Starting phenix.real_space_refine on Wed Mar 4 05:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7waz_32390/03_2026/7waz_32390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7waz_32390/03_2026/7waz_32390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7waz_32390/03_2026/7waz_32390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7waz_32390/03_2026/7waz_32390.map" model { file = "/net/cci-nas-00/data/ceres_data/7waz_32390/03_2026/7waz_32390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7waz_32390/03_2026/7waz_32390.cif" } resolution = 3.4 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 196 atoms to isotropic. 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 P 157 5.49 5 S 28 5.16 5 C 6424 2.51 5 N 1966 2.21 5 O 2459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11034 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7729 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 36, 'TRANS': 915} Chain breaks: 3 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 16, 'rna3p': 98} Chain breaks: 1 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Time building chain proxies: 2.84, per 1000 atoms: 0.26 Number of scatterers: 11034 At special positions: 0 Unit cell: (101.52, 144.76, 120.32, 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 28 16.00 P 157 15.00 O 2459 8.00 N 1966 7.00 C 6424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 505.2 milliseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.1% alpha, 17.9% beta 42 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.540A pdb=" N SER A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.611A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.694A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 222 through 272 removed outlier: 4.280A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 343 through 368 removed outlier: 4.688A pdb=" N GLU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.794A pdb=" N GLU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 442 removed outlier: 3.756A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 472 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.541A pdb=" N ARG A 774 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 790 removed outlier: 3.924A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 920 through 936 removed outlier: 3.506A pdb=" N GLN A 924 " --> pdb=" O HIS A 920 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 954 through 973 removed outlier: 4.351A pdb=" N PHE A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 545 removed outlier: 4.375A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 532 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 530 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 529 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 586 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 34 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 542 through 545 removed outlier: 4.375A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 532 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 530 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 529 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 586 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 34 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 619 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.121A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 144 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 152 " --> pdb=" O GLN A 144 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.851A pdb=" N GLN A 135 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 693 removed outlier: 3.874A pdb=" N LEU A 692 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 668 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 754 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE A 658 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N ARG A 660 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER A 799 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 753 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 830 through 832 removed outlier: 3.854A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.821A pdb=" N ASN A 855 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 860 " --> pdb=" O ASN A 855 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2403 1.33 - 1.45: 3223 1.45 - 1.57: 5600 1.57 - 1.69: 310 1.69 - 1.81: 41 Bond restraints: 11577 Sorted by residual: bond pdb=" CA VAL A 568 " pdb=" C VAL A 568 