Starting phenix.real_space_refine on Fri Aug 7 00:34:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubi_42089/08_2026/8ubi_42089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubi_42089/08_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_42089/08_2026/8ubi_42089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubi_42089/08_2026/8ubi_42089.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubi_42089/08_2026/8ubi_42089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubi_42089/08_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-2.2rc3-6140/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: 3.64, per 1000 atoms: 0.22 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: 1.27 Conformation dependent library (CDL) restraints added in 549.1 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: 2.08 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: 3.72 Time building geometry restraints manager: 1.81 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: 22477 1.45 - 2.90: 1855 2.90 - 4.35: 325 4.35 - 5.80: 44 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- 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 : 0.850 7.251 24720 Z= 0.697 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 0.85001 / 0.70 (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 : 0.455 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: 0.6324 (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: 0.7184 (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: 0.7972 time to fit residues: 173.8241 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 : 0.444 ------------------------------------------------------------------------------- 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: 9.9990 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 F 75 HIS F 93 GLN G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103983 restraints weight = 19161.610| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.67 r_work: 0.3103 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17264 Z= 0.254 Angle : 0.711 7.275 24720 Z= 0.408 Chirality : 0.051 0.232 2784 Planarity : 0.005 0.048 1996 Dihedral : 28.779 176.234 4906 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.56 % Allowed : 12.72 % Favored : 83.72 % 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: 1.89 (0.24), residues: 1198 helix: 2.28 (0.22), residues: 544 sheet: 1.37 (0.34), residues: 240 loop : -0.19 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.019 0.002 TYR H 42 PHE 0.016 0.002 PHE C 25 TRP 0.009 0.002 TRP M 185 HIS 0.006 0.002 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (17260) covalent geometry : angle 0.71050 / 0.41 (24712) SS BOND : bond 0.00827 / 0.42 ( 4) SS BOND : angle 1.61100 / 0.73 ( 8) hydrogen bonds : bond 0.06298 / 4.17 ( 958) hydrogen bonds : angle 3.67755 / 2.72 ( 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 213 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.389 Fit side-chains REVERT: B 59 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8202 (tttp) REVERT: C 73 ASN cc_start: 0.7640 (m-40) cc_final: 0.6819 (t160) REVERT: D 47 GLN cc_start: 0.8456 (tt0) cc_final: 0.8079 (mt0) REVERT: F 84 MET cc_start: 0.7784 (mmp) cc_final: 0.7353 (mmt) REVERT: G 51 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7688 (tp) REVERT: G 99 ARG cc_start: 0.8262 (mpp-170) cc_final: 0.7855 (mtm110) REVERT: M 52 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8580 (tp) REVERT: M 102 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8314 (t) REVERT: M 124 GLU cc_start: 0.8267 (pm20) cc_final: 0.8045 (pm20) REVERT: M 230 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.6854 (tpt) REVERT: N 230 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.6015 (tmm) REVERT: N 231 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6620 (mm-30) outliers start: 37 outliers final: 16 residues processed: 192 average time/residue: 0.8144 time to fit residues: 168.3629 Evaluate side-chains 182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 51 LEU 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: 7.9990 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.158798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106029 restraints weight = 19329.895| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.69 r_work: 0.3133 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1536 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= 0.149 Angle : 0.601 6.119 24720 Z= 0.354 Chirality : 0.044 0.254 2784 Planarity : 0.004 0.045 1996 Dihedral : 29.209 175.617 4906 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.60 % Allowed : 16.28 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.24), residues: 1198 helix: 2.58 (0.22), residues: 548 sheet: 1.43 (0.34), residues: 240 loop : -0.11 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 86 TYR 0.015 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 0.00288 / 0.15 (17260) covalent geometry : angle 0.60108 / 0.35 (24712) SS BOND : bond 0.00563 / 0.29 ( 4) SS BOND : angle 0.95740 / 0.45 ( 8) hydrogen bonds : bond 0.04822 / 3.19 ( 958) hydrogen bonds : angle 3.38113 / 2.49 ( 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 190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.439 