Starting phenix.real_space_refine on Fri Aug 7 13:38:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9t_64887/08_2026/9v9t_64887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9t_64887/08_2026/9v9t_64887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9t_64887/08_2026/9v9t_64887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9t_64887/08_2026/9v9t_64887.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9t_64887/08_2026/9v9t_64887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9t_64887/08_2026/9v9t_64887.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 11108 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 263 5.49 5 S 28 5.16 5 C 7422 2.51 5 N 2452 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13137 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 362 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 711 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2671 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39 SG CYS L 27 78.197 34.269 53.057 1.00 53.67 S ATOM 58 SG CYS L 30 76.326 32.534 50.130 1.00 53.74 S ATOM 146 SG CYS L 41 79.766 34.517 49.916 1.00 54.84 S ATOM 166 SG CYS L 44 76.560 36.219 49.956 1.00 56.02 S ATOM 401 SG CYS N 27 42.491 93.859 43.107 1.00 65.60 S ATOM 420 SG CYS N 30 41.687 93.175 39.591 1.00 69.15 S ATOM 508 SG CYS N 41 38.896 92.922 42.019 1.00 67.02 S ATOM 528 SG CYS N 44 41.615 90.268 42.201 1.00 67.95 S Time building chain proxies: 2.42, per 1000 atoms: 0.18 Number of scatterers: 13137 At special positions: 0 Unit cell: (123.2, 122.1, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 263 15.00 O 2970 8.00 N 2452 7.00 C 7422 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: 0.82 Conformation dependent library (CDL) restraints added in 367.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 30 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 27 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 41 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 44 " Number of angles added : 12 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 59.6% alpha, 3.9% beta 129 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'L' and resid 59 through 67 removed outlier: 3.632A pdb=" N ALA L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.193A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.731A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.928A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.547A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.666A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.063A pdb=" N SER D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.941A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 121 " --> pdb=" O CYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.567A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.590A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.581A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.586A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.567A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.835A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'N' and resid 25 through 26 removed outlier: 3.545A pdb=" N TRP N 25 " --> pdb=" O ASN N 34 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN N 34 " --> pdb=" O TRP N 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.021A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.942A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.088A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.222A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'K' and resid 48 through 49 removed outlier: 4.026A pdb=" N PHE K 45 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG K 42 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 3 through 4 removed outlier: 3.598A pdb=" N PHE O 4 " --> pdb=" O SER O 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'O' and resid 44 through 45 removed outlier: 3.793A pdb=" N PHE O 45 " --> pdb=" O LYS O 48 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 333 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3290 1.34 - 1.46: 4009 1.46 - 1.58: 6029 1.58 - 1.70: 524 1.70 - 1.82: 40 Bond restraints: 13892 Sorted by residual: bond pdb=" C1' DC I 3 " pdb=" N1 DC I 3 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" C3' DC J 115 " pdb=" C2' DC J 115 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG J 136 " pdb=" C2' DG J 136 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC I 118 " pdb=" C2' DC I 118 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 13887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19412 2.23 - 4.46: 453 4.46 - 6.69: 12 6.69 - 8.91: 0 8.91 - 11.14: 2 Bond angle restraints: 19879 Sorted by residual: angle pdb=" N3 DT J 35 " pdb=" C4 DT J 35 " pdb=" O4 DT J 35 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 19874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 6463 35.89 - 71.78: 1225 71.78 - 107.67: 18 107.67 - 143.56: 1 143.56 - 179.45: 3 Dihedral angle restraints: 7710 sinusoidal: 4876 harmonic: 2834 Sorted by residual: dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual 220.00 40.55 179.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 35.95 -175.95 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 70.27 149.73 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1223 0.030 - 0.060: 687 0.060 - 0.090: 248 0.090 - 0.119: 102 0.119 - 0.149: 16 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA ILE O 3 " pdb=" N ILE O 3 " pdb=" C ILE O 3 " pdb=" CB ILE O 3 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" C3' DT J 57 " pdb=" C4' DT J 57 " pdb=" O3' DT J 57 " pdb=" C2' DT J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C3' DG I 4 " pdb=" C4' DG I 4 " pdb=" O3' DG I 4 " pdb=" C2' DG I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2273 not shown) Planarity restraints: 1607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.18e+00 pdb=" N9 DA I 20 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO G 80 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.024 2.00e-02 2.50e+03 1.05e-02 3.01e+00 pdb=" N9 DA I 39 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " -0.001 2.00e-02 2.50e+03 ... (remaining 1604 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 206 2.65 - 3.21: 10613 3.21 - 3.77: 22377 3.77 - 4.34: 30972 4.34 - 4.90: 44570 Nonbonded interactions: 108738 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.085 2.496 nonbonded pdb=" OG1 THR L 50 " pdb=" OE1 GLU G 64 " model vdw 2.206 3.040 nonbonded pdb=" NE2 GLN K 31 " pdb=" O ILE K 36 " model vdw 2.271 3.120 nonbonded pdb=" OE1 GLN K 62 " pdb=" OG SER K 65 " model vdw 2.294 3.040 nonbonded pdb=" NH2 ARG L 53 " pdb=" OD2 ASP G 90 " model vdw 2.310 3.120 ... (remaining 108733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 119) } ncs_group { reference = (chain 'D' and resid 30 through 120) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'O' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.005 0.067 13900 Z= 0.488 Angle : 0.767 11.143 19891 Z= 0.644 Chirality : 0.044 0.149 2276 Planarity : 0.004 0.044 1607 Dihedral : 26.332 179.447 5872 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.63 (0.27), residues: 952 helix: 1.76 (0.22), residues: 555 sheet: -0.89 (0.94), residues: 32 loop : -1.67 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.015 0.002 TYR F 88 PHE 0.011 0.001 PHE E 84 TRP 0.004 0.001 TRP N 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.49 (13892) covalent geometry : angle 0.75267 / 0.64 (19879) hydrogen bonds : bond 0.12422 / 8.07 ( 754) hydrogen bonds : angle 4.16582 / 3.02 ( 1892) metal coordination : bond 0.00718 / 0.36 ( 8) metal coordination : angle 5.98401 / 3.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.368 Fit side-chains REVERT: A 77 ASP cc_start: 0.6292 (m-30) cc_final: 0.6068 (m-30) REVERT: C 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8610 (t0) REVERT: D 32 GLU cc_start: 0.6790 (pt0) cc_final: 0.6521 (pt0) REVERT: D 113 LYS cc_start: 0.7856 (tttm) cc_final: 0.7626 (tttp) REVERT: G 73 ASN cc_start: 0.7561 (t0) cc_final: 0.7109 (t0) REVERT: G 74 LYS cc_start: 0.7393 (mmtm) cc_final: 0.7175 (tppt) REVERT: H 102 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6564 (tp30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.8867 time to fit residues: 140.7755 Evaluate side-chains 135 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN G 84 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127700 restraints weight = 14313.046| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.27 r_work: 0.3067 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13900 Z= 0.275 Angle : 0.842 19.551 19891 Z= 0.459 Chirality : 0.058 0.285 2276 Planarity : 0.007 0.055 1607 Dihedral : 30.153 178.293 3934 