Starting phenix.real_space_refine on Tue Jun 10 05:14:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7waz_32390/06_2025/7waz_32390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7waz_32390/06_2025/7waz_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_32390/06_2025/7waz_32390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7waz_32390/06_2025/7waz_32390.map" model { file = "/net/cci-nas-00/data/ceres_data/7waz_32390/06_2025/7waz_32390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7waz_32390/06_2025/7waz_32390.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.26, per 1000 atoms: 0.66 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: 2.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.82 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: 4.96 Time building geometry restraints manager: 3.29 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.480 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- 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 : 11.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.009 0.001 TRP A 344 HIS 0.003 0.001 HIS A 405 PHE 0.007 0.001 PHE A 240 TYR 0.014 0.001 TYR A 85 ARG 0.005 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.14887 ( 494) hydrogen bonds : angle 5.96334 ( 1389) covalent geometry : bond 0.00244 (11577) covalent geometry : angle 0.58909 (16333) *********************** 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 : 1.096 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: 0.7536 (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: 0.4172 (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: 0.3013 time to fit residues: 69.2184 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 : 0.921 ------------------------------------------------------------------------------- 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 92 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 512 GLN A 534 ASN A 749 GLN A 947 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.167906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.136069 restraints weight = 33359.631| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 5.42 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 11577 Z= 0.349 Angle : 0.883 9.965 16333 Z= 0.463 Chirality : 0.049 0.329 1880 Planarity : 0.007 0.053 1513 Dihedral : 24.601 175.681 3283 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.73 % Favored : 91.95 % Rotamer: Outliers : 5.05 % Allowed : 11.66 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.26), residues: 944 helix: 0.90 (0.24), residues: 426 sheet: -2.08 (0.40), residues: 137 loop : -1.56 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 782 HIS 0.006 0.002 HIS A 286 PHE 0.030 0.003 PHE A 240 TYR 0.020 0.002 TYR A 789 ARG 0.009 0.001 ARG A 591 Details of bonding type rmsd hydrogen bonds : bond 0.08177 ( 494) hydrogen bonds : angle 5.55069 ( 1389) covalent geometry : bond 0.00741 (11577) covalent geometry : angle 0.88250 (16333) *********************** 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 131 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6716 (p0) REVERT: A 142 LEU cc_start: 0.6879 (tp) cc_final: 0.6677 (tp) REVERT: A 347 MET cc_start: 0.6402 (mtm) cc_final: 0.5928 (ptp) REVERT: A 396 ARG cc_start: 0.7219 (tpt-90) cc_final: 0.6925 (ptt180) REVERT: A 517 PHE cc_start: 0.5033 (OUTLIER) cc_final: 0.4416 (t80) REVERT: A 621 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7415 (tt) REVERT: A 937 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6643 (mtt90) REVERT: A 945 GLN cc_start: 0.6915 (mt0) cc_final: 0.6584 (mt0) REVERT: A 965 PHE cc_start: 0.6211 (t80) cc_final: 0.5691 (t80) REVERT: A 967 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7284 (ptt-90) outliers start: 42 outliers final: 27 residues processed: 119 average time/residue: 0.2995 time to fit residues: 47.9977 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 ASN 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 140 TYR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 237 VAL 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 568 VAL 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 663 ASN 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 698 TYR Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 779 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 286 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 928 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.133548 restraints weight = 32845.007| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 4.13 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11577 Z= 0.224 Angle : 0.716 9.674 16333 Z= 0.378 Chirality : 0.041 0.317 1880 Planarity : 0.005 0.052 1513 Dihedral : 24.457 176.882 3271 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 4.33 % Allowed : 15.50 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 944 helix: 1.21 (0.25), residues: 420 sheet: -1.91 (0.42), residues: 133 loop : -1.48 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 974 HIS 0.004 0.001 HIS A 405 PHE 0.052 0.002 PHE A 935 TYR 0.019 0.002 TYR A 140 ARG 0.005 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.06692 ( 494) hydrogen bonds : angle 5.10571 ( 1389) covalent geometry : bond 0.00475 (11577) covalent geometry : angle 0.71581 (16333) *********************** 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 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 412 GLU cc_start: 0.1832 (OUTLIER) cc_final: 0.1424 (mt-10) REVERT: A 517 PHE cc_start: 0.4888 (OUTLIER) cc_final: 0.4233 (t80) REVERT: A 621 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7646 (tt) REVERT: A 729 ASN cc_start: 0.8112 (m110) cc_final: 0.7674 (m-40) REVERT: A 776 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.4240 (m-80) REVERT: A 945 GLN cc_start: 0.6879 (mt0) cc_final: 0.6575 (mt0) REVERT: A 962 TRP cc_start: 0.1492 (OUTLIER) cc_final: -0.0393 (t-100) outliers start: 36 outliers final: 21 residues processed: 102 average time/residue: 0.2763 time to fit residues: 39.0125 Evaluate side-chains 90 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 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 559 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 LEU 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 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- 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 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.168617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.131622 restraints weight = 32323.110| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 4.31 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11577 Z= 0.211 Angle : 0.704 12.483 16333 Z= 0.370 Chirality : 0.041 0.306 1880 Planarity : 0.005 0.052 1513 Dihedral : 24.378 176.513 3262 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.10 % Favored : 92.80 % Rotamer: Outliers : 5.29 % Allowed : 14.18 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 944 helix: 1.31 (0.25), residues: 414 sheet: -1.69 (0.45), residues: 124 loop : -1.57 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 422 HIS 0.004 0.001 HIS A 286 PHE 0.030 0.002 PHE A 935 TYR 0.017 0.002 TYR A 789 ARG 0.004 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.06432 ( 494) hydrogen bonds : angle 4.93186 ( 1389) covalent geometry : bond 0.00442 (11577) covalent geometry : angle 0.70407 (16333) *********************** 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 121 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.6843 (p0) REVERT: A 37 MET cc_start: 0.6950 (tpp) cc_final: 0.6746 (tpp) REVERT: A 347 MET cc_start: 0.6061 (mtm) cc_final: 0.5840 (ptp) REVERT: A 412 GLU cc_start: 0.2048 (OUTLIER) cc_final: 0.1584 (mt-10) REVERT: A 776 TYR cc_start: 0.4932 (OUTLIER) cc_final: 0.4301 (m-80) REVERT: A 945 GLN cc_start: 0.7061 (mt0) cc_final: 0.6792 (mt0) outliers start: 44 outliers final: 27 residues processed: 112 average time/residue: 0.2838 time to fit residues: 44.8402 Evaluate side-chains 97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 258 ASN 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 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 581 LEU Chi-restraints excluded: chain A residue 620 THR 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 694 ILE Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 937 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN A 435 HIS A 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.171926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.136752 restraints weight = 32442.407| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 4.74 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11577 Z= 0.140 Angle : 0.622 13.264 16333 Z= 0.326 Chirality : 0.037 0.303 1880 Planarity : 0.004 0.049 1513 Dihedral : 24.224 175.666 3260 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 3.37 % Allowed : 16.71 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 944 helix: 1.70 (0.26), residues: 417 sheet: -1.46 (0.47), residues: 124 loop : -1.32 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 962 HIS 0.006 0.001 HIS A 405 PHE 0.043 0.002 PHE A 965 TYR 0.013 0.001 TYR A 789 ARG 0.003 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.05485 ( 494) hydrogen bonds : angle 4.50583 ( 1389) covalent geometry : bond 0.00291 (11577) covalent geometry : angle 0.62233 (16333) *********************** 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 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.6942 (p0) REVERT: A 44 ARG cc_start: 0.4382 (OUTLIER) cc_final: 0.3489 (ptm160) REVERT: A 240 PHE cc_start: 0.6567 (t80) cc_final: 0.6320 (t80) REVERT: A 334 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 435 HIS cc_start: 0.6325 (t-170) cc_final: 0.6118 (t-90) REVERT: A 504 LEU cc_start: 0.8382 (tt) cc_final: 0.8144 (tt) REVERT: A 611 LEU cc_start: 0.8577 (tp) cc_final: 0.7839 (pt) REVERT: A 728 LYS cc_start: 0.9045 (pttt) cc_final: 0.8813 (pttp) REVERT: A 776 TYR cc_start: 0.4632 (OUTLIER) cc_final: 0.4141 (m-80) REVERT: A 945 GLN cc_start: 0.6921 (mt0) cc_final: 0.6695 (mt0) outliers start: 28 outliers final: 14 residues processed: 92 average time/residue: 0.3268 time to fit residues: 43.2629 Evaluate side-chains 76 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 44 ARG Chi-restraints excluded: chain A residue 202 THR 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 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 776 TYR 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 99 optimal weight: 20.0000 chunk 56 optimal weight: 0.0970 chunk 35 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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 914 ASN A 928 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.169173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.132056 restraints weight = 32605.472| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 4.16 