Starting phenix.real_space_refine on Fri Feb 14 15:47:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6raf_4773/02_2025/6raf_4773.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raf_4773/02_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_4773/02_2025/6raf_4773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raf_4773/02_2025/6raf_4773.map" model { file = "/net/cci-nas-00/data/ceres_data/6raf_4773/02_2025/6raf_4773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raf_4773/02_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.44, per 1000 atoms: 0.63 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: 2.26 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: 1.07 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: 3.45 Time building geometry restraints manager: 2.61 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: 0.760 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.240 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- 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 10388 Z= 0.520 Angle : 1.584 22.525 14094 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 *********************** 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 : 1.132 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 353 LEU cc_start: 0.7580 (mt) cc_final: 0.7306 (mt) 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: 0.2988 time to fit residues: 90.7934 Evaluate side-chains 142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 = 0.164769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136599 restraints weight = 13635.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137145 restraints weight = 9601.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137750 restraints weight = 7747.407| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10388 Z= 0.212 Angle : 0.682 10.847 14094 Z= 0.355 Chirality : 0.043 0.191 1606 Planarity : 0.006 0.066 1782 Dihedral : 7.719 131.190 1481 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.10 % Favored : 98.82 % Rotamer: Outliers : 1.72 % Allowed : 9.73 % 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: 1.24 (0.23), residues: 1274 helix: 1.80 (0.18), residues: 788 sheet: 0.25 (0.42), residues: 125 loop : -1.15 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 446 HIS 0.006 0.001 HIS A 561 PHE 0.017 0.002 PHE A 296 TYR 0.018 0.001 TYR B 92 ARG 0.005 0.001 ARG B 394 *********************** 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 206 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8511 (mmp) cc_final: 0.8290 (tpp) REVERT: A 317 PHE cc_start: 0.6511 (m-10) cc_final: 0.5279 (t80) REVERT: A 338 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7430 (mttp) REVERT: B 9 LEU cc_start: 0.8061 (mt) cc_final: 0.7847 (mp) REVERT: B 303 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7427 (tm-30) REVERT: C 45 ARG cc_start: 0.6304 (ttp-170) cc_final: 0.5753 (ttm-80) outliers start: 18 outliers final: 11 residues processed: 199 average time/residue: 0.2622 time to fit residues: 70.9270 Evaluate side-chains 158 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 92 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132928 restraints weight = 13844.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136203 restraints weight = 8727.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138388 restraints weight = 6407.098| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10388 Z= 0.202 Angle : 0.643 10.523 14094 Z= 0.324 Chirality : 0.041 0.180 1606 Planarity : 0.005 0.054 1782 Dihedral : 7.386 117.713 1479 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.57 % Favored : 98.35 % Rotamer: Outliers : 3.34 % Allowed : 11.93 % 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: 1.60 (0.23), residues: 1274 helix: 2.11 (0.18), residues: 794 sheet: 0.13 (0.43), residues: 130 loop : -1.03 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 446 HIS 0.007 0.001 HIS A 561 PHE 0.012 0.001 PHE B 251 TYR 0.018 0.001 TYR B 92 ARG 0.005 0.000 ARG B 482 *********************** 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 198 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8341 (m-40) cc_final: 0.8021 (m-40) REVERT: A 317 PHE cc_start: 0.6454 (m-10) cc_final: 0.5440 (t80) REVERT: A 338 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7436 (mttp) REVERT: A 502 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7576 (mttp) REVERT: A 512 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6837 (mm) REVERT: B 9 LEU cc_start: 0.8019 (mt) cc_final: 0.7729 (mp) REVERT: B 288 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8975 (tt) REVERT: B 304 ARG cc_start: 0.7123 (ttp80) cc_final: 0.6899 (ttp80) REVERT: B 314 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7541 (tm-30) REVERT: C 83 MET cc_start: 0.5309 (mpp) cc_final: 0.4659 (mpp) outliers start: 35 outliers final: 18 residues processed: 178 average time/residue: 0.2595 time to fit residues: 63.4145 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 314 PHE Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain 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 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 373 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.169830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139583 restraints weight = 13502.