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.56 % Allowed : 10.68 % Favored : 87.76 % 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: -0.06 (0.26), residues: 952 helix: 1.18 (0.21), residues: 568 sheet: -0.97 (1.05), residues: 27 loop : -2.04 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.018 0.003 TYR A 54 PHE 0.021 0.003 PHE E 84 TRP 0.013 0.003 TRP N 25 HIS 0.005 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (13892) covalent geometry : angle 0.82153 / 0.46 (19879) hydrogen bonds : bond 0.08636 / 5.71 ( 754) hydrogen bonds : angle 3.57222 / 2.62 ( 1892) metal coordination : bond 0.01181 / 0.61 ( 8) metal coordination : angle 7.48620 / 4.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.378 Fit side-chains REVERT: A 77 ASP cc_start: 0.7266 (m-30) cc_final: 0.7025 (m-30) REVERT: D 32 GLU cc_start: 0.6990 (pt0) cc_final: 0.6572 (pt0) REVERT: D 56 MET cc_start: 0.8662 (mmt) cc_final: 0.8404 (tpt) REVERT: D 113 LYS cc_start: 0.8243 (tttm) cc_final: 0.7935 (tttp) REVERT: E 50 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7849 (mm-30) REVERT: G 56 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: G 73 ASN cc_start: 0.7792 (t0) cc_final: 0.7167 (t0) REVERT: G 84 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.7464 (tm130) REVERT: K 1 MET cc_start: 0.3193 (OUTLIER) cc_final: 0.2911 (ptt) outliers start: 13 outliers final: 2 residues processed: 139 average time/residue: 0.9049 time to fit residues: 133.1162 Evaluate side-chains 136 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 102 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 chunk 58 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.178582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134240 restraints weight = 14656.158| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.06 r_work: 0.3146 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13900 Z= 0.135 Angle : 0.651 12.406 19891 Z= 0.369 Chirality : 0.047 0.278 2276 Planarity : 0.004 0.061 1607 Dihedral : 30.064 176.084 3934 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 12.73 % Favored : 85.83 % 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: 0.98 (0.28), residues: 952 helix: 2.09 (0.22), residues: 565 sheet: -1.14 (0.92), residues: 34 loop : -1.66 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.010 0.001 TYR F 88 PHE 0.007 0.001 PHE A 67 TRP 0.005 0.001 TRP L 25 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.14 (13892) covalent geometry : angle 0.63706 / 0.37 (19879) hydrogen bonds : bond 0.05791 / 3.84 ( 754) hydrogen bonds : angle 3.16630 / 2.32 ( 1892) metal coordination : bond 0.00660 / 0.37 ( 8) metal coordination : angle 5.46030 / 3.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.273 Fit side-chains REVERT: L 34 ASN cc_start: 0.5599 (m-40) cc_final: 0.5388 (m110) REVERT: A 77 ASP cc_start: 0.7212 (m-30) cc_final: 0.6976 (m-30) REVERT: D 32 GLU cc_start: 0.6916 (pt0) cc_final: 0.6531 (pt0) REVERT: D 113 LYS cc_start: 0.8271 (tttm) cc_final: 0.7992 (tttp) REVERT: E 50 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7959 (mm-30) REVERT: G 56 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: G 73 ASN cc_start: 0.7712 (t0) cc_final: 0.7080 (t0) REVERT: G 91 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: H 105 LYS cc_start: 0.8273 (tttm) cc_final: 0.8051 (tttm) outliers start: 12 outliers final: 2 residues processed: 134 average time/residue: 0.7907 time to fit residues: 112.3015 Evaluate side-chains 131 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127139 restraints weight = 14288.431| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.10 r_work: 0.3045 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13900 Z= 0.271 Angle : 0.823 20.304 19891 Z= 0.445 Chirality : 0.057 0.284 2276 Planarity : 0.006 0.049 1607 Dihedral : 30.247 178.586 3934 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.40 % Allowed : 14.17 % Favored : 83.43 % 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: 0.18 (0.27), residues: 952 helix: 1.41 (0.21), residues: 567 sheet: -1.27 (0.92), residues: 34 loop : -1.98 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.016 0.003 TYR A 54 PHE 0.020 0.003 PHE E 84 TRP 0.016 0.003 TRP N 25 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.27 (13892) covalent geometry : angle 0.80433 / 0.44 (19879) hydrogen bonds : bond 0.08434 / 5.60 ( 754) hydrogen bonds : angle 3.41450 / 2.49 ( 1892) metal coordination : bond 0.01325 / 0.69 ( 8) metal coordination : angle 7.19572 / 4.