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.4929 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= 0.185 Angle : 0.671 13.772 16333 Z= 0.349 Chirality : 0.039 0.284 1880 Planarity : 0.004 0.051 1513 Dihedral : 24.265 175.787 3260 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 4.21 % Allowed : 17.55 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.28), residues: 944 helix: 1.61 (0.25), residues: 416 sheet: -1.49 (0.46), residues: 124 loop : -1.42 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 422 HIS 0.003 0.001 HIS A 286 PHE 0.021 0.002 PHE A 965 TYR 0.015 0.001 TYR A 789 ARG 0.003 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 494) hydrogen bonds : angle 4.74028 ( 1389) covalent geometry : bond 0.00391 (11577) covalent geometry : angle 0.67080 (16333) *********************** 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 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7009 (p0) REVERT: A 204 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.5843 (pp20) REVERT: A 412 GLU cc_start: 0.2082 (OUTLIER) cc_final: 0.1577 (mt-10) REVERT: A 611 LEU cc_start: 0.8510 (tp) cc_final: 0.7750 (pt) REVERT: A 776 TYR cc_start: 0.4807 (OUTLIER) cc_final: 0.4212 (m-80) REVERT: A 783 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 945 GLN cc_start: 0.6811 (mt0) cc_final: 0.6558 (mt0) outliers start: 35 outliers final: 20 residues processed: 96 average time/residue: 0.3115 time to fit residues: 43.2469 Evaluate side-chains 92 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 44 ARG Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 237 VAL 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 517 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 969 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 245 GLN ** 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 = 0.4796 r_free = 0.4796 target = 0.168016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.135088 restraints weight = 33517.902| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 4.33 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11577 Z= 0.194 Angle : 0.677 14.703 16333 Z= 0.350 Chirality : 0.039 0.272 1880 Planarity : 0.005 0.050 1513 Dihedral : 24.240 175.394 3260 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 4.33 % Allowed : 17.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 944 helix: 1.55 (0.25), residues: 416 sheet: -1.52 (0.45), residues: 124 loop : -1.52 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 422 HIS 0.004 0.001 HIS A 405 PHE 0.037 0.002 PHE A 965 TYR 0.016 0.001 TYR A 789 ARG 0.004 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.06142 ( 494) hydrogen bonds : angle 4.76349 ( 1389) covalent geometry : bond 0.00408 (11577) covalent geometry : angle 0.67682 (16333) *********************** 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 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7672 (mtt180) REVERT: A 19 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7004 (p0) REVERT: A 611 LEU cc_start: 0.8180 (tp) cc_final: 0.7611 (pt) REVERT: A 776 TYR cc_start: 0.4983 (OUTLIER) cc_final: 0.4272 (m-80) REVERT: A 945 GLN cc_start: 0.7047 (mt0) cc_final: 0.6725 (mt0) outliers start: 36 outliers final: 20 residues processed: 98 average time/residue: 0.4078 time to fit residues: 57.0937 Evaluate side-chains 90 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 19 ASN 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 507 SER Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 581 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 694 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 779 MET 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 20 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 65 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.172123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.136917 restraints weight = 33596.918| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 4.45 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11577 Z= 0.127 Angle : 0.626 15.930 16333 Z= 0.320 Chirality : 0.037 0.271 1880 Planarity : 0.004 0.053 1513 Dihedral : 24.072 175.000 3258 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 2.52 % Allowed : 19.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 944 helix: 1.87 (0.25), residues: 414 sheet: -1.38 (0.51), residues: 109 loop : -1.27 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 962 HIS 0.008 0.001 HIS A 435 PHE 0.039 0.001 PHE A 965 TYR 0.012 0.001 TYR A 372 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 494) hydrogen bonds : angle 4.44981 ( 1389) covalent geometry : bond 0.00262 (11577) covalent geometry : angle 0.62553 (16333) *********************** 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 91 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.3943 (OUTLIER) cc_final: 0.3297 (ptm160) REVERT: A 204 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5837 (pp20) REVERT: A 412 GLU cc_start: 0.2179 (OUTLIER) cc_final: 0.1545 (mt-10) REVERT: A 504 LEU cc_start: 0.8372 (tt) cc_final: 0.8132 (tt) REVERT: A 611 LEU cc_start: 0.8508 (tp) cc_final: 0.7791 (pt) REVERT: A 776 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.3870 (m-80) REVERT: A 945 GLN cc_start: 0.6866 (mt0) cc_final: 0.6592 (mt0) outliers start: 21 outliers final: 11 residues processed: 88 average time/residue: 0.2529 time to fit residues: 32.0137 Evaluate side-chains 78 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 