Fit side-chains REVERT: C 73 ASN cc_start: 0.7537 (m-40) cc_final: 0.6815 (t160) REVERT: D 47 GLN cc_start: 0.8426 (tt0) cc_final: 0.8089 (mt0) REVERT: D 71 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: E 120 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.6635 (mpp) REVERT: E 123 ASP cc_start: 0.8563 (m-30) cc_final: 0.8319 (m-30) REVERT: F 84 MET cc_start: 0.7811 (mmp) cc_final: 0.7362 (mmt) REVERT: G 90 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.7945 (t70) REVERT: G 99 ARG cc_start: 0.8279 (mpp-170) cc_final: 0.7798 (mtm110) REVERT: H 71 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: M 52 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8510 (tp) REVERT: M 102 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8125 (t) REVERT: M 124 GLU cc_start: 0.8424 (pm20) cc_final: 0.7988 (pm20) REVERT: M 230 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.6922 (tpt) REVERT: N 208 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8338 (ttmt) REVERT: N 231 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6468 (mm-30) outliers start: 27 outliers final: 13 residues processed: 177 average time/residue: 0.7420 time to fit residues: 142.1378 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 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 80 THR Chi-restraints excluded: chain E residue 120 MET 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 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 52 LEU 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: 0.3980 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: 0.4980 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103840 restraints weight = 19188.057| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.69 r_work: 0.3107 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1819 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= 0.181 Angle : 0.612 6.328 24720 Z= 0.353 Chirality : 0.045 0.254 2784 Planarity : 0.004 0.054 1996 Dihedral : 29.495 173.482 4906 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.43 % Allowed : 15.61 % Favored : 79.96 % 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: 2.09 (0.24), residues: 1198 helix: 2.53 (0.22), residues: 548 sheet: 1.31 (0.34), residues: 240 loop : -0.16 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.019 0.002 TYR H 42 PHE 0.011 0.002 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 0.00383 / 0.18 (17260) covalent geometry : angle 0.61178 / 0.35 (24712) SS BOND : bond 0.00642 / 0.33 ( 4) SS BOND : angle 1.27517 / 0.59 ( 8) hydrogen bonds : bond 0.05126 / 3.38 ( 958) hydrogen bonds : angle 3.31262 / 2.44 ( 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 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.480 Fit side-chains REVERT: A 79 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8138 (tttp) REVERT: A 133 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: B 59 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8182 (tttp) REVERT: C 73 ASN cc_start: 0.7470 (m-40) cc_final: 0.6769 (t160) REVERT: D 47 GLN cc_start: 0.8440 (tt0) cc_final: 0.8072 (mt0) REVERT: F 84 MET cc_start: 0.7840 (mmp) cc_final: 0.7421 (mmt) REVERT: G 51 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7628 (tp) REVERT: G 90 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.7940 (t70) REVERT: G 99 ARG cc_start: 0.8259 (mpp-170) cc_final: 0.7811 (mtm110) REVERT: H 71 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: M 52 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8479 (tp) REVERT: M 98 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: M 102 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7972 (t) REVERT: M 124 GLU cc_start: 0.8363 (pm20) cc_final: 0.7869 (pm20) REVERT: M 230 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.6906 (tpt) REVERT: N 112 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7419 (mm-30) REVERT: N 208 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8250 (ttmt) REVERT: N 228 VAL cc_start: 0.8718 (t) cc_final: 0.8467 (t) REVERT: N 231 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6420 (mm-30) outliers start: 46 outliers final: 19 residues processed: 187 average time/residue: 0.7861 time to fit residues: 159.1846 Evaluate side-chains 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR 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 G residue 114 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 71 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 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 200 ILE Chi-restraints excluded: chain N residue 208 LYS 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: 4.9990 chunk 89 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN 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 = 0.3824 r_free = 0.3824 target = 0.153962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100752 restraints weight = 19212.196| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.69 r_work: 0.3063 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2153 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= 0.259 Angle : 0.685 6.687 24720 Z= 0.383 Chirality : 0.049 0.271 2784 Planarity : 0.005 0.052 1996 Dihedral : 29.764 171.629 4906 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.72 % Allowed : 16.28 % Favored : 79.00 % 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: 1.55 (0.24), residues: 1198 helix: 2.13 (0.22), residues: 546 sheet: 0.99 (0.33), residues: 240 loop : -0.44 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 86 TYR 0.024 0.002 TYR H 42 PHE 0.016 0.002 PHE C 25 TRP 0.012 0.002 TRP M 60 HIS 0.008 0.002 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 (17260) covalent geometry : angle 0.68388 / 0.38 (24712) SS BOND : bond 0.00866 / 0.44 ( 4) SS BOND : angle 1.83609 / 0.87 ( 8) hydrogen bonds : bond 0.06092 / 4.05 ( 958) hydrogen bonds : angle 3.47434 / 2.55 ( 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 212 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.461 Fit side-chains REVERT: A 79 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8178 (tttp) REVERT: A 133 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: B 59 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8246 (tttp) REVERT: C 73 ASN cc_start: 0.7593 (m-40) cc_final: 0.6832 (t160) REVERT: D 47 GLN cc_start: 0.8454 (tt0) cc_final: 0.8054 (mt0) REVERT: E 133 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: F 84 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7436 (mmt) REVERT: G 51 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7653 (tp) REVERT: G 90 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.7953 (t70) REVERT: G 99 ARG cc_start: 0.8209 (mpp-170) cc_final: 0.7903 (mtm110) REVERT: H 71 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: M 49 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (mtm110) REVERT: M 52 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8525 (tp) REVERT: M 98 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: M 102 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.8008 (t) REVERT: M 124 GLU cc_start: 0.8346 (pm20) cc_final: 0.7799 (pm20) REVERT: M 230 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.6741 (tpt) REVERT: N 208 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8304 (ttmt) REVERT: N 231 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6481 (mm-30) outliers start: 49 outliers final: 28 residues processed: 189 average time/residue: 0.8303 time to fit residues: 169.4954 Evaluate side-chains 199 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 59 LYS 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 86 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 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 G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 52 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.156591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103596 restraints weight = 19081.621| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.69 r_work: 0.3107 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2140 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= 0.143 Angle : 0.616 7.036 24720 Z= 0.350 Chirality : 0.045 0.255 2784 Planarity : 0.004 0.061 1996 Dihedral : 29.740 171.975 4906 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.79 % Allowed : 18.79 % Favored : 78.42 % 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: 1.89 (0.24), residues: 1198 helix: 2.50 (0.22), residues: 546 sheet: 1.04 (0.34), residues: 240 loop : -0.33 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 191 TYR 0.014 0.001 TYR H 42 PHE 0.007 0.001 PHE F 61 TRP 0.012 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (17260) covalent geometry : angle 0.61588 / 0.35 (24712) SS BOND : bond 0.00572 / 0.29 ( 4) SS BOND : angle 1.12080 / 0.55 ( 8) hydrogen bonds : bond 0.04619 / 3.04 ( 958) hydrogen bonds : angle 3.26642 / 2.40 ( 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 190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8180 (tttp) REVERT: A 133 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: B 59 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8204 (tttp) REVERT: C 73 ASN cc_start: 0.7474 (m-40) cc_final: 0.6774 (t160) REVERT: D 47 GLN cc_start: 0.8427 (tt0) cc_final: 0.8058 (mt0) REVERT: E 115 LYS cc_start: 0.8411 (mtmp) cc_final: 0.8103 (mttp) REVERT: E 133 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: F 84 MET cc_start: 0.7904 (mmp) cc_final: 0.7438 (mmt) REVERT: G 90 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.7914 (t70) REVERT: G 99 ARG cc_start: 0.8173 (mpp-170) cc_final: 0.7866 (mtm110) REVERT: H 71 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: M 52 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8453 (tp) REVERT: M 98 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: M 102 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7967 (t) REVERT: M 124 GLU cc_start: 0.8182 (pm20) cc_final: 0.7657 (pm20) REVERT: N 208 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8257 (ttmt) REVERT: N 231 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6532 (mm-30) outliers start: 29 outliers final: 12 residues processed: 177 average time/residue: 0.8550 time to fit residues: 163.0843 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 133 GLU 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 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 52 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN M 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101654 