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.374 Fit side-chains REVERT: A 77 ASP cc_start: 0.7219 (m-30) cc_final: 0.6972 (m-30) REVERT: D 32 GLU cc_start: 0.6881 (pt0) cc_final: 0.6565 (pt0) REVERT: D 90 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: D 113 LYS cc_start: 0.8323 (tttm) cc_final: 0.8031 (tttp) REVERT: E 50 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7947 (mm-30) REVERT: G 56 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: G 71 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7544 (mtp180) REVERT: G 73 ASN cc_start: 0.7822 (t0) cc_final: 0.7175 (t0) REVERT: G 91 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: K 24 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6465 (tm-30) outliers start: 20 outliers final: 7 residues processed: 141 average time/residue: 0.9206 time to fit residues: 137.4688 Evaluate side-chains 144 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN L 64 GLN A 125 GLN C 110 ASN D 44 GLN D 46 HIS E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.177283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130385 restraints weight = 14551.026| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 0.99 r_work: 0.3121 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13900 Z= 0.146 Angle : 0.673 14.107 19891 Z= 0.375 Chirality : 0.049 0.267 2276 Planarity : 0.004 0.040 1607 Dihedral : 30.176 176.229 3934 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.92 % Allowed : 15.61 % Favored : 82.47 % 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: 0.93 (0.28), residues: 952 helix: 2.09 (0.22), residues: 564 sheet: -1.18 (0.94), residues: 34 loop : -1.75 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 53 TYR 0.009 0.002 TYR F 51 PHE 0.009 0.001 PHE L 39 TRP 0.007 0.002 TRP N 25 HIS 0.003 0.001 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (13892) covalent geometry : angle 0.65927 / 0.37 (19879) hydrogen bonds : bond 0.06095 / 4.05 ( 754) hydrogen bonds : angle 3.12495 / 2.27 ( 1892) metal coordination : bond 0.00799 / 0.44 ( 8) metal coordination : angle 5.55515 / 3.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.387 Fit side-chains REVERT: A 59 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: A 77 ASP cc_start: 0.7290 (m-30) cc_final: 0.7067 (m-30) REVERT: D 32 GLU cc_start: 0.6617 (pt0) cc_final: 0.6338 (pt0) REVERT: D 90 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: D 113 LYS cc_start: 0.8219 (tttm) cc_final: 0.7923 (tttp) REVERT: E 50 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7925 (mm-30) REVERT: F 74 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: G 56 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: G 73 ASN cc_start: 0.7891 (t0) cc_final: 0.7176 (t0) REVERT: G 91 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: K 24 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6228 (tm-30) outliers start: 16 outliers final: 7 residues processed: 135 average time/residue: 0.9338 time to fit residues: 133.3572 Evaluate side-chains 138 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 87 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.184353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143360 restraints weight = 14161.300| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 0.96 r_work: 0.3323 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13900 Z= 0.125 Angle : 0.587 9.349 19891 Z= 0.343 Chirality : 0.044 0.256 2276 Planarity : 0.004 0.039 1607 Dihedral : 29.961 176.339 3934 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.32 % Allowed : 16.93 % Favored : 81.75 % 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: 1.48 (0.28), residues: 952 helix: 2.51 (0.22), residues: 566 sheet: -0.95 (0.97), residues: 32 loop : -1.49 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 53 TYR 0.012 0.001 TYR F 88 PHE 0.008 0.001 PHE L 39 TRP 0.004 0.001 TRP N 25 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.12 (13892) covalent geometry : angle 0.58409 / 0.34 (19879) hydrogen bonds : bond 0.04910 / 3.29 ( 754) hydrogen bonds : angle 2.89368 / 2.09 ( 1892) metal coordination : bond 0.00927 / 0.49 ( 8) metal coordination : angle 2.44628 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.369 Fit side-chains REVERT: A 77 ASP cc_start: 