Starting phenix.real_space_refine on Sun Sep 13 05:16:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roo_54126/09_2026/9roo_54126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roo_54126/09_2026/9roo_54126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9roo_54126/09_2026/9roo_54126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roo_54126/09_2026/9roo_54126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9roo_54126/09_2026/9roo_54126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roo_54126/09_2026/9roo_54126.map" } resolution = 3.5 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= 0.001 sd= 0.012 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 56 5.16 5 C 6509 2.51 5 N 1697 2.21 5 O 1898 1.98 5 H 10197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20357 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 15274 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 938} Chain: "B" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4540 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 259} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 2.66, per 1000 atoms: 0.13 Number of scatterers: 20357 At special positions: 0 Unit cell: (75.439, 90.361, 174.09, 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 56 16.00 O 1898 8.00 N 1697 7.00 C 6509 6.00 H 10197 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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: 1.74 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 50.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.680A pdb=" N GLU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 100 through 122 Processing helix chain 'A' and resid 127 through 161 removed outlier: 3.747A pdb=" N SER A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 332 removed outlier: 4.675A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.493A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.519A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.582A pdb=" N ARG A 445 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.533A pdb=" N ALA A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.659A pdb=" N LEU A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.777A pdb=" N VAL A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 708 removed outlier: 3.578A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.746A pdb=" N LEU A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 784 Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 816 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.687A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 removed outlier: 3.624A pdb=" N GLN A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.067A pdb=" N LEU A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 938 removed outlier: 3.749A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.724A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.987A pdb=" N TRP A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 984 through 990' Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.708A pdb=" N GLU A1003 " --> pdb=" O PHE A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 28 through 60 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.708A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.830A pdb=" N SER B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.147A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.172A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 197 through 198 removed outlier: 5.262A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 7.002A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 399 removed outlier: 3.548A pdb=" N THR A 387 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 490 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU A 479 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 492 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 399 removed outlier: 3.548A pdb=" N THR A 387 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS A 518 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 585 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER A 520 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY A 587 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N LEU A 522 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ILE A 589 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.267A pdb=" N ASN B 226 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.514A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 514 hydrogen bonds defined for protein. 1467 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: 5.51 Time building geometry restraints manager: 2.41 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: 10173 1.03 - 1.23: 87 1.23 - 1.43: 4190 1.43 - 1.62: 6038 1.62 - 1.82: 82 Bond restraints: 20570 Sorted by residual: bond pdb=" CB MET A 673 " pdb=" CG MET A 673 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" CA TYR B 169 " pdb=" C TYR B 169 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.80e+00 bond pdb=" CA SER A 369 " pdb=" C SER A 369 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.80e-02 3.09e+03 1.48e+00 bond pdb=" CB LYS A 727 " pdb=" CG LYS A 727 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CA PHE B 139 " pdb=" CB PHE B 139 " ideal model delta sigma weight residual 1.537 1.522 0.015 1.45e-02 4.76e+03 1.09e+00 ... (remaining 20565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 36883 1.79 - 3.57: 363 3.57 - 5.36: 35 5.36 - 7.15: 3 7.15 - 8.94: 4 Bond angle restraints: 37288 Sorted by residual: angle pdb=" N ILE