Starting phenix.real_space_refine on Thu Aug 6 16:13:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s3f_54532/08_2026/9s3f_54532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s3f_54532/08_2026/9s3f_54532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s3f_54532/08_2026/9s3f_54532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s3f_54532/08_2026/9s3f_54532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s3f_54532/08_2026/9s3f_54532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s3f_54532/08_2026/9s3f_54532.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 4841 2.51 5 N 1341 2.21 5 O 1467 1.98 5 H 7757 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15449 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 6402 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 385} Chain: "B" Number of atoms: 6639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6639 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 399} Chain: "C" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2408 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.85, per 1000 atoms: 0.18 Number of scatterers: 15449 At special positions: 0 Unit cell: (68.88, 94.08, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 1467 8.00 N 1341 7.00 C 4841 6.00 H 7757 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 536.9 milliseconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 17 sheets defined 28.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.957A pdb=" N HIS A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 564 Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 627 through 648 removed outlier: 3.936A pdb=" N VAL A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Proline residue: A 641 - end of helix Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.535A pdb=" N ILE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 removed outlier: 4.305A pdb=" N MET B 351 " --> pdb=" O ARG B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.670A pdb=" N LEU B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.814A pdb=" N HIS B 537 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 565 removed outlier: 3.502A pdb=" N SER B 563 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 589 removed outlier: 3.661A pdb=" N VAL B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 638 removed outlier: 3.771A pdb=" N VAL B 632 " --> pdb=" O PRO B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.822A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.780A pdb=" N ALA C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.909A pdb=" N VAL C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 97 through 103 removed outlier: 3.702A pdb=" N LYS C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.832A pdb=" N VAL C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 Processing helix chain 'C' and resid 161 through 175 removed outlier: 3.857A pdb=" N ALA C 170 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 342 through 346 Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 4.029A pdb=" N LEU A 471 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 426 removed outlier: 3.661A pdb=" N MET A 409 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 408 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE A 389 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ARG A 410 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 391 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 443 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A 442 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU A 435 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU A 444 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 543 removed outlier: 6.903A pdb=" N VAL A 501 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 571 " --> pdb=" O MET A 504 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 568 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 609 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA7, first strand: chain 'A' and resid 613 through 614 Processing sheet with id=AA8, first strand: chain 'A' and resid 656 through 661 removed outlier: 7.292A pdb=" N ALA A 689 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ARG A 660 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER A 691 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 690 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ARG A 675 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP A 729 " --> pdb=" O MET A 711 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 665 through 666 Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.813A