0.7119 (m-30) cc_final: 0.6917 (m-30) REVERT: D 32 GLU cc_start: 0.6593 (pt0) cc_final: 0.6390 (pt0) REVERT: D 44 GLN cc_start: 0.7540 (mt0) cc_final: 0.7336 (mt0) REVERT: D 113 LYS cc_start: 0.8180 (tttm) cc_final: 0.7935 (tttp) REVERT: G 73 ASN cc_start: 0.7609 (t0) cc_final: 0.7127 (t0) REVERT: G 91 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7237 (tt0) outliers start: 11 outliers final: 3 residues processed: 136 average time/residue: 0.8470 time to fit residues: 122.3479 Evaluate side-chains 132 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 107 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN H 106 HIS K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.177120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135443 restraints weight = 13887.895| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.00 r_work: 0.3165 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13900 Z= 0.258 Angle : 0.780 8.563 19891 Z= 0.429 Chirality : 0.056 0.299 2276 Planarity : 0.006 0.048 1607 Dihedral : 30.211 178.091 3934 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.40 % Allowed : 17.41 % Favored : 80.19 % 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: 0.52 (0.27), residues: 952 helix: 1.73 (0.21), residues: 568 sheet: -2.15 (0.81), residues: 43 loop : -1.77 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 40 TYR 0.015 0.003 TYR H 118 PHE 0.017 0.003 PHE E 84 TRP 0.014 0.003 TRP N 25 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 (13892) covalent geometry : angle 0.77751 / 0.43 (19879) hydrogen bonds : bond 0.08074 / 5.35 ( 754) hydrogen bonds : angle 3.27242 / 2.37 ( 1892) metal coordination : bond 0.01042 / 0.55 ( 8) metal coordination : angle 2.76120 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.360 Fit side-chains REVERT: A 77 ASP cc_start: 0.7237 (m-30) cc_final: 0.7035 (m-30) REVERT: D 32 GLU cc_start: 0.6728 (pt0) cc_final: 0.6432 (pt0) REVERT: D 90 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: D 113 LYS cc_start: 0.8268 (tttm) cc_final: 0.8002 (tttp) REVERT: G 73 ASN cc_start: 0.7829 (t0) cc_final: 0.7127 (t160) REVERT: G 91 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: K 24 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6253 (tm-30) outliers start: 20 outliers final: 11 residues processed: 140 average time/residue: 0.8143 time to fit residues: 121.2281 Evaluate side-chains 144 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.180242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139058 restraints weight = 13923.853| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.00 r_work: 0.3218 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13900 Z= 0.138 Angle : 0.660 12.567 19891 Z= 0.373 Chirality : 0.049 0.247 2276 Planarity : 0.004 0.041 1607 Dihedral : 30.169 176.154 3934 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.32 % Allowed : 19.09 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.28), residues: 952 helix: 2.18 (0.22), residues: 567 sheet: -2.12 (0.83), residues: 43 loop : -1.63 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.012 0.002 TYR K 59 PHE 0.007 0.001 PHE L 39 TRP 0.009 0.002 TRP N 25 HIS 0.003 0.001 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (13892) covalent geometry : angle 0.65823 / 0.37 (19879) hydrogen bonds : bond 0.05983 / 3.96 ( 754) hydrogen bonds : angle 3.08610 / 2.24 ( 1892) metal coordination : bond 0.00474 / 0.28 ( 8) metal coordination : angle 2.17941 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.253 Fit side-chains REVERT: A 59 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: D 32 GLU cc_start: 0.6626 (pt0) cc_final: 0.6358 (pt0) REVERT: D 113 LYS cc_start: 0.8215 (tttm) cc_final: 0.7955 (tttp) REVERT: G 73 ASN cc_start: 0.7906 (t0) cc_final: 0.7208 (t0) REVERT: G 91 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: K 24 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6168 (tm-30) outliers start: 11 outliers final: 7 residues processed: 134 average time/residue: 0.7957 time to fit residues: 113.1722 Evaluate side-chains 137 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 68 GLN A 125 GLN C 110 ASN E 76 GLN E 125 GLN H 106 HIS K 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138267 restraints weight = 14061.009| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.08 r_work: 0.3205 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13900 