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.05e-02 9.07e+03 3.19e+00 bond pdb=" C LYS A 493 " pdb=" N PRO A 494 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.51e-02 4.39e+03 3.00e+00 bond pdb=" N VAL A 568 " pdb=" CA VAL A 568 " ideal model delta sigma weight residual 1.461 1.442 0.019 1.23e-02 6.61e+03 2.40e+00 bond pdb=" C ASP A 92 " pdb=" O ASP A 92 " ideal model delta sigma weight residual 1.249 1.238 0.010 8.50e-03 1.38e+04 1.52e+00 bond pdb=" O4' DC C 1 " pdb=" C1' DC C 1 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 11572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 16135 2.20 - 4.41: 187 4.41 - 6.61: 9 6.61 - 8.81: 1 8.81 - 11.01: 1 Bond angle restraints: 16333 Sorted by residual: angle pdb=" N GLU A 674 " pdb=" CA GLU A 674 " pdb=" C GLU A 674 " ideal model delta sigma weight residual 113.19 107.45 5.74 1.58e+00 4.01e-01 1.32e+01 angle pdb=" C2' A D 109 " pdb=" C1' A D 109 " pdb=" N9 A D 109 " ideal model delta sigma weight residual 112.00 117.20 -5.20 1.50e+00 4.44e-01 1.20e+01 angle pdb=" C GLY A 791 " pdb=" N LEU A 792 " pdb=" CA LEU A 792 " ideal model delta sigma weight residual 122.15 111.14 11.01 3.47e+00 8.31e-02 1.01e+01 angle pdb=" O3' C D 40 " pdb=" C3' C D 40 " pdb=" C2' C D 40 " ideal model delta sigma weight residual 109.50 113.56 -4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" C1' C D 19 " pdb=" N1 C D 19 " pdb=" C2 C D 19 " ideal model delta sigma weight residual 118.80 126.79 -7.99 3.00e+00 1.11e-01 7.10e+00 ... (remaining 16328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6447 35.75 - 71.50: 530 71.50 - 107.25: 47 107.25 - 143.00: 4 143.00 - 178.75: 5 Dihedral angle restraints: 7033 sinusoidal: 4254 harmonic: 2779 Sorted by residual: dihedral pdb=" C4' C D 40 " pdb=" C3' C D 40 " pdb=" C2' C D 40 " pdb=" C1' C D 40 " ideal model delta sinusoidal sigma weight residual -35.00 32.42 -67.42 1 8.00e+00 1.56e-02 9.24e+01 dihedral pdb=" C5' C D 40 " pdb=" C4' C D 40 " pdb=" C3' C D 40 " pdb=" O3' C D 40 " ideal model delta sinusoidal sigma weight residual 147.00 80.46 66.54 1 8.00e+00 1.56e-02 9.03e+01 dihedral pdb=" O4' U D 9 " pdb=" C1' U D 9 " pdb=" N1 U D 9 " pdb=" C2 U D 9 " ideal model delta sinusoidal sigma weight residual -160.00 -12.34 -147.66 1 1.50e+01 4.44e-03 7.87e+01 ... (remaining 7030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1738 0.062 - 0.124: 135 0.124 - 0.187: 4 0.187 - 0.249: 1 0.249 - 0.311: 2 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C1' A D 109 " pdb=" O4' A D 109 " pdb=" C2' A D 109 " pdb=" N9 A D 109 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C3' C D 40 " pdb=" C4' C D 40 " pdb=" O3' C D 40 " pdb=" C2' C D 40 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C2' C D 40 " pdb=" C3' C D 40 " pdb=" O2' C D 40 " pdb=" C1' C D 40 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1877 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 109 " 0.029 2.00e-02 2.50e+03 1.44e-02 5.69e+00 pdb=" N9 A D 109 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A D 109 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A D 109 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A D 109 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 109 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 109 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A D 109 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 109 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 109 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 109 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 110 " 0.032 2.00e-02 2.50e+03 1.37e-02 5.67e+00 pdb=" N9 G D 110 " -0.033 2.00e-02 2.50e+03 pdb=" C8 G D 110 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G D 110 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G D 110 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G D 110 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G D 110 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G D 110 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G D 110 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G D 110 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 110 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G D 110 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 96 " 0.025 2.00e-02 2.50e+03 1.07e-02 3.18e+00 pdb=" N9 A D 96 " -0.021 2.00e-02 2.50e+03 pdb=" C8 A D 96 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A D 96 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 96 