Starting phenix.real_space_refine on Sat Jul 4 04:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubi_42089/07_2026/8ubi_42089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubi_42089/07_2026/8ubi_42089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubi_42089/07_2026/8ubi_42089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubi_42089/07_2026/8ubi_42089.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubi_42089/07_2026/8ubi_42089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubi_42089/07_2026/8ubi_42089.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.119 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 2242 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 324 5.49 5 S 32 5.16 5 C 9232 2.51 5 N 2970 2.21 5 O 3730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16288 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3311 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3331 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 3.40, per 1000 atoms: 0.21 Number of scatterers: 16288 At special positions: 0 Unit cell: (137.214, 138.484, 144.837, 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 32 16.00 P 324 15.00 O 3730 8.00 N 2970 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.04 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 634.8 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 22 sheets defined 48.0% alpha, 21.4% beta 162 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.932A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 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: 3.810A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.577A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.321A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) 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 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.631A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.890A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.524A 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 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.326A 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 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.728A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.388A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.609A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 removed outlier: 3.515A pdb=" N SER M 240 " --> pdb=" O SER M 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.708A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 236 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.925A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.201A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.566A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.913A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.293A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.201A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.201A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR M 116 " --> pdb=" O GLN M 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.520A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.520A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.712A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.349A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N 32 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.349A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N 32 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.584A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 4.006A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 412 hydrogen bonds 824 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 1.47 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: 3784 1.34 - 1.46: 4894 1.46 - 1.57: 7884 1.57 - 1.69: 646 1.69 - 1.81: 52 Bond restraints: 17260 Sorted by residual: bond pdb=" C1' DC I 39 " pdb=" N1 DC I 39 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" C1' DC J 4 " pdb=" N1 DC J 4 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" C1' DC I 91 " pdb=" N1 DC I 91 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.97e+01 bond pdb=" C1' DC I 131 " pdb=" N1 DC I 131 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.84e+01 bond pdb=" C1' DT I 59 " pdb=" N1 DT I 59 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.63e+01 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 22505 1.45 - 2.90: 1827 2.90 - 4.35: 