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143001 restraints weight = 8581.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145284 restraints weight = 6279.452| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10388 Z= 0.206 Angle : 0.619 10.380 14094 Z= 0.310 Chirality : 0.041 0.169 1606 Planarity : 0.005 0.053 1782 Dihedral : 6.887 101.530 1479 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.24 % Allowed : 13.17 % Favored : 83.59 % 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: 1.77 (0.23), residues: 1274 helix: 2.25 (0.18), residues: 790 sheet: -0.05 (0.46), residues: 121 loop : -0.83 (0.30), residues: 363 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 0.018 0.001 TYR B 92 ARG 0.005 0.000 ARG A 560 *********************** 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 191 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8281 (m-40) cc_final: 0.7954 (m-40) REVERT: A 145 ASN cc_start: 0.8093 (t0) cc_final: 0.7500 (t0) REVERT: A 257 PHE cc_start: 0.7508 (t80) cc_final: 0.7295 (t80) REVERT: A 317 PHE cc_start: 0.6631 (m-10) cc_final: 0.5508 (t80) REVERT: A 338 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7384 (mttp) REVERT: A 502 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7494 (mtmm) REVERT: A 512 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6865 (mm) REVERT: A 535 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6999 (ptp-110) REVERT: A 582 LEU cc_start: 0.8177 (tp) cc_final: 0.7780 (tp) REVERT: B 9 LEU cc_start: 0.7821 (mt) cc_final: 0.7592 (mp) REVERT: B 288 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9022 (tt) REVERT: B 304 ARG cc_start: 0.7066 (ttp80) cc_final: 0.6832 (ttp80) REVERT: C 82 GLN cc_start: 0.6143 (tp40) cc_final: 0.5879 (tp-100) outliers start: 34 outliers final: 25 residues processed: 173 average time/residue: 0.2586 time to fit residues: 60.9509 Evaluate side-chains 172 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 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 65 LYS 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: 2.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.157768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129170 restraints weight = 13019.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131653 restraints weight = 8990.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133386 restraints weight = 6935.148| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10388 Z= 0.211 Angle : 0.596 6.985 14094 Z= 0.300 Chirality : 0.040 0.169 1606 Planarity : 0.004 0.048 1782 Dihedral : 6.310 88.087 1479 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.34 % Allowed : 14.31 % Favored : 82.35 % 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: 1.80 (0.23), residues: 1274 helix: 2.29 (0.18), residues: 791 sheet: 0.02 (0.44), residues: 131 loop : -0.91 (0.31), residues: 352 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 0.014 0.002 PHE A 171 TYR 0.017 0.001 TYR B 92 ARG 0.005 0.000 ARG A 560 *********************** 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: 35 poor density : 160 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8275 (m-40) cc_final: 0.7941 (m-40) REVERT: A 145 ASN cc_start: 0.8046 (t0) cc_final: 0.7522 (t0) REVERT: A 317 PHE cc_start: 0.6565 (m-10) cc_final: 0.5581 (t80) REVERT: A 502 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7421 (mttp) REVERT: A 512 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6748 (mm) REVERT: A 535 ARG cc_start: 0.7361 (mtp85) cc_final: 0.7147 (ptp-110) REVERT: A 582 LEU cc_start: 0.8271 (tp) cc_final: 0.7743 (tp) REVERT: B 288 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9035 (tt) REVERT: B 304 ARG cc_start: 0.7295 (ttp80) cc_final: 0.7092 (tmm-80) outliers start: 35 outliers final: 29 residues processed: 178 average time/residue: 0.2701 time to fit residues: 66.1720 Evaluate side-chains 173 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 430 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139597 restraints weight = 13717.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140627 restraints weight = 8893.