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A D 96 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A D 96 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A D 96 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 96 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 96 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 96 " -0.004 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 544 2.71 - 3.26: 10465 3.26 - 3.80: 19316 3.80 - 4.35: 22749 4.35 - 4.90: 35295 Nonbonded interactions: 88369 Sorted by model distance: nonbonded pdb=" OG SER A 171 " pdb=" OG SER A 185 " model vdw 2.160 3.040 nonbonded pdb=" O2' A D 114 " pdb=" O5' A D 115 " model vdw 2.166 3.040 nonbonded pdb=" O2' A D 109 " pdb=" O4' G D 110 " model vdw 2.167 3.040 nonbonded pdb=" O THR A 946 " pdb=" OG1 THR A 949 " model vdw 2.234 3.040 nonbonded pdb=" NE1 TRP A 836 " pdb=" OD1 ASP A 871 " model vdw 2.243 3.120 ... (remaining 88364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 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 : 0.002 0.029 11577 Z= 0.137 Angle : 0.589 11.013 16333 Z= 0.337 Chirality : 0.035 0.311 1880 Planarity : 0.003 0.035 1513 Dihedral : 21.359 178.745 5237 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.03 % Favored : 95.76 % Rotamer: Outliers : 5.53 % Allowed : 6.73 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.28), residues: 944 helix: 2.27 (0.26), residues: 420 sheet: -1.43 (0.43), residues: 135 loop : -0.77 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.014 0.001 TYR A 85 PHE 0.007 0.001 PHE A 240 TRP 0.009 0.001 TRP A 344 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00244 (11577) covalent geometry : angle 0.58909 (16333) hydrogen bonds : bond 0.14887 ( 494) hydrogen bonds : angle 5.96334 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.297 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: A 19 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7218 (p0) REVERT: A 142 LEU cc_start: 0.5693 (tp) cc_final: 0.5411 (tp) REVERT: A 485 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4690 (pttp) REVERT: A 517 PHE cc_start: 0.4740 (OUTLIER) cc_final: 0.4171 (t80) REVERT: A 551 PHE cc_start: 0.6445 (m-80) cc_final: 0.6183 (m-80) REVERT: A 591 ARG cc_start: 0.6476 (ttt90) cc_final: 0.6193 (ttt180) REVERT: A 601 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 604 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.4159 (mp) REVERT: A 621 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7152 (tt) REVERT: A 660 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.4984 (mtt-85) outliers start: 46 outliers final: 10 residues processed: 172 average time/residue: 0.1357 time to fit residues: 30.9501 Evaluate side-chains 89 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 660 ARG Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 512 GLN A 534 ASN A 749 GLN A 914 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.176345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.140257 restraints weight = 34494.615| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 4.89 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11577 Z= 0.172 Angle : 0.650 10.495 16333 Z= 0.340 Chirality : 0.039 0.315 1880 Planarity : 0.005 0.045 1513 Dihedral : 24.306 177.473 3283 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 3.25 % Allowed : 11.42 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 944 helix: 1.96 (0.25), residues: 429 sheet: -1.40 (0.44), residues: 135 loop : -0.93 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 478 TYR 0.020 0.001 TYR A 140 PHE 0.023 0.002 PHE A 935 TRP 0.015 0.002 TRP A 422 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00358 (11577) covalent geometry : angle 0.65007 (16333) hydrogen bonds : bond 0.05836 ( 494) hydrogen bonds : angle 4.75750 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.6596 (t80) cc_final: 0.6367 (t80) REVERT: A 347 MET cc_start: 0.6224 (mtm) cc_final: 0.5958 (ptt) REVERT: A 398 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 517 PHE cc_start: 0.4853 (OUTLIER) cc_final: 0.4274 (t80) REVERT: A 551 PHE cc_start: 0.7553 (m-80) cc_final: 0.7045 (m-80) REVERT: A 595 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 621 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7644 (tt) REVERT: A 797 TYR cc_start: 0.6167 (m-10) cc_final: 0.5966 (m-10) outliers start: 27 outliers final: 19 residues processed: 115 average time/residue: 0.1139 time to fit residues: 18.0804 Evaluate side-chains 