pdb=" N ARG B 598 " --> pdb=" O THR B 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AB4, first strand: chain 'B' and resid 423 through 426 removed outlier: 3.815A pdb=" N ALA B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 425 " --> pdb=" O TYR B 376 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 375 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 409 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL B 408 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE B 388 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ARG B 410 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE B 390 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 445 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 434 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG B 446 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU B 432 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 547 removed outlier: 10.829A pdb=" N VAL B 501 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N GLY B 545 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 503 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL B 547 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER B 505 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 502 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER B 571 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N MET B 504 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 608 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 609 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB7, first strand: chain 'B' and resid 708 through 711 removed outlier: 3.594A pdb=" N HIS B 674 " --> pdb=" O LEU B 710 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA B 689 " --> pdb=" O LYS B 658 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG B 660 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER B 691 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 665 through 666 236 hydrogen bonds defined for protein. 639 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: 4.12 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7747 1.03 - 1.23: 18 1.23 - 1.42: 3055 1.42 - 1.62: 4694 1.62 - 1.81: 76 Bond restraints: 15590 Sorted by residual: bond pdb=" CA SER B 702 " pdb=" CB SER B 702 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.56e-02 4.11e+03 8.06e+00 bond pdb=" N GLY B 693 " pdb=" CA GLY B 693 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.08e-02 8.57e+03 8.05e+00 bond pdb=" N THR B 692 " pdb=" H THR B 692 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" N ASN A 694 " pdb=" H ASN A 694 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" N LEU A 700 " pdb=" H LEU A 700 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 15585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 27850 1.72 - 3.44: 441 3.44 - 5.17: 70 5.17 - 6.89: 5 6.89 - 8.61: 3 Bond angle restraints: 28369 Sorted by residual: angle pdb=" N MET A 696 " pdb=" CA MET A 696 " pdb=" C MET A 696 " ideal model delta sigma weight residual 111.71 103.10 8.61 1.15e+00 7.56e-01 5.61e+01 angle pdb=" CA GLY B 693 " pdb=" C GLY B 693 " pdb=" O GLY B 693 " ideal model delta sigma weight residual 122.57 118.13 4.44 9.20e-01 1.18e+00 2.33e+01 angle pdb=" CA ARG B 699 " pdb=" C ARG B 699 " pdb=" O ARG B 699 " ideal model delta sigma weight residual 121.56 117.36 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N THR B 692 " pdb=" CA THR B 692 " pdb=" C THR B 692 " ideal model delta sigma weight residual 113.16 108.38 4.78 1.24e+00 6.50e-01 1.49e+01 angle pdb=" N ASN A 694 " pdb=" CA ASN A 694 " pdb=" C ASN A 694 " ideal model delta sigma weight residual 114.12 108.91 5.21 1.39e+00 5.18e-01 1.40e+01 ... (remaining 28364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6309 17.95 - 35.89: 708 35.89 - 53.84: 231 53.84 - 71.79: 53 71.79 - 89.73: 25 Dihedral angle restraints: 7326 sinusoidal: 4138 harmonic: 3188 Sorted by residual: dihedral pdb=" CA HIS B 681 " pdb=" C HIS B 681 " pdb=" N HIS B 682 " pdb=" CA HIS B 682 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CD ARG A 699 " pdb=" NE ARG A 699 " pdb=" CZ ARG A 699 " pdb=" NH1 ARG A 699 " ideal model delta sinusoidal sigma weight residual 0.00 -29.49 29.49 1 1.00e+01 1.00e-02 1.24e+01 dihedral pdb=" CA VAL A 730 " pdb=" C VAL A 730 " pdb=" N MET A 731 " pdb=" CA MET A 731 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 852 0.036 - 0.071: 254 0.071 - 0.107: 91 0.107 - 0.143: 43 0.143 - 0.178: 4 Chirality restraints: 1244 Sorted by residual: chirality pdb=" CA MET B 701 " pdb=" N MET B 701 " pdb=" C MET B 701 " pdb=" CB MET B 701 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA MET A 696 " pdb=" N MET A 696 " pdb=" C MET A 696 " pdb=" CB MET A 696 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA LEU B 700 " pdb=" N LEU B 700 " pdb=" C LEU B 700 " pdb=" CB LEU B 700 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1241 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 699 " -0.531 9.50e-02 1.11e+02 2.38e-01 3.46e+01 pdb=" NE ARG A 699 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 699 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 699 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 699 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 694 " -0.035 2.00e-02 2.50e+03 3.87e-02 2.24e+01 pdb=" CG ASN A 694 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 694 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 694 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 694 " 0.058 2.00e-02 2.50e+03 pdb="HD22 ASN A 694 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 695 " 0.037 2.00e-02 2.50e+03 3.72e-02 2.08e+01 pdb=" CD GLN B 695 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN B 695 " -0.032 2.00e-02 2.50e+03 pdb=" NE2 GLN B 695 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 695 " -0.053 2.00e-02 2.50e+03 pdb="HE22 GLN B 695 " 0.056 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1530 2.22 - 2.82: 33955 2.82 - 3.41: 41350 3.41 - 4.01: 55366 4.01 - 4.60: 84923 Nonbonded interactions: 217124 Sorted by model distance: nonbonded pdb=" H HIS B 682 " pdb=" HD1 HIS B 682 " model vdw 1.628 2.100 nonbonded pdb=" H LYS C 19 " pdb=" HG2 LYS C 19 " model vdw 1.833 2.270 nonbonded pdb="HH11 ARG A 527 " pdb="HD22 ASN A 543 " model vdw 1.838 2.100 nonbonded pdb=" H ILE A 482 " pdb="HG13 ILE A 482 " model vdw 1.855 2.270 nonbonded pdb=" H ILE C 64 " pdb="HG12 ILE C 64 " model vdw 1.862 2.270 ... (remaining 217119 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 319 through 736) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.110 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.600 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.003 0.044 7833 Z= 0.189 Angle : 0.698 8.612 10652 Z= 0.394 Chirality : 0.044 0.178 1244 Planarity : 0.009 0.238 1407 Dihedral : 16.650 89.732 2949 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.42 % Allowed : 29.03 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.26), residues: 1005 helix: 0.72 (0.33), residues: 238 sheet: -1.02 (0.40), residues: 155 loop : 0.04 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 33 TYR 0.010 0.001 TYR C 125 PHE 0.013 0.001 PHE A 321 TRP 0.006 0.001 TRP A 680 HIS 0.009 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 ( 7833) covalent geometry : angle 0.69838 / 0.39 (10652) hydrogen bonds : bond 0.20715 / 13.80 ( 236) hydrogen bonds : angle 7.36855 / 5.07 ( 639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 560 GLU cc_start: 0.8706 (tp30) cc_final: 0.8290 (tp30) REVERT: B 524 ASP cc_start: 0.7754 (t0) cc_final: 0.7523 (t0) REVERT: B 553 ASP cc_start: 0.8523 (m-30) cc_final: 0.8235 (m-30) REVERT: C 70 LYS cc_start: 0.9272 (mmtp) cc_final: 0.8894 (mmtm) REVERT: C 165 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8411 (mp0) REVERT: C 172 LYS cc_start: 0.7542 (mtmm) cc_final: 0.6452 (tptp) outliers start: 12 outliers final: 7 residues processed: 159 average time/residue: 0.2165 time to fit residues: 46.4291 Evaluate side-chains 153 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 695 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** 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 = 0.3919 r_free = 0.3919 target = 0.142264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099880 restraints weight = 37417.260| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.62 r_work: 0.3202 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7833 Z= 0.123 Angle : 0.556 4.715 10652 Z= 0.277 Chirality : 0.043 0.144 1244 Planarity : 0.004 0.045 1407 Dihedral : 5.644 56.787 1095 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.25 % Allowed : 24.64 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1005 helix: 1.31 (0.33), residues: 243 sheet: -0.86 (0.41), residues: 153 loop : 0.01 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 33 TYR 0.006 0.001 TYR B 376 PHE 0.008 0.001 PHE B 622 TRP 0.009 0.001 TRP C 58 HIS 0.009 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 7833) covalent geometry : angle 0.55578 / 0.28 (10652) hydrogen bonds : bond 0.04044 / 2.71 ( 236) hydrogen bonds : angle 5.41289 / 3.74 ( 639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 560 GLU cc_start: 