B 122 " pdb=" CA ILE B 122 " pdb=" C ILE B 122 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.42e+01 angle pdb=" CB LYS A 727 " pdb=" CG LYS A 727 " pdb=" CD LYS A 727 " ideal model delta sigma weight residual 111.30 119.45 -8.15 2.30e+00 1.89e-01 1.26e+01 angle pdb=" N GLY B 161 " pdb=" CA GLY B 161 " pdb=" C GLY B 161 " ideal model delta sigma weight residual 114.67 110.39 4.28 1.41e+00 5.03e-01 9.22e+00 angle pdb=" CB MET B 121 " pdb=" CG MET B 121 " pdb=" SD MET B 121 " ideal model delta sigma weight residual 112.70 121.64 -8.94 3.00e+00 1.11e-01 8.88e+00 angle pdb=" N ASP A 43 " pdb=" CA ASP A 43 " pdb=" C ASP A 43 " ideal model delta sigma weight residual 113.43 109.77 3.66 1.26e+00 6.30e-01 8.45e+00 ... (remaining 37283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8576 17.92 - 35.83: 770 35.83 - 53.75: 234 53.75 - 71.66: 66 71.66 - 89.58: 22 Dihedral angle restraints: 9668 sinusoidal: 5309 harmonic: 4359 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -122.85 36.85 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA TYR B 167 " pdb=" C TYR B 167 " pdb=" N GLY B 168 " pdb=" CA GLY B 168 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLU A 404 " pdb=" CA GLU A 404 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 9665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 967 0.029 - 0.057: 408 0.057 - 0.086: 128 0.086 - 0.114: 67 0.114 - 0.143: 23 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CA VAL A 358 " pdb=" N VAL A 358 " pdb=" C VAL A 358 " pdb=" CB VAL A 358 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CB VAL A 135 " pdb=" CA VAL A 135 " pdb=" CG1 VAL A 135 " pdb=" CG2 VAL A 135 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 480 " pdb=" N ILE A 480 " pdb=" C ILE A 480 " pdb=" CB ILE A 480 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1590 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 235 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 236 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 74 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 75 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 81 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 82 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.019 5.00e-02 4.00e+02 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1155 2.16 - 2.77: 41581 2.77 - 3.38: 61278 3.38 - 3.99: 77265 3.99 - 4.60: 118303 Nonbonded interactions: 299582 Sorted by model distance: nonbonded pdb=" O GLY A 731 " pdb=" H ASP A 747 " model vdw 1.553 2.450 nonbonded pdb=" H GLY A 196 " pdb=" O CYS A 249 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASN A 896 " pdb=" H TYR A 908 " model vdw 1.563 2.450 nonbonded pdb=" O PHE B 90 " pdb=" H LYS B 302 " model vdw 1.572 2.450 nonbonded pdb=" O SER A 739 " pdb=" HG SER A 742 " model vdw 1.573 2.450 ... (remaining 299577 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.450 Find NCS groups from input model: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 0.046 10376 Z= 0.152 Angle : 0.607 8.937 14072 Z= 0.334 Chirality : 0.040 0.143 1593 Planarity : 0.004 0.057 1816 Dihedral : 15.708 89.579 3844 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.09 % Allowed : 17.99 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.98 (0.23), residues: 1290 helix: -0.10 (0.22), residues: 556 sheet: -1.20 (0.43), residues: 143 loop : -0.91 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.014 0.001 TYR A 869 PHE 0.017 0.001 PHE A 999 TRP 0.018 0.001 TRP A 418 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (10373) covalent geometry : angle 0.60731 / 0.33 (14066) SS BOND : bond 0.00295 / 0.15 ( 3) SS BOND : angle 0.86109 / 0.57 ( 6) hydrogen bonds : bond 0.15722 / 10.65 ( 505) hydrogen bonds : angle 6.80420 / 4.73 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.545 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: 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: symmetry clash revert: symmetry clash REVERT: A 748 MET cc_start: 0.8887 (ttm) cc_final: 0.8223 (tpp) outliers start: 1 outliers final: 1 residues processed: 143 average time/residue: 0.1789 time to fit residues: 38.9990 Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN A 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.108963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.070941 restraints weight = 96511.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073821 restraints weight = 37472.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.075635 restraints weight = 21786.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076442 restraints weight = 16208.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.077006 restraints weight = 14167.094| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10376 Z= 0.193 Angle : 0.581 6.981 14072 Z= 0.313 Chirality : 0.040 0.140 1593 Planarity : 0.005 0.051 1816 Dihedral : 4.673 41.131 1399 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.71 % Allowed : 17.00 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.71 (0.23), residues: 1290 helix: 0.22 (0.21), residues: 579 sheet: -0.96 (0.46), residues: 137 loop : -0.97 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 837 TYR 0.016 0.001 TYR A 869 PHE 0.013 0.001 PHE B 108 TRP 0.006 0.001 TRP A 418 HIS 0.004 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (10373) covalent geometry : angle 0.58082 / 0.31 (14066) SS BOND : bond 0.00236 / 0.12 ( 3) SS BOND : angle 0.61544 / 0.40 ( 6) hydrogen bonds : bond 0.04591 / 3.09 ( 505) hydrogen bonds : angle 5.41892 / 3.74 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.531 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: 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 102 MET cc_start: 0.8937 (ptt) cc_final: 0.8711 (ppp) REVERT: A 816 MET cc_start: 0.8279 (mmp) cc_final: 0.8009 (mmp) REVERT: A 974 MET cc_start: 0.8994 (mmm) cc_final: 0.8560 (mmm) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.1759 time to fit residues: 39.0597 Evaluate side-chains 146 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 30.0000 chunk 123 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.107156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069033 restraints weight = 98716.