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140722 restraints weight = 7527.362| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10388 Z= 0.225 Angle : 0.604 8.548 14094 Z= 0.301 Chirality : 0.040 0.173 1606 Planarity : 0.004 0.045 1782 Dihedral : 6.053 89.892 1479 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.63 % Allowed : 16.03 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.23), residues: 1274 helix: 2.28 (0.18), residues: 790 sheet: -0.09 (0.46), residues: 120 loop : -0.86 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.005 0.001 HIS A 561 PHE 0.014 0.001 PHE A 171 TYR 0.018 0.001 TYR B 92 ARG 0.005 0.000 ARG A 560 *********************** 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 186 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8357 (m-40) cc_final: 0.8051 (m-40) REVERT: A 145 ASN cc_start: 0.8156 (t0) cc_final: 0.7566 (t0) REVERT: A 168 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: A 317 PHE cc_start: 0.6614 (m-10) cc_final: 0.5456 (t80) REVERT: A 473 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 512 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6764 (mm) REVERT: A 535 ARG cc_start: 0.7398 (mtp85) cc_final: 0.7178 (ptp-110) REVERT: A 582 LEU cc_start: 0.8391 (tp) cc_final: 0.7962 (tp) REVERT: B 288 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9052 (tt) REVERT: B 304 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7178 (ttp80) outliers start: 38 outliers final: 26 residues processed: 167 average time/residue: 0.2515 time to fit residues: 57.6122 Evaluate side-chains 170 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 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 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 512 LEU Chi-restraints excluded: chain A residue 548 THR 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 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: 0.5980 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.161810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133988 restraints weight = 13917.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134913 restraints weight = 9392.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134953 restraints weight = 7440.106| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10388 Z= 0.179 Angle : 0.578 8.145 14094 Z= 0.288 Chirality : 0.039 0.174 1606 Planarity : 0.004 0.044 1782 Dihedral : 5.808 88.756 1479 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.15 % Allowed : 16.98 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.23), residues: 1274 helix: 2.40 (0.18), residues: 786 sheet: -0.15 (0.46), residues: 119 loop : -0.72 (0.31), residues: 369 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 0.015 0.001 TYR B 92 ARG 0.005 0.000 ARG A 560 *********************** 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 186 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8270 (m-40) cc_final: 0.7924 (m-40) REVERT: A 145 ASN cc_start: 0.8098 (t0) cc_final: 0.7522 (t0) REVERT: A 168 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: A 317 PHE cc_start: 0.6838 (m-10) cc_final: 0.5398 (t80) REVERT: A 473 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 512 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6756 (mm) REVERT: A 560 ARG cc_start: 0.8359 (ttm110) cc_final: 0.8111 (ptp-110) REVERT: A 582 LEU cc_start: 0.8317 (tp) cc_final: 0.7864 (tp) REVERT: B 288 LEU cc_start: 0.9368 (tp) cc_final: 0.9060 (tt) REVERT: B 304 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7206 (ttp80) outliers start: 33 outliers final: 26 residues processed: 171 average time/residue: 0.2576 time to fit residues: 60.2116 Evaluate side-chains 174 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 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 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR 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: 0.6980 chunk 7 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137763 restraints weight = 13810.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141105 restraints weight = 8888.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143377 restraints weight = 6534.740| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10388 Z= 0.211 Angle : 0.603 9.241 14094 Z= 0.298 Chirality : 0.040 0.164 1606 Planarity : 0.004 0.042 1782 Dihedral : 5.688 87.970 1479 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.86 % Allowed : 17.56 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.81 (0.23), residues: 1274 helix: 2.32 (0.18), residues: 788 sheet: -0.33 (0.45), residues: 121 loop : -0.77 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.005 0.001 HIS A 121 PHE 0.014 0.001 PHE A 171 TYR 0.016 0.001 TYR B 92 ARG 0.004 0.000 ARG A 560 *********************** 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 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8337 (m-40) cc_final: 0.8060 (m-40) REVERT: A 145 ASN cc_start: 0.8149 (t0) cc_final: 0.7565 (t0) REVERT: A 168 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: A 317 PHE cc_start: 0.6594 (m-10) cc_final: 0.5619 (t80) REVERT: A 512 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6756 (mm) REVERT: A 582 LEU cc_start: 0.8300 (tp) cc_final: 0.7919 (tp) REVERT: B 288 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9059 (tt) outliers start: 30 outliers final: 24 residues processed: 165 average time/residue: 0.2536 time to fit residues: 57.1347 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 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 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 428 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: 0.9980 chunk 116 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.167026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139559 restraints weight = 13727.