: 0.5858 (tp-100) outliers start: 34 outliers final: 24 residues processed: 181 average time/residue: 0.2688 time to fit residues: 67.3014 Evaluate side-chains 170 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 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 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 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.0020 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.159387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130852 restraints weight = 12944.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133367 restraints weight = 8887.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135126 restraints weight = 6842.196| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3765 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= 0.132 Angle : 0.582 7.087 14098 Z= 0.291 Chirality : 0.040 0.166 1606 Planarity : 0.004 0.045 1782 Dihedral : 6.359 87.292 1479 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.53 % Allowed : 14.22 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1274 helix: 2.39 (0.18), residues: 793 sheet: -0.12 (0.46), residues: 121 loop : -0.80 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.006 0.001 HIS A 561 PHE 0.014 0.001 PHE A 171 TYR 0.018 0.001 TYR A 589 ARG 0.006 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 667) hydrogen bonds : angle 3.88975 ( 1956) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.17440 ( 4) covalent geometry : bond 0.00290 (10388) covalent geometry : angle 0.58229 (14094) *********************** 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 195 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8272 (m-40) cc_final: 0.7943 (m-40) REVERT: A 145 ASN cc_start: 0.8006 (t0) cc_final: 0.7468 (t0) REVERT: A 317 PHE cc_start: 0.6799 (m-10) cc_final: 0.5564 (t80) REVERT: A 473 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 502 LYS cc_start: 0.7764 (mtmm) cc_final: 0.7454 (mttp) REVERT: A 512 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6875 (mm) REVERT: A 535 ARG cc_start: 0.7312 (mtp85) cc_final: 0.7092 (ptp-110) REVERT: B 288 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 37 outliers final: 27 residues processed: 175 average time/residue: 0.3156 time to fit residues: 74.6985 Evaluate side-chains 171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 532 THR 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 184 ASP Chi-restraints excluded: chain B residue 288 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 550 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL 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 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.167370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139879 restraints weight = 13665.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140333 restraints weight = 9498.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141095 restraints weight = 7385.964| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3963 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= 0.152 Angle : 0.608 7.604 14098 Z= 0.303 Chirality : 0.040 0.173 1606 Planarity : 0.004 0.042 1782 Dihedral : 6.091 88.604 1479 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.44 % Allowed : 15.46 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1274 helix: 2.30 (0.18), residues: 791 sheet: -0.11 (0.46), residues: 121 loop : -0.80 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 352 HIS 0.005 0.001 HIS A 561 PHE 0.014 0.001 PHE A 171 TYR 0.019 0.001 TYR A 589 ARG 0.005 0.000 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 667) hydrogen bonds : angle 3.93984 ( 1956) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.33532 ( 4) covalent geometry : bond 0.00346 (10388) covalent geometry : angle 0.60849 (14094) *********************** 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: 36 poor density : 152 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8297 (m-40) cc_final: 0.7983 (m-40) REVERT: A 145 ASN cc_start: 0.8138 (t0) cc_final: 0.7553 (t0) REVERT: A 168 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: A 317 PHE cc_start: 0.6600 (m-10) cc_final: 0.5469 (t80) REVERT: A 473 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8102 (tp) REVERT: A 512 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6713 (mm) REVERT: A 535 ARG cc_start: 0.7336 (mtp85) cc_final: 0.7096 (ptp-110) REVERT: B 288 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9031 (tt) outliers start: 36 outliers final: 29 residues processed: 169 average time/residue: 0.2607 time to fit residues: 61.1347 Evaluate side-chains 177 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain 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 184 ASP Chi-restraints excluded: chain B residue 288 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 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 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 70 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 0.0870 chunk 109 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.163204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133702 restraints weight = 13841.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136765 restraints weight = 8960.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138920 restraints weight = 6671.331| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10390 Z= 0.120 Angle : 0.578 8.935 14098 Z= 0.286 Chirality : 0.039 0.173 1606 Planarity : 0.004 0.042 1782 Dihedral : 5.824 89.341 1479 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.67 % Allowed : 17.27 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1274 helix: 2.42 (0.18), residues: 793 sheet: 0.04 (0.46), residues: 124 loop : -0.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 352 HIS 0.006 0.001 HIS A 561 PHE 0.016 0.001 PHE A 171 TYR 0.014 0.001 TYR B 92 ARG 0.006 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 667) hydrogen bonds : angle 3.77207 ( 1956) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.15717 ( 4) covalent geometry : bond 0.00258 (10388) covalent geometry : angle 0.57839 (14094) *********************** 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 183 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8281 (m-40) cc_final: 0.7942 (m-40) REVERT: A 145 ASN cc_start: 0.8007 (t0) cc_final: 0.7446 (t0) REVERT: A 317 PHE cc_start: 0.6793 (m-10) cc_final: 0.5564 (t80) REVERT: A 473 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 512 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6899 (mm) REVERT: A 560 ARG cc_start: 0.8295 (ttm110) cc_final: 0.8084 (ptp-110) REVERT: B 288 LEU cc_start: 0.9374 (tp) cc_final: 0.9062 (tt) outliers start: 28 outliers final: 22 residues processed: 168 average time/residue: 0.2604 time to fit residues: 60.7149 Evaluate side-chains 169 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 148 ILE 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 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 550 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 108 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 56 optimal weight: 0.0370 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 0.0050 chunk 87 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 overall best weight: 0.4072 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.171560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142208 restraints weight = 13682.