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071792 restraints weight = 38568.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073535 restraints weight = 22685.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.074438 restraints weight = 17026.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075010 restraints weight = 14803.424| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10376 Z= 0.324 Angle : 0.635 7.213 14072 Z= 0.351 Chirality : 0.042 0.139 1593 Planarity : 0.005 0.053 1816 Dihedral : 4.899 43.980 1399 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.25 % Allowed : 18.08 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1290 helix: -0.04 (0.20), residues: 572 sheet: -1.02 (0.46), residues: 136 loop : -1.35 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 911 TYR 0.021 0.002 TYR A 869 PHE 0.017 0.002 PHE A 769 TRP 0.007 0.001 TRP A 418 HIS 0.006 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.32 (10373) covalent geometry : angle 0.63520 / 0.35 (14066) SS BOND : bond 0.00314 / 0.16 ( 3) SS BOND : angle 0.87015 / 0.54 ( 6) hydrogen bonds : bond 0.04454 / 3.04 ( 505) hydrogen bonds : angle 5.54084 / 3.86 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.572 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: 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 816 MET cc_start: 0.8311 (mmp) cc_final: 0.7919 (mmp) outliers start: 25 outliers final: 21 residues processed: 145 average time/residue: 0.1802 time to fit residues: 39.5912 Evaluate side-chains 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 48 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 38 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 396 GLN A 771 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.109341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071154 restraints weight = 96345.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074039 restraints weight = 37015.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.075876 restraints weight = 21510.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076911 restraints weight = 16014.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077307 restraints weight = 13753.530| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10376 Z= 0.139 Angle : 0.557 6.893 14072 Z= 0.293 Chirality : 0.040 0.139 1593 Planarity : 0.004 0.052 1816 Dihedral : 4.770 46.396 1399 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.98 % Allowed : 18.71 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.63 (0.23), residues: 1290 helix: 0.42 (0.21), residues: 573 sheet: -1.15 (0.44), residues: 147 loop : -0.99 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.015 0.001 TYR A 869 PHE 0.015 0.001 PHE A 769 TRP 0.008 0.001 TRP A 418 HIS 0.008 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10373) covalent geometry : angle 0.55712 / 0.29 (14066) SS BOND : bond 0.00186 / 0.09 ( 3) SS BOND : angle 0.83373 / 0.51 ( 6) hydrogen bonds : bond 0.03846 / 2.60 ( 505) hydrogen bonds : angle 5.04677 / 3.49 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.530 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.1713 time to fit residues: 39.4949 Evaluate side-chains 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 68 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071021 restraints weight = 96854.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.073931 restraints weight = 37592.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075784 restraints weight = 21852.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.076794 restraints weight = 16265.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077356 restraints weight = 13988.670| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10376 Z= 0.167 Angle : 0.555 6.597 14072 Z= 0.294 Chirality : 0.040 0.138 1593 Planarity : 0.004 0.058 1816 Dihedral : 4.746 48.092 1399 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.89 % Allowed : 19.24 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.52 (0.23), residues: 1290 helix: 0.51 (0.21), residues: 577 sheet: -1.07 (0.44), residues: 148 loop : -0.96 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.015 0.001 TYR A 869 PHE 0.011 0.001 PHE A 769 TRP 0.009 0.001 TRP A 418 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (10373) covalent geometry : angle 0.55466 / 0.29 (14066) SS BOND : bond 0.00937 / 0.49 ( 3) SS BOND : angle 0.83033 / 0.49 ( 6) hydrogen bonds : bond 0.03682 / 2.49 ( 505) hydrogen bonds : angle 4.96112 / 3.43 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.543 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9238 (mt) REVERT: A 816 MET cc_start: 0.8125 (mmp) cc_final: 0.7745 (mmp) REVERT: A 954 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9300 (mp) outliers start: 21 outliers final: 19 residues processed: 146 average time/residue: 0.1897 time to fit residues: 41.4793 Evaluate side-chains 156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.108706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070593 restraints weight = 97938.