319 GLU 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 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 776 TYR 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 56 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 103 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 350 ASN A 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.170219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.134592 restraints weight = 33430.143| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 4.31 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5628 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= 0.149 Angle : 0.637 16.041 16333 Z= 0.325 Chirality : 0.037 0.260 1880 Planarity : 0.004 0.050 1513 Dihedral : 24.054 175.206 3258 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.72 % Favored : 94.17 % Rotamer: Outliers : 2.64 % Allowed : 20.31 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 944 helix: 1.73 (0.25), residues: 418 sheet: -1.29 (0.50), residues: 109 loop : -1.38 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 962 HIS 0.004 0.001 HIS A 405 PHE 0.042 0.002 PHE A 965 TYR 0.012 0.001 TYR A 789 ARG 0.004 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 494) hydrogen bonds : angle 4.47350 ( 1389) covalent geometry : bond 0.00314 (11577) covalent geometry : angle 0.63659 (16333) *********************** 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 91 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7085 (tpp) cc_final: 0.6867 (tpp) REVERT: A 204 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5898 (pp20) REVERT: A 319 GLU cc_start: 0.4452 (OUTLIER) cc_final: 0.3604 (mp0) REVERT: A 412 GLU cc_start: 0.1890 (OUTLIER) cc_final: 0.1391 (mt-10) REVERT: A 435 HIS cc_start: 0.6113 (t-170) cc_final: 0.5862 (t-90) REVERT: A 439 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 611 LEU cc_start: 0.8530 (tp) cc_final: 0.7771 (pt) REVERT: A 776 TYR cc_start: 0.4606 (OUTLIER) cc_final: 0.4075 (m-80) REVERT: A 945 GLN cc_start: 0.6878 (mt0) cc_final: 0.6600 (mt0) outliers start: 22 outliers final: 16 residues processed: 88 average time/residue: 0.2917 time to fit residues: 37.5418 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 : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 204 GLU 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 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 969 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.167341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.135440 restraints weight = 33653.404| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 4.39 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11577 Z= 0.196 Angle : 0.700 16.396 16333 Z= 0.360 Chirality : 0.039 0.251 1880 Planarity : 0.005 0.051 1513 Dihedral : 24.166 175.194 3256 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 2.64 % Allowed : 20.79 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 944 helix: 1.58 (0.25), residues: 413 sheet: -1.30 (0.48), residues: 113 loop : -1.47 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 782 HIS 0.004 0.001 HIS A 405 PHE 0.045 0.003 PHE A 965 TYR 0.015 0.001 TYR A 789 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.06050 ( 494) hydrogen bonds : angle 4.84951 ( 1389) covalent geometry : bond 0.00415 (11577) covalent geometry : angle 0.69955 (16333) ********************** 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 91 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5789 (pp20) REVERT: A 319 GLU cc_start: 0.4118 (OUTLIER) cc_final: 0.3036 (mp0) REVERT: A 398 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 412 GLU cc_start: 0.2142 (OUTLIER) cc_final: 0.1580 (mt-10) REVERT: A 776 TYR cc_start: 0.4873 (OUTLIER) cc_final: 0.4278 (m-80) REVERT: A 937 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6361 (mtt90) REVERT: A 945 GLN cc_start: 0.7068 (mt0) cc_final: 0.6670 (mt0) outliers start: 22 outliers final: 14 residues processed: 87 average time/residue: 0.2643 time to fit residues: 33.9033 Evaluate side-chains 81 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 GLU 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 655 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 851 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 38 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN A 729 ASN A 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.166775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.131959 restraints weight = 32668.724| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.95 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11577 Z= 0.195 Angle : 0.698 16.077 16333 Z= 0.359 Chirality : 0.040 0.248 1880 Planarity : 0.005 0.055 1513 Dihedral : 24.209 175.092 3256 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.99 % Favored : 92.80 % Rotamer: Outliers : 2.52 % Allowed : 20.55 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.27), residues: 944 helix: 1.46 (0.25), residues: 407 sheet: -1.62 (0.43), residues: 134 loop : -1.56 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 962 HIS 0.004 0.001 HIS A 405 PHE 0.046 0.003 PHE A 965 TYR 0.015 0.001 TYR A 789 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.06096 ( 494) hydrogen bonds : angle 4.85971 ( 1389) covalent geometry : bond 0.00414 (11577) covalent geometry : angle 0.69796 (16333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5813.44 seconds wall clock time: 104 minutes 55.60 seconds (6295.60 seconds total)