326 4.35 - 5.80: 43 5.80 - 7.25: 11 Bond angle restraints: 24712 Sorted by residual: angle pdb=" O4' DT J 143 " pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" O4' DC J 5 " pdb=" C1' DC J 5 " pdb=" N1 DC J 5 " ideal model delta sigma weight residual 108.00 111.06 -3.06 7.00e-01 2.04e+00 1.91e+01 angle pdb=" O5' DC J 4 " pdb=" C5' DC J 4 " pdb=" C4' DC J 4 " ideal model delta sigma weight residual 109.40 112.86 -3.46 8.00e-01 1.56e+00 1.87e+01 angle pdb=" N3 DT J 87 " pdb=" C4 DT J 87 " pdb=" O4 DT J 87 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 24707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 8147 34.86 - 69.73: 1361 69.73 - 104.59: 36 104.59 - 139.46: 0 139.46 - 174.32: 2 Dihedral angle restraints: 9546 sinusoidal: 6000 harmonic: 3546 Sorted by residual: dihedral pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " pdb=" P DG J 144 " ideal model delta sinusoidal sigma weight residual 220.00 45.68 174.32 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 109 " pdb=" C3' DT J 109 " pdb=" O3' DT J 109 " pdb=" P DG J 110 " ideal model delta sinusoidal sigma weight residual 220.00 70.17 149.83 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA ASP D 51 " pdb=" CB ASP D 51 " pdb=" CG ASP D 51 " pdb=" OD1 ASP D 51 " ideal model delta sinusoidal sigma weight residual -30.00 -87.31 57.31 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1570 0.033 - 0.066: 726 0.066 - 0.099: 139 0.099 - 0.132: 218 0.132 - 0.165: 131 Chirality restraints: 2784 Sorted by residual: chirality pdb=" C3' DC I 113 " pdb=" C4' DC I 113 " pdb=" O3' DC I 113 " pdb=" C2' DC I 113 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" C3' DC I 62 " pdb=" C4' DC I 62 " pdb=" O3' DC I 62 " pdb=" C2' DC I 62 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C3' DA I 82 " pdb=" C4' DA I 82 " pdb=" O3' DA I 82 " pdb=" C2' DA I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 2781 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 73 " 0.027 2.00e-02 2.50e+03 1.37e-02 5.16e+00 pdb=" N9 DA J 73 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 73 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 73 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 73 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA J 73 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 73 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DA J 73 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 73 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 23 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ARG F 23 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP F 24 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 91 " -0.025 2.00e-02 2.50e+03 1.37e-02 4.24e+00 pdb=" N1 DC I 91 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DC I 91 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC I 91 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC I 91 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 91 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 91 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC I 91 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 91 " -0.000 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2183 2.77 - 3.30: 13586 3.30 - 3.83: 30358 3.83 - 4.37: 36507 4.37 - 4.90: 54357 Nonbonded interactions: 136991 Sorted by model distance: nonbonded pdb=" OD2 ASP M 222 " pdb=" OG SER M 225 " model vdw 2.234 3.040 nonbonded pdb=" N GLU M 124 " pdb=" OE1 GLU M 124 " model vdw 2.249 3.120 nonbonded pdb=" N GLU N 124 " pdb=" OE1 GLU N 124 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLU G 91 " pdb=" OG SER N 180 " model vdw 2.262 3.040 nonbonded pdb=" O GLU M 162 " pdb=" OG1 THR M 165 " model vdw 2.407 3.040 ... (remaining 136986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.007 0.080 17264 Z= 0.586 Angle : 0.844 7.251 24720 Z= 0.691 Chirality : 0.056 0.165 2784 Planarity : 0.005 0.067 1996 Dihedral : 25.375 174.322 7262 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.48 % Allowed : 11.46 % Favored : 88.05 % 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: 2.20 (0.24), residues: 1198 helix: 2.72 (0.22), residues: 532 sheet: 1.46 (0.34), residues: 226 loop : -0.13 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 86 TYR 0.021 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP M 196 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.59 (17260) covalent geometry : angle 0.84448 / 0.69 (24712) SS