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073467 restraints weight = 38179.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.075299 restraints weight = 22367.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076329 restraints weight = 16630.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076740 restraints weight = 14284.097| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10376 Z= 0.203 Angle : 0.560 7.215 14072 Z= 0.300 Chirality : 0.040 0.137 1593 Planarity : 0.004 0.053 1816 Dihedral : 4.749 49.859 1399 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.07 % Allowed : 19.78 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.61 (0.23), residues: 1290 helix: 0.50 (0.21), residues: 576 sheet: -1.05 (0.44), residues: 148 loop : -1.10 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 911 TYR 0.017 0.001 TYR A 869 PHE 0.011 0.001 PHE A 769 TRP 0.009 0.001 TRP A 418 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (10373) covalent geometry : angle 0.55994 / 0.30 (14066) SS BOND : bond 0.00358 / 0.19 ( 3) SS BOND : angle 0.80360 / 0.49 ( 6) hydrogen bonds : bond 0.03669 / 2.49 ( 505) hydrogen bonds : angle 4.95384 / 3.43 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.522 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: 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 678 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9245 (mt) REVERT: A 816 MET cc_start: 0.8240 (mmp) cc_final: 0.7892 (mmp) REVERT: A 954 LEU cc_start: 0.9534 (mp) cc_final: 0.9317 (mp) outliers start: 23 outliers final: 20 residues processed: 147 average time/residue: 0.1831 time to fit residues: 40.8239 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 46 optimal weight: 40.0000 chunk 67 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.108187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070043 restraints weight = 97672.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072897 restraints weight = 38041.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.074638 restraints weight = 22130.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075662 restraints weight = 16579.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076074 restraints weight = 14208.774| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10376 Z= 0.227 Angle : 0.570 7.754 14072 Z= 0.307 Chirality : 0.040 0.137 1593 Planarity : 0.004 0.054 1816 Dihedral : 4.599 32.105 1397 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.25 % Allowed : 19.87 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.67 (0.23), residues: 1290 helix: 0.46 (0.21), residues: 576 sheet: -1.06 (0.44), residues: 148 loop : -1.15 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.017 0.001 TYR A 869 PHE 0.014 0.001 PHE A 769 TRP 0.009 0.001 TRP A 418 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (10373) covalent geometry : angle 0.56966 / 0.31 (14066) SS BOND : bond 0.00391 / 0.20 ( 3) SS BOND : angle 0.81082 / 0.48 ( 6) hydrogen bonds : bond 0.03675 / 2.50 ( 505) hydrogen bonds : angle 4.98746 / 3.46 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.534 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: 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 678 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9256 (mt) REVERT: A 954 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9331 (mp) outliers start: 25 outliers final: 22 residues processed: 147 average time/residue: 0.1719 time to fit residues: 39.0189 Evaluate side-chains 155 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.109412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071380 restraints weight = 97184.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074303 restraints weight = 37461.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.076150 restraints weight = 21793.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.077087 restraints weight = 16147.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077714 restraints weight = 14012.444| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10376 Z= 0.139 Angle : 0.544 8.689 14072 Z= 0.285 Chirality : 0.040 0.140 1593 Planarity : 0.004 0.053 1816 Dihedral : 4.485 31.479 1397 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.89 % Allowed : 20.41 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.23), residues: 1290 helix: 0.71 (0.22), residues: 576 sheet: -1.00 (0.44), residues: 148 loop : -1.03 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.014 0.001 TYR A 869 PHE 0.010 0.001 PHE B 108 TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10373) covalent geometry : angle 0.54362 / 0.28 (14066) SS BOND : bond 0.00210 / 0.11 ( 3) SS BOND : angle 0.67051 / 0.41 ( 6) hydrogen bonds : bond 0.03482 / 2.35 ( 505) hydrogen bonds : angle 4.75636 / 3.28 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.522 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: 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: symmetry clash REVERT: A 678 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9244 (mt) REVERT: A 954 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9338 (mp) REVERT: C 43 ILE cc_start: 0.8712 (mt) cc_final: 0.8373 (tt) outliers start: 21 outliers final: 19 residues processed: 153 average time/residue: 0.1744 time to fit residues: 41.7245 Evaluate side-chains 155 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 40.0000 chunk 54 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 50 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.109097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071100 restraints weight = 97820.