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145448 restraints weight = 8857.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147712 restraints weight = 6538.452| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10390 Z= 0.121 Angle : 0.594 8.264 14098 Z= 0.292 Chirality : 0.039 0.167 1606 Planarity : 0.004 0.041 1782 Dihedral : 5.628 88.231 1479 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.05 % Allowed : 16.98 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.23), residues: 1274 helix: 2.46 (0.18), residues: 793 sheet: 0.05 (0.46), residues: 120 loop : -0.71 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.005 0.001 HIS A 561 PHE 0.018 0.001 PHE A 171 TYR 0.014 0.001 TYR B 92 ARG 0.006 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 667) hydrogen bonds : angle 3.72333 ( 1956) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.21743 ( 4) covalent geometry : bond 0.00260 (10388) covalent geometry : angle 0.59358 (14094) *********************** 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 188 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8314 (m-40) cc_final: 0.8020 (m-40) REVERT: A 145 ASN cc_start: 0.7973 (t0) cc_final: 0.7409 (t0) REVERT: A 317 PHE cc_start: 0.6706 (m-10) cc_final: 0.5607 (t80) REVERT: A 473 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8167 (tp) REVERT: A 512 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6838 (mm) REVERT: B 122 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8428 (tt) REVERT: B 288 LEU cc_start: 0.9356 (tp) cc_final: 0.9049 (tt) REVERT: B 416 VAL cc_start: 0.8967 (t) cc_final: 0.8654 (p) outliers start: 32 outliers final: 26 residues processed: 174 average time/residue: 0.2469 time to fit residues: 59.6369 Evaluate side-chains 170 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 122 LEU 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 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 69 THR Chi-restraints excluded: chain C residue 108 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 0.0370 chunk 2 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.169749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142007 restraints weight = 13668.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142901 restraints weight = 9573.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143535 restraints weight = 7691.098| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10390 Z= 0.137 Angle : 0.613 9.354 14098 Z= 0.303 Chirality : 0.040 0.166 1606 Planarity : 0.004 0.041 1782 Dihedral : 5.585 87.990 1479 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.34 % Allowed : 16.89 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1274 helix: 2.42 (0.18), residues: 793 sheet: 0.03 (0.45), residues: 125 loop : -0.71 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.005 0.001 HIS A 121 PHE 0.024 0.001 PHE C 68 TYR 0.016 0.001 TYR B 92 ARG 0.007 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 667) hydrogen bonds : angle 3.78088 ( 1956) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.18266 ( 4) covalent geometry : bond 0.00309 (10388) covalent geometry : angle 0.61343 (14094) *********************** 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 181 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8358 (t70) cc_final: 0.8158 (t0) REVERT: A 128 ASN cc_start: 0.8341 (m-40) cc_final: 0.8081 (m-40) REVERT: A 145 ASN cc_start: 0.8059 (t0) cc_final: 0.7507 (t0) REVERT: A 168 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: A 317 PHE cc_start: 0.6848 (m-10) cc_final: 0.5553 (t80) REVERT: A 473 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 512 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6930 (mm) REVERT: B 288 LEU cc_start: 0.9373 (tp) cc_final: 0.9076 (tt) outliers start: 35 outliers final: 24 residues processed: 166 average time/residue: 0.2427 time to fit residues: 57.0586 Evaluate side-chains 170 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 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 69 THR Chi-restraints excluded: chain C residue 108 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.169134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141125 restraints weight = 13676.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142793 restraints weight = 9183.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142927 restraints weight = 7373.293| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4514 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= 0.141 Angle : 0.634 9.949 14098 Z= 0.308 Chirality : 0.040 0.166 1606 Planarity : 0.004 0.040 1782 Dihedral : 5.609 89.076 1479 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 17.65 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1274 helix: 2.35 (0.18), residues: 790 sheet: 0.03 (0.45), residues: 125 loop : -0.75 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS A 561 PHE 0.026 0.001 PHE C 68 TYR 0.017 0.001 TYR B 92 ARG 0.009 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 667) hydrogen bonds : angle 3.80522 ( 1956) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.29066 ( 4) covalent geometry : bond 0.00321 (10388) covalent geometry : angle 0.63372 (14094) ********************** 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 177 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8375 (t70) cc_final: 0.8125 (t0) REVERT: A 128 ASN cc_start: 0.8390 (m-40) cc_final: 0.8138 (m-40) REVERT: A 145 ASN cc_start: 0.8125 (t0) cc_final: 0.7521 (t0) REVERT: A 168 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: A 317 PHE cc_start: 0.6869 (m-10) cc_final: 0.5607 (t80) REVERT: A 473 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 512 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6779 (mm) REVERT: B 288 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9077 (tt) REVERT: C 3 GLN cc_start: 0.6258 (mp10) cc_final: 0.5049 (pp30) outliers start: 31 outliers final: 25 residues processed: 161 average time/residue: 0.2719 time to fit residues: 61.7516 Evaluate side-chains 172 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 108 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 103 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.161518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130783 restraints weight = 13964.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133893 restraints weight = 9109.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136017 restraints weight = 6821.490| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4588 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= 0.144 Angle : 0.638 9.545 14098 Z= 0.311 Chirality : 0.040 0.166 1606 Planarity : 0.004 0.041 1782 Dihedral : 5.604 89.963 1479 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.77 % Allowed : 18.32 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.23), residues: 1274 helix: 2.32 (0.18), residues: 789 sheet: -0.04 (0.45), residues: 125 loop : -0.73 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS A 561 PHE 0.019 0.001 PHE C 68 TYR 0.017 0.001 TYR B 92 ARG 0.009 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 667) hydrogen bonds : angle 3.82869 ( 1956) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.33565 ( 4) covalent geometry : bond 0.00331 (10388) covalent geometry : angle 0.63771 (14094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.65 seconds wall clock time: 77 minutes 38.30 seconds (4658.30 seconds total)