BOND : bond 0.00292 / 0.15 ( 4) SS BOND : angle 0.76345 / 0.34 ( 8) hydrogen bonds : bond 0.13506 / 8.96 ( 958) hydrogen bonds : angle 4.71220 / 3.45 ( 2387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.386 Fit side-chains REVERT: A 73 GLU cc_start: 0.6218 (tt0) cc_final: 0.6016 (tt0) REVERT: A 112 ILE cc_start: 0.6529 (mt) cc_final: 0.6325 (mp) REVERT: B 79 LYS cc_start: 0.7240 (mtmm) cc_final: 0.7016 (mttp) REVERT: B 91 LYS cc_start: 0.7413 (ttpm) cc_final: 0.7185 (ttpp) REVERT: B 93 GLN cc_start: 0.7455 (mt0) cc_final: 0.7242 (mt0) REVERT: C 24 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7237 (mm-40) REVERT: C 73 ASN cc_start: 0.6831 (m-40) cc_final: 0.6097 (t160) REVERT: M 30 MET cc_start: 0.7482 (ptp) cc_final: 0.7235 (ptm) REVERT: N 228 VAL cc_start: 0.9216 (t) cc_final: 0.8943 (t) outliers start: 5 outliers final: 0 residues processed: 202 average time/residue: 0.8412 time to fit residues: 183.0778 Evaluate side-chains 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 89 ASN D 84 ASN D 95 GLN F 75 HIS F 93 GLN G 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103762 restraints weight = 19176.910| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.71 r_work: 0.3102 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17264 Z= 0.257 Angle : 0.690 6.950 24720 Z= 0.404 Chirality : 0.050 0.228 2784 Planarity : 0.005 0.043 1996 Dihedral : 28.732 175.619 4906 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.37 % Allowed : 13.01 % Favored : 83.62 % 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: 1.96 (0.24), residues: 1198 helix: 2.32 (0.22), residues: 546 sheet: 1.39 (0.34), residues: 240 loop : -0.14 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.021 0.002 TYR H 42 PHE 0.016 0.002 PHE C 25 TRP 0.011 0.002 TRP M 185 HIS 0.006 0.002 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.26 (17260) covalent geometry : angle 0.68909 / 0.40 (24712) SS BOND : bond 0.00818 / 0.42 ( 4) SS BOND : angle 1.62671 / 0.74 ( 8) hydrogen bonds : bond 0.06176 / 4.08 ( 958) hydrogen bonds : angle 3.69176 / 2.73 ( 2387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.464 Fit side-chains REVERT: B 59 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8195 (tttp) REVERT: C 73 ASN cc_start: 0.7633 (m-40) cc_final: 0.6816 (t160) REVERT: D 47 GLN cc_start: 0.8460 (tt0) cc_final: 0.8086 (mt0) REVERT: G 99 ARG cc_start: 0.8263 (mpp-170) cc_final: 0.7848 (mtm110) REVERT: M 52 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8572 (tp) REVERT: M 102 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8306 (t) REVERT: M 124 GLU cc_start: 0.8242 (pm20) cc_final: 0.8019 (pm20) REVERT: M 230 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.6820 (tpt) REVERT: N 230 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.5607 (tmm) REVERT: N 231 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.5907 (mm-30) outliers start: 35 outliers final: 16 residues processed: 190 average time/residue: 0.8138 time to fit residues: 166.5967 Evaluate side-chains 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106368 restraints weight = 19355.183| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.70 r_work: 0.3137 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17264 Z= 0.146 Angle : 0.592 6.079 24720 Z= 0.351 Chirality : 0.043 0.236 2784 Planarity : 0.004 0.041 1996 Dihedral : 29.200 174.992 4906 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.79 % Allowed : 15.80 % Favored : 81.41 % 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: 2.21 (0.24), residues: 1198 helix: 2.60 (0.22), residues: 548 sheet: 1.46 (0.34), residues: 240 loop : -0.11 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.016 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.010 0.001 TRP M 60 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (17260) covalent geometry : angle 0.59160 / 0.35 (24712) SS BOND : bond 0.00542 / 0.28 ( 4) SS BOND : angle 0.92199 / 0.43 ( 8) hydrogen bonds : bond 0.04796 / 3.17 ( 958) hydrogen bonds : angle 3.39618 / 2.50 ( 2387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8197 (tttp) REVERT: B 93 GLN cc_start: 0.8321 (mt0) cc_final: 0.8116 (mt0) REVERT: C 73 ASN cc_start: 0.7454 (m-40) cc_final: 0.6762 (t160) REVERT: D 47 GLN cc_start: 0.8429 (tt0) cc_final: 0.8025 (mt0) REVERT: D 71 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: E 120 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.6605 (mpp) REVERT: E 123 ASP cc_start: 