Z= 0.167 Angle : 0.671 12.446 19891 Z= 0.378 Chirality : 0.049 0.266 2276 Planarity : 0.005 0.041 1607 Dihedral : 30.143 176.898 3934 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.56 % Allowed : 18.85 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.27), residues: 952 helix: 2.12 (0.21), residues: 567 sheet: -1.18 (0.96), residues: 34 loop : -1.73 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.011 0.002 TYR F 51 PHE 0.013 0.002 PHE E 84 TRP 0.010 0.002 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (13892) covalent geometry : angle 0.66922 / 0.38 (19879) hydrogen bonds : bond 0.06417 / 4.25 ( 754) hydrogen bonds : angle 3.08924 / 2.24 ( 1892) metal coordination : bond 0.00722 / 0.40 ( 8) metal coordination : angle 2.34584 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.356 Fit side-chains REVERT: D 32 GLU cc_start: 0.6696 (pt0) cc_final: 0.6407 (pt0) REVERT: D 90 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: D 113 LYS cc_start: 0.8244 (tttm) cc_final: 0.7990 (tttp) REVERT: G 73 ASN cc_start: 0.7804 (t0) cc_final: 0.7041 (t160) REVERT: G 91 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: K 24 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6152 (tm-30) outliers start: 13 outliers final: 9 residues processed: 132 average time/residue: 0.7658 time to fit residues: 107.3043 Evaluate side-chains 138 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 68 GLN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137590 restraints weight = 14021.236| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.09 r_work: 0.3192 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13900 Z= 0.179 Angle : 0.692 13.077 19891 Z= 0.387 Chirality : 0.050 0.280 2276 Planarity : 0.005 0.042 1607 Dihedral : 30.172 176.647 3934 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.80 % Allowed : 18.73 % Favored : 79.47 % 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: 0.83 (0.27), residues: 952 helix: 1.98 (0.21), residues: 569 sheet: -1.26 (0.96), residues: 34 loop : -1.77 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 36 TYR 0.014 0.002 TYR H 34 PHE 0.014 0.002 PHE E 84 TRP 0.012 0.002 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (13892) covalent geometry : angle 0.68980 / 0.39 (19879) hydrogen bonds : bond 0.06687 / 4.43 ( 754) hydrogen bonds : angle 3.11789 / 2.26 ( 1892) metal coordination : bond 0.00782 / 0.44 ( 8) metal coordination : angle 2.57424 / 1.49 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.333 Fit side-chains REVERT: D 32 GLU cc_start: 0.6758 (pt0) cc_final: 0.6439 (pt0) REVERT: D 90 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: D 113 LYS cc_start: 0.8258 (tttm) cc_final: 0.8005 (tttp) REVERT: E 56 LYS cc_start: 0.8696 (tppp) cc_final: 0.8352 (tttt) REVERT: G 73 ASN cc_start: 0.7807 (t0) cc_final: 0.7191 (t160) REVERT: G 91 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: K 24 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6142 (tm-30) outliers start: 15 outliers final: 7 residues processed: 139 average time/residue: 0.7778 time to fit residues: 114.7368 Evaluate side-chains 143 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 84 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 68 GLN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136728 restraints weight = 13916.936| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.01 r_work: 0.3189 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13900 Z= 0.189 Angle : 0.707 12.827 19891 Z= 0.394 Chirality : 0.051 0.281 2276 Planarity : 0.005 0.043 1607 Dihedral : 30.196 176.851 3934 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.56 % Allowed : 19.09 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.27), residues: 952 helix: 1.91 (0.21), residues: 569 sheet: -1.31 (0.96), residues: 34 loop : -1.78 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 40 TYR 0.018 0.002 TYR F 88 PHE 0.016 0.002 PHE E 84 TRP 0.012 0.002 TRP N 25 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (13892) covalent geometry : angle 0.70347 / 0.39 (19879) hydrogen bonds : bond 0.06882 / 4.56 ( 754) hydrogen bonds : angle 3.14603 / 2.28 ( 1892) metal coordination : bond 0.00917 / 0.50 ( 8) metal coordination : angle 2.90202 / 1.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4483.90 seconds wall clock time: 76 minutes 43.55 seconds (4603.55 seconds total)