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140481 restraints weight = 9764.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140530 restraints weight = 7332.727| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10388 Z= 0.227 Angle : 0.620 10.418 14094 Z= 0.307 Chirality : 0.040 0.166 1606 Planarity : 0.004 0.041 1782 Dihedral : 5.691 89.018 1479 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.15 % Allowed : 17.37 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.23), residues: 1274 helix: 2.27 (0.18), residues: 789 sheet: -0.33 (0.45), residues: 121 loop : -0.77 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.005 0.001 HIS A 121 PHE 0.013 0.001 PHE A 261 TYR 0.018 0.001 TYR B 92 ARG 0.008 0.000 ARG B 304 *********************** 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 179 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8397 (t70) cc_final: 0.8133 (t0) REVERT: A 128 ASN cc_start: 0.8376 (m-40) cc_final: 0.8097 (m-40) REVERT: A 145 ASN cc_start: 0.8238 (t0) cc_final: 0.7677 (t0) REVERT: A 168 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: A 317 PHE cc_start: 0.6693 (m-10) cc_final: 0.5563 (t80) REVERT: A 502 LYS cc_start: 0.7748 (mtmm) cc_final: 0.7432 (mttp) REVERT: A 512 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6706 (mm) REVERT: A 582 LEU cc_start: 0.8224 (tp) cc_final: 0.7772 (tp) REVERT: B 288 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9083 (tt) outliers start: 33 outliers final: 25 residues processed: 163 average time/residue: 0.2581 time to fit residues: 58.5918 Evaluate side-chains 170 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 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 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 0.0000 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5522 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.169240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141455 restraints weight = 13789.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141785 restraints weight = 11045.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143961 restraints weight = 8213.322| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10388 Z= 0.187 Angle : 0.606 10.405 14094 Z= 0.298 Chirality : 0.039 0.169 1606 Planarity : 0.004 0.041 1782 Dihedral : 5.598 89.119 1479 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.96 % Allowed : 17.56 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.23), residues: 1274 helix: 2.38 (0.18), residues: 793 sheet: -0.03 (0.47), residues: 113 loop : -0.75 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.004 0.001 HIS A 561 PHE 0.011 0.001 PHE A 261 TYR 0.014 0.001 TYR B 92 ARG 0.004 0.000 ARG B 56 ********************** 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 185 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8354 (t70) cc_final: 0.8118 (t0) REVERT: A 128 ASN cc_start: 0.8385 (m-40) cc_final: 0.8121 (m-40) REVERT: A 145 ASN cc_start: 0.8161 (t0) cc_final: 0.7561 (t0) REVERT: A 168 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: A 317 PHE cc_start: 0.6898 (m-10) cc_final: 0.5618 (t80) REVERT: A 502 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7387 (mttp) REVERT: A 512 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6805 (mm) REVERT: A 582 LEU cc_start: 0.8229 (tp) cc_final: 0.7770 (tp) REVERT: B 277 GLU cc_start: 0.7421 (pp20) cc_final: 0.6747 (pp20) REVERT: B 288 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9114 (tt) outliers start: 31 outliers final: 26 residues processed: 167 average time/residue: 0.2428 time to fit residues: 56.3526 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 : 1.139 ------------------------------------------------------------------------------- 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 142 ASP 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 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 132 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 103 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 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 = 0.4007 r_free = 0.4007 target = 0.167586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137764 restraints weight = 13723.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141101 restraints weight = 8884.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143266 restraints weight = 6513.676| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10388 Z= 0.213 Angle : 0.626 9.726 14094 Z= 0.307 Chirality : 0.040 0.164 1606 Planarity : 0.004 0.040 1782 Dihedral : 5.601 89.972 1479 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.15 % Allowed : 17.84 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.23), residues: 1274 helix: 2.32 (0.18), residues: 790 sheet: -0.14 (0.47), residues: 115 loop : -0.75 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.004 0.001 HIS A 561 PHE 0.012 0.001 PHE A 261 TYR 0.017 0.001 TYR B 92 ARG 0.005 0.000 ARG B 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2995.26 seconds wall clock time: 54 minutes 23.04 seconds (3263.04 seconds total)