0.8558 (m-30) cc_final: 0.8310 (m-30) REVERT: F 84 MET cc_start: 0.7867 (mmt) cc_final: 0.7438 (mmt) REVERT: G 90 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.7979 (t70) REVERT: G 99 ARG cc_start: 0.8277 (mpp-170) cc_final: 0.7789 (mtm110) REVERT: M 102 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8167 (t) REVERT: M 124 GLU cc_start: 0.8416 (pm20) cc_final: 0.7980 (pm20) REVERT: M 230 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.6874 (tpt) REVERT: N 208 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8326 (ttmt) REVERT: N 231 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6429 (mm-30) outliers start: 29 outliers final: 12 residues processed: 184 average time/residue: 0.8248 time to fit residues: 163.8171 Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 54 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 126 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107097 restraints weight = 19221.428| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.69 r_work: 0.3154 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17264 Z= 0.137 Angle : 0.560 5.982 24720 Z= 0.333 Chirality : 0.042 0.223 2784 Planarity : 0.004 0.049 1996 Dihedral : 29.431 173.799 4906 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.60 % Allowed : 17.05 % Favored : 80.35 % 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: 2.37 (0.24), residues: 1198 helix: 2.79 (0.22), residues: 550 sheet: 1.48 (0.34), residues: 240 loop : -0.09 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.015 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.011 0.001 TRP M 60 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (17260) covalent geometry : angle 0.55963 / 0.33 (24712) SS BOND : bond 0.00522 / 0.27 ( 4) SS BOND : angle 0.88402 / 0.41 ( 8) hydrogen bonds : bond 0.04328 / 2.86 ( 958) hydrogen bonds : angle 3.19374 / 2.34 ( 2387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.464 Fit side-chains REVERT: A 133 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: C 73 ASN cc_start: 0.7391 (m-40) cc_final: 0.6748 (t160) REVERT: D 47 GLN cc_start: 0.8428 (tt0) cc_final: 0.8068 (mt0) REVERT: E 120 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7613 (mmt) REVERT: E 123 ASP cc_start: 0.8575 (m-30) cc_final: 0.8123 (m-30) REVERT: F 84 MET cc_start: 0.7887 (mmt) cc_final: 0.7445 (mmt) REVERT: G 15 LYS cc_start: 0.7036 (pttm) cc_final: 0.6577 (pmtt) REVERT: G 90 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.7932 (t70) REVERT: G 99 ARG cc_start: 0.8245 (mpp-170) cc_final: 0.7764 (mtm110) REVERT: M 102 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8067 (t) REVERT: M 124 GLU cc_start: 0.8376 (pm20) cc_final: 0.7891 (pm20) REVERT: M 230 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.6868 (tpt) REVERT: N 228 VAL cc_start: 0.8717 (t) cc_final: 0.8471 (t) REVERT: N 231 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6427 (mm-30) outliers start: 27 outliers final: 10 residues processed: 177 average time/residue: 0.8166 time to fit residues: 156.2003 Evaluate side-chains 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 73 ASN H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101913 restraints weight = 19214.618| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.70 r_work: 0.3077 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17264 Z= 0.250 Angle : 0.648 6.207 24720 Z= 0.369 Chirality : 0.047 0.250 2784 Planarity : 0.005 0.049 1996 Dihedral : 29.673 171.721 4906 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.34 % Allowed : 16.18 % Favored : 79.48 % 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: 1.88 (0.24), residues: 1198 helix: 2.36 (0.22), residues: 546 sheet: 1.25 (0.34), residues: 240 loop : -0.28 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.021 0.002 TYR H 42 PHE 0.015 0.002 PHE C 25 TRP 0.011 0.002 TRP M 60 HIS 0.008 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (17260) covalent geometry : angle 0.64745 / 0.37 (24712) SS BOND : bond 0.00809 / 0.41 ( 4) SS BOND : angle 1.74025 / 0.82 ( 8) hydrogen bonds : bond 0.05844 / 3.88 ( 958) hydrogen bonds : angle 3.37616 / 2.48 ( 2387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.434 Fit side-chains REVERT: A 79 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8132 (tttp) REVERT: A 133 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: C 73 ASN cc_start: 0.7618 (m-40) cc_final: 0.6762 (t0) REVERT: D 47 GLN cc_start: 0.8447 (tt0) cc_final: 0.8097 (mt0) REVERT: F 84 MET cc_start: 0.7870 (mmt) cc_final: 0.7515 (mmt) REVERT: G 15 LYS cc_start: 0.7324 (pttm) cc_final: 0.6819 (pmtt) REVERT: G 90 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.7979 (t70) REVERT: G 99 ARG cc_start: 0.8206 (mpp-170) cc_final: 0.7864 (mtm110) REVERT: M 98 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: M 102 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7968 (t) REVERT: M 124 GLU cc_start: 0.8362 (pm20) cc_final: 0.7839 (pm20) REVERT: M 230 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.6661 (tpt) REVERT: N 208 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8327 (ttmt) REVERT: N 228 VAL cc_start: 0.8731 (t) cc_final: 0.8500 (t) REVERT: N 231 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6418 (mm-30) outliers start: 45 outliers final: 24 residues processed: 196 average time/residue: 0.8142 time to fit residues: 171.6814 Evaluate side-chains 192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 0.0970 chunk 103 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 10.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104672 restraints weight = 19074.792| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.71 r_work: 0.3114 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17264 Z= 0.131 Angle : 0.600 9.232 24720 Z= 0.347 Chirality : 0.045 0.233 2784 Planarity : 0.004 0.071 1996 Dihedral : 29.667 171.925 4906 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.70 % Allowed : 17.82 % Favored : 79.48 % 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: 2.17 (0.24), residues: 1198 helix: 2.68 (0.22), residues: 546 sheet: 1.29 (0.34), residues: 240 loop : -0.18 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 191 TYR 0.014 0.001 TYR H 42 PHE 0.006 0.001 PHE F 61 TRP 0.011 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (17260) covalent geometry : angle 0.59960 / 0.35 (24712) SS BOND : bond 0.00530 / 0.27 ( 4) SS BOND : angle 0.98813 / 0.46 ( 8) hydrogen bonds : bond 0.04494 / 2.95 ( 958) hydrogen bonds : angle 3.24301 / 2.38 ( 2387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.441 Fit side-chains REVERT: A 79 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8131 (tttp) REVERT: C 73 ASN cc_start: 0.7455 (m-40) cc_final: 0.6657 (t0) REVERT: D 47 GLN cc_start: 0.8394 (tt0) cc_final: 0.8039 (mt0) REVERT: F 84 MET cc_start: 0.7807 (mmt) cc_final: 0.7435 (mmt) REVERT: G 90 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.7916 (t70) REVERT: G 99 ARG cc_start: 0.8238 (mpp-170) cc_final: 0.7819 (mtm110) REVERT: M 98 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: M 102 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7944 (t) REVERT: M 124 GLU cc_start: 0.8234 (pm20) cc_final: 0.7679 (pm20) REVERT: M 191 ARG cc_start: 0.8688 (ttp-110) cc_final: 0.8322 (ttp80) REVERT: N 208 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8306 (ttmt) REVERT: N 231 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6502 (mm-30) outliers start: 28 outliers final: 15 residues processed: 189 average time/residue: 0.8013 time to fit residues: 163.1596 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103756 restraints weight = 19151.161| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.70 r_work: 0.3107 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17264 Z= 0.167 Angle : 0.594 7.056 24720 Z= 0.344 Chirality : 0.044 0.235 2784 Planarity : 0.004 0.048 1996 Dihedral : 29.713 171.373 4906 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.70 % Allowed : 18.59 % Favored : 78.71 % 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: 2.08 (0.24), residues: 1198 helix: 2.61 (0.22), residues: 548 sheet: 1.25 (0.34), residues: 240 loop : -0.27 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.018 0.002 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.012 0.002 TRP M 60 HIS 0.005 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (17260) covalent geometry : angle 0.59366 / 0.34 (24712) SS BOND : bond 0.00608 / 0.31 ( 4) SS BOND : angle 1.16136 / 0.55 ( 8) hydrogen bonds : bond 0.04745 / 3.13 ( 958) hydrogen bonds : angle 3.21451 / 2.36 ( 2387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.349 Fit side-chains REVERT: A 79 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8128 (tttp) REVERT: A 133 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: C 73 ASN cc_start: 0.7509 (m-40) cc_final: 0.6794 (t160) REVERT: D 47 GLN cc_start: 0.8435 (tt0) cc_final: 0.8068 (mt0) REVERT: F 84 MET cc_start: 0.7847 (mmt) cc_final: 0.7468 (mmt) REVERT: G 90 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.7934 (t70) REVERT: G 99 ARG cc_start: 0.8159 (mpp-170) cc_final: 0.7856 (mtm110) REVERT: M 98 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: M 102 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7950 (t) REVERT: M 124 GLU cc_start: 0.8225 (pm20) cc_final: 0.7717 (pm20) REVERT: N 112 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7427 (mm-30) REVERT: N 208 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: N 231 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6447 (mm-30) outliers start: 28 outliers final: 17 residues processed: 182 average time/residue: 0.7912 time to fit residues: 155.0354 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 50.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104245 restraints weight = 19112.181| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.69 r_work: 0.3114 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17264 Z= 0.146 Angle : 0.588 7.756 24720 Z= 0.342 Chirality : 0.043 0.234 2784 Planarity : 0.004 0.071 1996 Dihedral : 29.713 171.426 4906 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.99 % Allowed : 18.40 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.24), residues: 1198 helix: 2.67 (0.22), residues: 548 sheet: 1.26 (0.34), residues: 240 loop : -0.25 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 191 TYR 0.016 0.001 TYR H 42 PHE 0.008 0.001 PHE C 25 TRP 0.011 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (17260) covalent geometry : angle 0.58810 / 0.34 (24712) SS BOND : bond 0.00569 / 0.29 ( 4) SS BOND : angle 1.06634 / 0.51 ( 8) hydrogen bonds : bond 0.04531 / 2.98 ( 958) hydrogen bonds : angle 3.18838 / 2.34 ( 2387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.502 Fit side-chains REVERT: A 79 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8131 (tttp) REVERT: A 133 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: C 73 ASN cc_start: 0.7492 (m-40) cc_final: 0.6786 (t160) REVERT: D 47 GLN cc_start: 0.8261 (tt0) cc_final: 0.7918 (mt0) REVERT: E 133 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: F 84 MET cc_start: 0.7781 (mmt) cc_final: 0.7433 (mmt) REVERT: G 90 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.7929 (t70) REVERT: G 99 ARG cc_start: 0.8158 (mpp-170) cc_final: 0.7858 (mtm110) REVERT: M 98 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: M 102 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7944 (t) REVERT: M 124 GLU cc_start: 0.8226 (pm20) cc_final: 0.7713 (pm20) REVERT: N 112 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7364 (mm-30) REVERT: N 208 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8283 (ttmt) REVERT: N 231 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6447 (mm-30) outliers start: 31 outliers final: 19 residues processed: 184 average time/residue: 0.8253 time to fit residues: 163.8328 Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 92 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105780 restraints weight = 19154.627| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.68 r_work: 0.3133 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17264 Z= 0.126 Angle : 0.579 8.147 24720 Z= 0.338 Chirality : 0.043 0.229 2784 Planarity : 0.004 0.065 1996 Dihedral : 29.691 171.793 4906 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.50 % Allowed : 18.98 % Favored : 78.52 % 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: 2.26 (0.24), residues: 1198 helix: 2.80 (0.22), residues: 548 sheet: 1.30 (0.34), residues: 240 loop : -0.19 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 191 TYR 0.018 0.001 TYR M 209 PHE 0.006 0.001 PHE F 61 TRP 0.011 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (17260) covalent geometry : angle 0.57866 / 0.34 (24712) SS BOND : bond 0.00495 / 0.25 ( 4) SS BOND : angle 0.88067 / 0.43 ( 8) hydrogen bonds : bond 0.04209 / 2.76 ( 958) hydrogen bonds : angle 3.13642 / 2.30 ( 2387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.452 Fit side-chains REVERT: A 79 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8133 (tttp) REVERT: C 73 ASN cc_start: 0.7406 (m-40) cc_final: 0.6739 (t160) REVERT: D 47 GLN cc_start: 0.8245 (tt0) cc_final: 0.7888 (mt0) REVERT: E 115 LYS cc_start: 0.8345 (mtmp) cc_final: 0.8074 (mttp) REVERT: E 133 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: F 84 