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.074002 restraints weight = 37957.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075836 restraints weight = 22099.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.076874 restraints weight = 16422.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.077272 restraints weight = 14077.296| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10376 Z= 0.182 Angle : 0.555 8.968 14072 Z= 0.295 Chirality : 0.040 0.138 1593 Planarity : 0.004 0.054 1816 Dihedral : 4.477 30.996 1397 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.07 % Allowed : 20.41 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.44 (0.23), residues: 1290 helix: 0.66 (0.21), residues: 576 sheet: -0.96 (0.43), residues: 152 loop : -1.04 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.016 0.001 TYR A 869 PHE 0.022 0.001 PHE A 291 TRP 0.014 0.001 TRP A 418 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (10373) covalent geometry : angle 0.55522 / 0.30 (14066) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 0.70535 / 0.42 ( 6) hydrogen bonds : bond 0.03511 / 2.37 ( 505) hydrogen bonds : angle 4.79834 / 3.32 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.487 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: 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 334 GLU cc_start: 0.6975 (pm20) cc_final: 0.6666 (pm20) REVERT: A 678 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9233 (mt) REVERT: A 727 LYS cc_start: 0.9582 (tppt) cc_final: 0.9353 (tppt) REVERT: A 816 MET cc_start: 0.8110 (mmp) cc_final: 0.7351 (mmp) REVERT: A 954 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9342 (mp) REVERT: C 43 ILE cc_start: 0.8744 (mt) cc_final: 0.8402 (tt) outliers start: 23 outliers final: 21 residues processed: 149 average time/residue: 0.1693 time to fit residues: 39.0619 Evaluate side-chains 154 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 71 optimal weight: 0.0070 chunk 8 optimal weight: 10.0000 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.110502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.072477 restraints weight = 95969.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.075501 restraints weight = 37107.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077401 restraints weight = 21397.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078470 restraints weight = 15783.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078856 restraints weight = 13494.016| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10376 Z= 0.105 Angle : 0.539 9.327 14072 Z= 0.278 Chirality : 0.040 0.141 1593 Planarity : 0.004 0.054 1816 Dihedral : 4.326 29.366 1397 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.53 % Allowed : 20.95 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.24), residues: 1290 helix: 0.95 (0.22), residues: 575 sheet: -0.89 (0.45), residues: 143 loop : -0.93 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.012 0.001 TYR B 101 PHE 0.019 0.001 PHE A 291 TRP 0.016 0.001 TRP A 418 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10373) covalent geometry : angle 0.53943 / 0.28 (14066) SS BOND : bond 0.00116 / 0.06 ( 3) SS BOND : angle 0.55964 / 0.33 ( 6) hydrogen bonds : bond 0.03288 / 2.20 ( 505) hydrogen bonds : angle 4.53318 / 3.12 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.565 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: 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 334 GLU cc_start: 0.6903 (pm20) cc_final: 0.6624 (pm20) REVERT: A 678 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9218 (mt) REVERT: A 727 LYS cc_start: 0.9586 (tppt) cc_final: 0.9369 (tppt) REVERT: A 816 MET cc_start: 0.8141 (mmp) cc_final: 0.7397 (mmp) REVERT: C 43 ILE cc_start: 0.8690 (mt) cc_final: 0.8362 (tt) outliers start: 17 outliers final: 15 residues processed: 149 average time/residue: 0.1833 time to fit residues: 41.4101 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.110262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072054 restraints weight = 96516.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075029 restraints weight = 37689.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076896 restraints weight = 21864.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.077813 restraints weight = 16201.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078490 restraints weight = 14055.619| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10376 Z= 0.115 Angle : 0.538 9.589 14072 Z= 0.277 Chirality : 0.040 0.139 1593 Planarity : 0.004 0.054 1816 Dihedral : 4.255 28.244 1397 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.35 % Allowed : 21.22 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.08 (0.24), residues: 1290 helix: 1.02 (0.22), residues: 575 sheet: -0.91 (0.44), residues: 143 loop : -0.88 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.012 0.001 TYR A 869 PHE 0.020 0.001 PHE A 291 TRP 0.018 0.001 TRP A 418 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10373) covalent geometry : angle 0.53810 / 0.28 (14066) SS BOND : bond 0.00137 / 0.07 ( 3) SS BOND : angle 0.58407 / 0.34 ( 6) hydrogen bonds : bond 0.03239 / 2.17 ( 505) hydrogen bonds : angle 4.49250 / 3.09 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.27 seconds wall clock time: 68 minutes 34.98 seconds (4114.98 seconds total)