0.8705 (tp30) cc_final: 0.8337 (tp30) REVERT: B 553 ASP cc_start: 0.8496 (m-30) cc_final: 0.8263 (m-30) REVERT: C 167 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8288 (mm) REVERT: C 172 LYS cc_start: 0.7603 (mtmm) cc_final: 0.6488 (tptp) outliers start: 19 outliers final: 13 residues processed: 168 average time/residue: 0.2003 time to fit residues: 46.3146 Evaluate side-chains 160 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097575 restraints weight = 37938.117| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.69 r_work: 0.3198 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7833 Z= 0.148 Angle : 0.542 4.520 10652 Z= 0.269 Chirality : 0.043 0.140 1244 Planarity : 0.004 0.042 1407 Dihedral : 5.104 56.159 1089 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 22.75 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1005 helix: 1.39 (0.33), residues: 242 sheet: -0.84 (0.40), residues: 155 loop : -0.06 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 523 TYR 0.007 0.001 TYR C 91 PHE 0.008 0.001 PHE B 622 TRP 0.007 0.001 TRP C 58 HIS 0.007 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7833) covalent geometry : angle 0.54173 / 0.27 (10652) hydrogen bonds : bond 0.03744 / 2.51 ( 236) hydrogen bonds : angle 5.25498 / 3.62 ( 639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 560 GLU cc_start: 0.8774 (tp30) cc_final: 0.8399 (tp30) REVERT: A 729 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: B 553 ASP cc_start: 0.8572 (m-30) cc_final: 0.8296 (m-30) REVERT: B 729 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: C 91 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7882 (p90) REVERT: C 172 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7378 (pttm) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.1880 time to fit residues: 42.7450 Evaluate side-chains 160 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 157 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098209 restraints weight = 37696.330| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.68 r_work: 0.3207 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7833 Z= 0.115 Angle : 0.527 5.697 10652 Z= 0.257 Chirality : 0.042 0.137 1244 Planarity : 0.004 0.039 1407 Dihedral : 5.007 57.674 1089 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.42 % Allowed : 23.34 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1005 helix: 1.44 (0.33), residues: 246 sheet: -0.77 (0.40), residues: 157 loop : 0.04 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 452 TYR 0.007 0.001 TYR C 91 PHE 0.007 0.001 PHE B 622 TRP 0.006 0.001 TRP C 58 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7833) covalent geometry : angle 0.52722 / 0.26 (10652) hydrogen bonds : bond 0.03143 / 2.11 ( 236) hydrogen bonds : angle 4.99882 / 3.45 ( 639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8459 (mp) REVERT: A 560 GLU cc_start: 0.8761 (tp30) cc_final: 0.8400 (tp30) REVERT: A 711 MET cc_start: 0.7895 (mtt) cc_final: 0.7555 (mtt) REVERT: B 553 ASP cc_start: 0.8587 (m-30) cc_final: 0.8229 (m-30) REVERT: C 172 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7381 (pttm) outliers start: 12 outliers final: 9 residues processed: 162 average time/residue: 0.1861 time to fit residues: 42.1448 Evaluate side-chains 159 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN C 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096122 restraints weight = 38139.364| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.68 r_work: 0.3173 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7833 Z= 0.182 Angle : 0.544 5.314 10652 Z= 0.270 Chirality : 0.043 0.140 1244 Planarity : 0.004 0.040 1407 Dihedral : 4.908 59.360 1087 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 23.22 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1005 helix: 1.32 (0.33), residues: 247 sheet: -0.91 (0.40), residues: 157 loop : -0.04 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.007 0.001 TYR B 673 PHE 0.008 0.001 PHE B 622 TRP 0.006 0.001 TRP B 688 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 7833) covalent geometry : angle 0.54401 / 0.27 (10652) hydrogen bonds : bond 0.03251 / 2.17 ( 236) hydrogen bonds : angle 5.06527 / 3.50 ( 639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 560 GLU cc_start: 0.8785 (tp30) cc_final: 0.8446 (tp30) REVERT: A 729 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: B 550 ASN cc_start: 0.6813 (t0) cc_final: 0.5966 (t0) REVERT: B 553 ASP cc_start: 0.8607 (m-30) cc_final: 0.7932 (m-30) REVERT: B 729 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: C 172 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7438 (pttm) outliers start: 21 outliers final: 18 residues processed: 166 average time/residue: 0.1960 time to fit residues: 45.2301 Evaluate side-chains 167 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 157 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.139562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096321 restraints weight = 37921.694| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.68 r_work: 0.3180 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7833 Z= 0.146 Angle : 0.537 5.837 10652 Z= 0.263 Chirality : 0.043 0.139 1244 Planarity : 0.004 0.047 1407 Dihedral : 4.866 59.691 1087 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.25 % Allowed : 23.82 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1005 helix: 1.41 (0.33), residues: 247 sheet: -0.92 (0.44), residues: 129 loop : 0.02 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 410 TYR 0.009 0.001 TYR B 673 PHE 0.007 0.001 PHE A 609 TRP 0.006 0.001 TRP C 58 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7833) covalent geometry : angle 0.53722 / 0.26 (10652) hydrogen bonds : bond 0.03020 / 2.01 ( 236) hydrogen bonds : angle 4.95335 / 3.43 ( 639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 560 GLU cc_start: 0.8781 (tp30) cc_final: 0.8444 (tp30) REVERT: A 729 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: B 550 ASN cc_start: 0.6871 (t0) cc_final: 0.6022 (t0) REVERT: B 553 ASP cc_start: 0.8630 (m-30) cc_final: 0.7941 (m-30) REVERT: B 729 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: C 167 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8303 (mm) REVERT: C 172 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7406 (pttm) outliers start: 19 outliers final: 13 residues processed: 166 average time/residue: 0.1878 time to fit residues: 43.7275 Evaluate side-chains 158 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.140028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097034 restraints weight = 37785.420| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.70 r_work: 0.3187 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7833 Z= 0.116 Angle : 0.530 6.005 10652 Z= 0.257 Chirality : 0.042 0.137 1244 Planarity : 0.004 0.046 1407 Dihedral : 4.787 58.648 1087 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.90 % Allowed : 24.29 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1005 helix: 1.53 (0.33), residues: 247 sheet: -0.83 (0.44), residues: 129 loop : 0.08 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 410 TYR 0.009 0.001 TYR B 673 PHE 0.006 0.001 PHE B 596 TRP 0.004 0.001 TRP B 688 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7833) covalent geometry : angle 0.53013 / 0.26 (10652) hydrogen bonds : bond 0.02864 / 1.92 ( 236) hydrogen bonds : angle 4.87111 / 3.37 ( 639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 536 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 560 GLU cc_start: 0.8768 (tp30) cc_final: 0.8451 (tp30) REVERT: A 729 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: B 550 ASN cc_start: 0.6895 (t0) cc_final: 0.6037 (t0) REVERT: B 553 ASP cc_start: 0.8641 (m-30) cc_final: 0.7947 (m-30) REVERT: B 729 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: C 172 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7473 (pttm) outliers start: 16 outliers final: 11 residues processed: 160 average time/residue: 0.1904 time to fit residues: 42.3664 Evaluate side-chains 159 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain C residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 28 optimal weight: 0.0570 chunk 33 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098008 restraints weight = 38027.564| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.72 r_work: 0.3207 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7833 Z= 0.095 Angle : 0.530 6.244 10652 Z= 0.255 Chirality : 0.042 0.135 1244 Planarity : 0.004 0.055 1407 Dihedral : 4.677 57.426 1087 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.66 % Allowed : 24.