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 55 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 947 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.170480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.132028 restraints weight = 33571.640| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 4.25 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11577 Z= 0.251 Angle : 0.749 9.407 16333 Z= 0.393 Chirality : 0.043 0.302 1880 Planarity : 0.005 0.049 1513 Dihedral : 24.392 178.180 3271 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 5.17 % Allowed : 12.02 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 944 helix: 1.44 (0.24), residues: 415 sheet: -1.62 (0.43), residues: 135 loop : -1.26 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 660 TYR 0.018 0.002 TYR A 789 PHE 0.046 0.003 PHE A 935 TRP 0.029 0.003 TRP A 782 HIS 0.008 0.002 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00532 (11577) covalent geometry : angle 0.74873 (16333) hydrogen bonds : bond 0.06973 ( 494) hydrogen bonds : angle 5.07264 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6205 (p0) REVERT: A 102 GLN cc_start: 0.8655 (tt0) cc_final: 0.8454 (tt0) REVERT: A 347 MET cc_start: 0.5867 (mtm) cc_final: 0.5659 (mtm) REVERT: A 396 ARG cc_start: 0.7303 (tpt-90) cc_final: 0.7022 (ptm160) REVERT: A 517 PHE cc_start: 0.4940 (OUTLIER) cc_final: 0.4418 (t80) REVERT: A 621 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7759 (tt) REVERT: A 729 ASN cc_start: 0.8080 (m110) cc_final: 0.7658 (m-40) REVERT: A 775 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6772 (pp30) outliers start: 43 outliers final: 26 residues processed: 111 average time/residue: 0.1114 time to fit residues: 17.2178 Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN A 512 GLN ** A 729 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 = 0.4846 r_free = 0.4846 target = 0.173100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.138778 restraints weight = 32460.111| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 4.05 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11577 Z= 0.152 Angle : 0.619 9.819 16333 Z= 0.327 Chirality : 0.038 0.303 1880 Planarity : 0.004 0.044 1513 Dihedral : 24.224 176.254 3269 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.72 % Favored : 94.17 % Rotamer: Outliers : 3.37 % Allowed : 15.14 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 944 helix: 1.65 (0.25), residues: 420 sheet: -1.05 (0.48), residues: 120 loop : -1.14 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 660 TYR 0.017 0.001 TYR A 776 PHE 0.035 0.002 PHE A 965 TRP 0.023 0.002 TRP A 422 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00313 (11577) covalent geometry : angle 0.61922 (16333) hydrogen bonds : bond 0.05646 ( 494) hydrogen bonds : angle 4.58590 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4179 (OUTLIER) cc_final: 0.3473 (ttm170) REVERT: A 102 GLN cc_start: 0.8392 (tt0) cc_final: 0.8178 (tt0) REVERT: A 240 PHE cc_start: 0.6646 (t80) cc_final: 0.6339 (t80) REVERT: A 517 PHE cc_start: 0.4603 (OUTLIER) cc_final: 0.3899 (t80) REVERT: A 551 PHE cc_start: 0.7681 (m-80) cc_final: 0.7128 (m-80) REVERT: A 621 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7658 (tt) REVERT: A 728 LYS cc_start: 0.8895 (pttt) cc_final: 0.8684 (pttp) REVERT: A 962 TRP cc_start: 0.1249 (OUTLIER) cc_final: -0.0271 (t-100) outliers start: 28 outliers final: 15 residues processed: 100 average time/residue: 0.1109 time to fit residues: 15.7012 Evaluate side-chains 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 0.0870 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 512 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.174207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.142429 restraints weight = 33440.047| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 4.26 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11577 Z= 0.133 Angle : 0.589 9.715 16333 Z= 0.309 Chirality : 0.036 0.291 1880 Planarity : 0.004 0.049 1513 Dihedral : 24.063 175.636 3264 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 3.25 % Allowed : 15.99 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.28), residues: 944 helix: 1.95 (0.25), residues: 416 sheet: -0.98 (0.47), residues: 124 loop : -0.99 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 956 TYR 0.013 0.001 TYR A 776 PHE 0.021 0.001 PHE A 965 TRP 0.020 0.002 TRP A 422 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00274 (11577) covalent geometry : angle 0.58885 (16333) hydrogen bonds : bond 0.05130 ( 494) hydrogen bonds : angle 4.34339 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4581 (OUTLIER) cc_final: 0.3644 (ttm170) REVERT: A 102 GLN cc_start: 0.8274 (tt0) cc_final: 0.8032 (tt0) REVERT: A 240 PHE cc_start: 0.6570 (t80) cc_final: 0.6334 (t80) REVERT: A 517 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.3811 (t80) REVERT: A 551 PHE cc_start: 0.7444 (m-80) cc_final: 0.6944 (m-80) REVERT: A 621 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7673 (tt) outliers start: 27 outliers final: 17 residues processed: 95 average time/residue: 0.1110 time to fit residues: 14.8616 Evaluate side-chains 84 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN A 435 HIS A 512 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.171824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.135255 restraints weight = 33881.636| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 4.49 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11577 Z= 0.165 Angle : 0.634 9.495 16333 Z= 0.331 Chirality : 0.037 0.275 1880 Planarity : 0.004 0.050 1513 Dihedral : 24.085 175.269 3264 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.75 % Rotamer: Outliers : 3.49 % Allowed : 17.07 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 944 helix: 1.83 (0.25), residues: 417 sheet: -1.24 (0.44), residues: 133 loop : -1.01 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.013 0.001 TYR A 789 PHE 0.029 0.002 PHE A 965 TRP 0.021 0.002 TRP A 422 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00348 (11577) covalent geometry : angle 0.63399 (16333) hydrogen bonds : bond 0.05538 ( 494) hydrogen bonds : angle 4.50599 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4400 (OUTLIER) cc_final: 0.3327 (ttm170) REVERT: A 439 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 517 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.4057 (t80) REVERT: A 621 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7736 (tt) outliers start: 29 outliers final: 19 residues processed: 92 average time/residue: 0.1097 time to fit residues: 14.4117 Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 36 optimal weight: 0.0970 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 512 GLN A 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.169755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.133733 restraints weight = 33155.848| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 4.14 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11577 Z= 0.188 Angle : 0.667 9.395 16333 Z= 0.348 Chirality : 0.038 0.269 1880 Planarity : 0.005 0.049 1513 Dihedral : 24.196 174.971 3264 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.25 % Favored : 93.64 % Rotamer: Outliers : 3.61 % Allowed : 17.91 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.27), residues: 944 helix: 1.63 (0.25), residues: 417 sheet: -1.38 (0.44), residues: 133 loop : -1.18 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.034 0.002 TYR A 776 PHE 0.037 0.002 PHE A 965 TRP 0.022 0.002 TRP A 422 HIS 0.005 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00393 (11577) covalent geometry : angle 0.66672 (16333) hydrogen bonds : bond 0.05928 ( 494) hydrogen bonds : angle 4.69873 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4540 (OUTLIER) cc_final: 0.3354 (ttm170) REVERT: A 412 GLU cc_start: 0.1776 (OUTLIER) cc_final: 0.1334 (mt-10) REVERT: A 517 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.4068 (t80) outliers start: 30 outliers final: 17 residues processed: 93 average time/residue: 0.1124 time to fit residues: 14.4781 Evaluate side-chains 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 512 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.170226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.136425 restraints weight = 33578.596| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 4.11 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11577 Z= 0.169 Angle : 0.643 9.405 16333 Z= 0.336 Chirality : 0.038 0.262 1880 Planarity : 0.004 0.049 1513 Dihedral : 24.119 174.473 3260 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.43 % Rotamer: Outliers : 3.12 % Allowed : 18.27 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.28), residues: 944 helix: 1.63 (0.25), residues: 416 sheet: -1.41 (0.44), residues: 129 loop : -1.21 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 627 TYR 0.027 0.001 TYR A 776 PHE 0.040 0.002 PHE A 965 TRP 0.020 0.002 TRP A 422 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00355 (11577) covalent geometry : angle 0.64258 (16333) hydrogen bonds : bond 0.05684 ( 494) hydrogen bonds : angle 4.58079 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.3628 (ttm170) REVERT: A 412 GLU cc_start: 0.1792 (OUTLIER) cc_final: 0.1333 (mt-10) REVERT: A 517 PHE cc_start: 0.4793 (OUTLIER) cc_final: 0.4000 (t80) outliers start: 26 outliers final: 18 residues processed: 89 average time/residue: 0.0992 time to fit residues: 12.8943 Evaluate side-chains 85 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.171419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.135689 restraints weight = 32230.919| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 4.36 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11577 Z= 0.143 Angle : 0.628 12.026 16333 Z= 0.323 Chirality : 0.037 0.257 1880 Planarity : 0.004 0.049 1513 Dihedral : 24.017 174.011 3260 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 2.52 % Allowed : 19.35 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.28), residues: 944 helix: 1.75 (0.25), residues: 416 sheet: -1.10 (0.47), residues: 120 loop : -1.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.013 0.001 TYR A 776 PHE 0.036 0.002 PHE A 965 TRP 0.020 0.002 TRP A 422 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00299 (11577) covalent geometry : angle 0.62790 (16333) hydrogen bonds : bond 0.05265 ( 494) hydrogen bonds : angle 4.39752 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.4248 (OUTLIER) cc_final: 0.3524 (ttm170) REVERT: A 319 GLU cc_start: 0.4446 (OUTLIER) cc_final: 0.3669 (mp0) REVERT: A 412 GLU cc_start: 0.1734 (OUTLIER) cc_final: 0.1242 (mt-10) REVERT: A 517 PHE cc_start: 0.4855 (OUTLIER) cc_final: 0.4109 (t80) outliers start: 21 outliers final: 14 residues processed: 85 average time/residue: 0.0992 time to fit residues: 12.2198 Evaluate side-chains 86 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 62 optimal weight: 0.0000 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 75 optimal weight: 0.2980 overall best weight: 2.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.169849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.133514 restraints weight = 33316.640| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 4.03 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11577 Z= 0.174 Angle : 0.665 10.811 16333 Z= 0.345 Chirality : 0.038 0.248 1880 Planarity : 0.004 0.049 1513 Dihedral : 24.062 174.298 3260 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 2.28 % Allowed : 19.83 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 944 helix: 1.54 (0.25), residues: 421 sheet: -1.34 (0.43), residues: 129 loop : -1.25 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.019 0.002 TYR A 776 PHE 0.047 0.002 PHE A 965 TRP 0.022 0.002 TRP A 782 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00368 (11577) covalent geometry : angle 0.66486 (16333) hydrogen bonds : bond 0.05671 ( 494) hydrogen bonds : angle 4.62525 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.4562 (OUTLIER) cc_final: 0.3833 (mp0) REVERT: A 412 GLU cc_start: 0.1686 (OUTLIER) cc_final: 0.1233 (mt-10) REVERT: A 439 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 517 PHE cc_start: 0.4809 (OUTLIER) cc_final: 0.4155 (t80) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.0889 time to fit residues: 10.6375 Evaluate side-chains 82 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN A 512 GLN A 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.170538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.134150 restraints weight = 33460.633| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 4.14 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11577 Z= 0.154 Angle : 0.647 11.826 16333 Z= 0.333 Chirality : 0.037 0.242 1880 Planarity : 0.004 0.049 1513 Dihedral : 24.016 174.095 3260 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 2.28 % Allowed : 19.35 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 944 helix: 1.69 (0.25), residues: 416 sheet: -1.24 (0.44), residues: 129 loop : -1.14 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 703 TYR 0.016 0.001 TYR A 372 PHE 0.046 0.002 PHE A 965 TRP 0.021 0.002 TRP A 422 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00323 (11577) covalent geometry : angle 0.64677 (16333) hydrogen bonds : bond 0.05441 ( 494) hydrogen bonds : angle 4.45273 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.72 seconds wall clock time: 44 minutes 12.80 seconds (2652.80 seconds total)