MET cc_start: 0.7789 (mmt) cc_final: 0.7435 (mmt) REVERT: G 90 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7887 (t70) REVERT: G 99 ARG cc_start: 0.8162 (mpp-170) cc_final: 0.7843 (mtm110) REVERT: M 98 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: M 102 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7914 (t) REVERT: M 124 GLU cc_start: 0.8224 (pm20) cc_final: 0.7708 (pm20) REVERT: N 112 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7347 (mm-30) REVERT: N 208 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8272 (ttmt) REVERT: N 231 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6500 (mm-30) outliers start: 26 outliers final: 14 residues processed: 185 average time/residue: 0.8191 time to fit residues: 163.5135 Evaluate side-chains 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 9.9990 chunk 107 optimal weight: 0.0010 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 0.0000 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN G 73 ASN H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106211 restraints weight = 19122.800| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.68 r_work: 0.3139 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17264 Z= 0.122 Angle : 0.583 9.523 24720 Z= 0.339 Chirality : 0.043 0.227 2784 Planarity : 0.004 0.087 1996 Dihedral : 29.683 171.954 4906 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.83 % Allowed : 19.94 % Favored : 78.23 % 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: 2.33 (0.25), residues: 1198 helix: 2.86 (0.22), residues: 548 sheet: 1.32 (0.34), residues: 240 loop : -0.16 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.015 0.001 TYR H 42 PHE 0.007 0.001 PHE E 67 TRP 0.013 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.12 (17260) covalent geometry : angle 0.58289 / 0.34 (24712) SS BOND : bond 0.00452 / 0.23 ( 4) SS BOND : angle 0.81977 / 0.40 ( 8) hydrogen bonds : bond 0.04106 / 2.70 ( 958) hydrogen bonds : angle 3.11469 / 2.28 ( 2387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.456 Fit side-chains REVERT: A 79 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8008 (tttp) REVERT: C 73 ASN cc_start: 0.7380 (m-40) cc_final: 0.6724 (t160) REVERT: D 47 GLN cc_start: 0.8240 (tt0) cc_final: 0.7882 (mt0) REVERT: E 115 LYS cc_start: 0.8330 (mtmp) cc_final: 0.8065 (mttp) REVERT: E 123 ASP cc_start: 0.8500 (m-30) cc_final: 0.8180 (m-30) REVERT: E 133 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: F 84 MET cc_start: 0.7774 (mmt) cc_final: 0.7429 (mmt) REVERT: G 90 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7879 (t70) REVERT: G 99 ARG cc_start: 0.8167 (mpp-170) cc_final: 0.7848 (mtm110) REVERT: M 98 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: M 102 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7908 (t) REVERT: M 124 GLU cc_start: 0.8258 (pm20) cc_final: 0.7754 (pm20) REVERT: M 191 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8229 (ttp80) REVERT: N 112 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7331 (mm-30) REVERT: N 208 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8266 (ttmt) REVERT: N 231 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6506 (mm-30) outliers start: 19 outliers final: 11 residues processed: 179 average time/residue: 0.8091 time to fit residues: 156.2838 Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106204 restraints weight = 19091.259| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.69 r_work: 0.3142 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17264 Z= 0.133 Angle : 0.564 8.494 24720 Z= 0.331 Chirality : 0.042 0.225 2784 Planarity : 0.004 0.062 1996 Dihedral : 29.649 172.718 4906 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.93 % Allowed : 19.85 % Favored : 78.23 % 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: 2.33 (0.24), residues: 1198 helix: 2.86 (0.22), residues: 548 sheet: 1.32 (0.34), residues: 240 loop : -0.16 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 191 TYR 0.016 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.021 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (17260) covalent geometry : angle 0.56380 / 0.33 (24712) SS BOND : bond 0.00473 / 0.24 ( 4) SS BOND : angle 0.90791 / 0.43 ( 8) hydrogen bonds : bond 0.04101 / 2.70 ( 958) hydrogen bonds : angle 3.05170 / 2.23 ( 2387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6587.58 seconds wall clock time: 112 minutes 33.97 seconds (6753.97 seconds total)