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1005 helix: 1.69 (0.33), residues: 247 sheet: -0.85 (0.46), residues: 117 loop : 0.10 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 410 TYR 0.007 0.001 TYR B 673 PHE 0.007 0.001 PHE A 388 TRP 0.004 0.001 TRP C 58 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.09 ( 7833) covalent geometry : angle 0.53035 / 0.26 (10652) hydrogen bonds : bond 0.02688 / 1.81 ( 236) hydrogen bonds : angle 4.74172 / 3.30 ( 639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 536 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 560 GLU cc_start: 0.8765 (tp30) cc_final: 0.8438 (tp30) REVERT: B 553 ASP cc_start: 0.8627 (m-30) cc_final: 0.8256 (m-30) REVERT: C 167 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8190 (mm) REVERT: C 172 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7433 (pttm) outliers start: 14 outliers final: 11 residues processed: 165 average time/residue: 0.1821 time to fit residues: 41.4873 Evaluate side-chains 159 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.097371 restraints weight = 37915.837| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.70 r_work: 0.3198 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7833 Z= 0.116 Angle : 0.537 6.555 10652 Z= 0.260 Chirality : 0.042 0.134 1244 Planarity : 0.004 0.058 1407 Dihedral : 4.659 56.125 1087 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.66 % Allowed : 23.93 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1005 helix: 1.64 (0.33), residues: 247 sheet: -0.89 (0.45), residues: 127 loop : 0.12 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 410 TYR 0.007 0.001 TYR B 673 PHE 0.006 0.001 PHE B 622 TRP 0.005 0.001 TRP B 688 HIS 0.008 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7833) covalent geometry : angle 0.53707 / 0.26 (10652) hydrogen bonds : bond 0.02693 / 1.81 ( 236) hydrogen bonds : angle 4.72785 / 3.30 ( 639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 550 ASN cc_start: 0.6900 (t0) cc_final: 0.6273 (t0) REVERT: B 553 ASP cc_start: 0.8645 (m-30) cc_final: 0.8169 (m-30) REVERT: C 33 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8339 (mtp-110) REVERT: C 167 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8194 (mm) REVERT: C 172 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7440 (pttm) outliers start: 14 outliers final: 12 residues processed: 163 average time/residue: 0.1781 time to fit residues: 39.6911 Evaluate side-chains 160 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097823 restraints weight = 37845.906| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.68 r_work: 0.3203 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7833 Z= 0.111 Angle : 0.543 7.343 10652 Z= 0.263 Chirality : 0.042 0.134 1244 Planarity : 0.004 0.058 1407 Dihedral : 4.299 43.206 1085 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.42 % Allowed : 24.05 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1005 helix: 1.75 (0.33), residues: 247 sheet: -0.88 (0.46), residues: 123 loop : 0.15 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 410 TYR 0.007 0.001 TYR B 673 PHE 0.008 0.001 PHE A 388 TRP 0.005 0.001 TRP B 688 HIS 0.008 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 7833) covalent geometry : angle 0.54278 / 0.26 (10652) hydrogen bonds : bond 0.02649 / 1.77 ( 236) hydrogen bonds : angle 4.67753 / 3.26 ( 639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Residue MET 696 is missing expected H atoms. Skipping. Residue SER 698 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 GLU cc_start: 0.8678 (tp30) cc_final: 0.8362 (tp30) REVERT: B 553 ASP cc_start: 0.8634 (m-30) cc_final: 0.8187 (m-30) REVERT: C 33 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8341 (mtp-110) REVERT: C 66 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9096 (mm-30) REVERT: C 167 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8196 (mm) REVERT: C 172 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7473 (pttm) outliers start: 12 outliers final: 11 residues processed: 160 average time/residue: 0.1757 time to fit residues: 38.8775 Evaluate side-chains 160 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 31 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098484 restraints weight = 37704.912| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.69 r_work: 0.3211 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7833 Z= 0.099 Angle : 0.540 6.996 10652 Z= 0.260 Chirality : 0.042 0.133 1244 Planarity : 0.004 0.060 1407 Dihedral : 4.179 43.101 1084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.54 % Allowed : 23.82 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1005 helix: 1.84 (0.33), residues: 247 sheet: -0.80 (0.47), residues: 123 loop : 0.21 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 410 TYR 0.007 0.001 TYR B 673 PHE 0.006 0.001 PHE B 596 TRP 0.004 0.001 TRP B 688 HIS 0.007 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 7833) covalent geometry : angle 0.53966 / 0.26 (10652) hydrogen bonds : bond 0.02556 / 1.73 ( 236) hydrogen bonds : angle 4.60571 / 3.22 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.62 seconds wall clock time: 65 minutes 47.98 seconds (3947.98 seconds total)