restraints weight = 19168.922| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.67 r_work: 0.3076 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17264 Z= 0.231 Angle : 0.655 6.342 24720 Z= 0.368 Chirality : 0.047 0.263 2784 Planarity : 0.005 0.063 1996 Dihedral : 29.789 171.578 4906 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.56 % Allowed : 18.59 % Favored : 77.84 % 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: 1.65 (0.24), residues: 1198 helix: 2.28 (0.22), residues: 546 sheet: 0.97 (0.34), residues: 240 loop : -0.45 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 191 TYR 0.020 0.002 TYR H 42 PHE 0.013 0.002 PHE C 25 TRP 0.012 0.002 TRP M 60 HIS 0.007 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (17260) covalent geometry : angle 0.65479 / 0.37 (24712) SS BOND : bond 0.00750 / 0.38 ( 4) SS BOND : angle 1.61278 / 0.77 ( 8) hydrogen bonds : bond 0.05540 / 3.67 ( 958) hydrogen bonds : angle 3.36370 / 2.47 ( 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 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.374 Fit side-chains REVERT: A 79 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8233 (tttp) REVERT: A 133 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: B 59 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8244 (tttp) REVERT: C 73 ASN cc_start: 0.7526 (m-40) cc_final: 0.6749 (t160) REVERT: D 47 GLN cc_start: 0.8456 (tt0) cc_final: 0.8070 (mt0) REVERT: E 115 LYS cc_start: 0.8456 (mtmp) cc_final: 0.8133 (mttp) REVERT: E 133 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: G 51 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7664 (tp) REVERT: G 75 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7650 (mmmt) REVERT: G 90 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.7961 (t70) REVERT: G 99 ARG cc_start: 0.8248 (mpp-170) cc_final: 0.7934 (mtm110) REVERT: H 71 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: M 52 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8459 (tp) REVERT: M 98 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: M 102 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7996 (t) REVERT: M 124 GLU cc_start: 0.8188 (pm20) cc_final: 0.7569 (pm20) REVERT: N 36 GLU cc_start: 0.8297 (pt0) cc_final: 0.8072 (pt0) REVERT: N 208 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8271 (ttmt) REVERT: N 230 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.6438 (tpt) REVERT: N 231 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6553 (mm-30) outliers start: 37 outliers final: 18 residues processed: 194 average time/residue: 0.8089 time to fit residues: 169.0155 Evaluate side-chains 201 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 59 LYS 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 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 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 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 52 LEU 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 230 MET Chi-restraints excluded: chain N residue 231 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: 0.6980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 119 optimal weight: 0.0010 chunk 147 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 50.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104125 restraints weight = 19102.683| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.69 r_work: 0.3113 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2229 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= 0.129 Angle : 0.611 7.935 24720 Z= 0.349 Chirality : 0.045 0.249 2784 Planarity : 0.004 0.067 1996 Dihedral : 29.744 172.363 4906 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.89 % Allowed : 19.27 % Favored : 77.84 % 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: 1.98 (0.25), residues: 1198 helix: 2.62 (0.22), residues: 546 sheet: 1.04 (0.34), residues: 240 loop : -0.31 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.013 0.001 TYR H 40 PHE 0.007 0.001 PHE A 67 TRP 0.014 0.001 TRP M 60 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (17260) covalent geometry : angle 0.61070 / 0.35 (24712) SS BOND : bond 0.00563 / 0.29 ( 4) SS BOND : angle 1.05168 / 0.51 ( 8) hydrogen bonds : bond 0.04417 / 2.90 ( 958) hydrogen bonds : angle 3.22768 / 2.37 ( 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 200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.531 Fit side-chains REVERT: A 64 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.8010 (mmtm) REVERT: A 79 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8063 (tttp) REVERT: C 73 ASN cc_start: 0.7423 (m-40) cc_final: 0.6730 (t160) REVERT: D 47 GLN cc_start: 0.8420 (tt0) cc_final: 0.8063 (mt0) REVERT: E 115 LYS cc_start: 0.8396 (mtmp) cc_final: 0.8118 (mttp) REVERT: E 133 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: F 84 MET cc_start: 0.7778 (mmt) cc_final: 0.7447 (mmt) REVERT: G 90 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.7913 (t70) REVERT: G 99 ARG cc_start: 0.8229 (mpp-170) cc_final: 0.7908 (mtm110) REVERT: M 52 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8428 (tp) REVERT: M 98 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: M 102 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7945 (t) REVERT: M 124 GLU cc_start: 0.8209 (pm20) cc_final: 0.7755 (pm20) REVERT: M 230 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.6708 (tpt) REVERT: N 208 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8235 (ttmt) REVERT: N 231 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6602 (mm-30) outliers start: 30 outliers final: 11 residues processed: 188 average time/residue: 0.8021 time to fit residues: 162.6525 Evaluate side-chains 185 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 133 GLU 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 52 LEU 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 200 ILE Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 24 optimal weight: 0.0000 chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 143 optimal weight: 0.0570 overall best weight: 0.3540 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.157946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105159 restraints weight = 19183.610| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.69 r_work: 0.3129 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17264 Z= 0.122 Angle : 0.602 9.148 24720 Z= 0.345 Chirality : 0.044 0.245 2784 Planarity : 0.004 0.061 1996 Dihedral : 29.711 172.946 4906 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.22 % Allowed : 20.13 % Favored : 77.65 % 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 (0.25), residues: 1198 helix: 2.76 (0.22), residues: 548 sheet: 1.09 (0.34), residues: 240 loop : -0.28 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.015 0.001 TYR H 40 PHE 0.007 0.001 PHE D 70 TRP 0.014 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (17260) covalent geometry : angle 0.60186 / 0.35 (24712) SS BOND : bond 0.00446 / 0.23 ( 4) SS BOND : angle 0.75834 / 0.37 ( 8) hydrogen bonds : bond 0.04166 / 2.73 ( 958) hydrogen bonds : angle 3.15857 / 2.32 ( 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 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.474 Fit side-chains REVERT: A 79 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8091 (tttp) REVERT: D 47 GLN cc_start: 0.8417 (tt0) cc_final: 0.8063 (mt0) REVERT: E 115 LYS cc_start: 0.8347 (mtmp) cc_final: 0.8041 (mttp) REVERT: E 133 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: G 20 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8113 (ttm170) REVERT: G 51 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7564 (tp) REVERT: G 90 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.7883 (t70) REVERT: G 99 ARG cc_start: 0.8236 (mpp-170) cc_final: 0.7973 (mtm110) REVERT: M 52 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8352 (tp) REVERT: M 98 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: M 102 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7931 (t) REVERT: M 124 GLU cc_start: 0.8221 (pm20) cc_final: 0.7755 (pm20) REVERT: M 230 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.6671 (tpt) REVERT: N 208 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8259 (ttmt) REVERT: N 231 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6621 (mm-30) outliers start: 23 outliers final: 10 residues processed: 185 average time/residue: 0.7923 time to fit residues: 157.9142 Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 LEU 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 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 52 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 10.0000 chunk 107 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.159960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107745 restraints weight = 19184.915| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.68 r_work: 0.3164 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17264 Z= 0.123 Angle : 0.564 7.351 24720 Z= 0.331 Chirality : 0.042 0.238 2784 Planarity : 0.004 0.043 1996 Dihedral : 29.564 174.713 4906 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.93 % Allowed : 20.62 % Favored : 77.46 % 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: 2.32 (0.25), residues: 1198 helix: 2.91 (0.22), residues: 548 sheet: 1.22 (0.34), residues: 240 loop : -0.20 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG M 191 TYR 0.014 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.024 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 (17260) covalent geometry : angle 0.56441 / 0.33 (24712) SS BOND : bond 0.00443 / 0.23 ( 4) SS BOND : angle 0.78667 / 0.38 ( 8) hydrogen bonds : bond 0.03813 / 2.51 ( 958) hydrogen bonds : angle 3.01026 / 2.20 ( 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 195 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.447 Fit side-chains REVERT: A 79 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8114 (tttp) REVERT: D 47 GLN cc_start: 0.8416 (tt0) cc_final: 0.8056 (mt0) REVERT: E 115 LYS cc_start: 0.8128 (mtmp) cc_final: 0.7894 (mttp) REVERT: E 123 ASP cc_start: 0.8436 (m-30) cc_final: 0.8120 (m-30) REVERT: E 133 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: G 20 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8077 (ttm170) REVERT: G 51 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7640 (tp) REVERT: G 99 ARG cc_start: 0.8276 (mpp-170) cc_final: 0.7927 (mtm110) REVERT: M 36 GLU cc_start: 0.8256 (pm20) cc_final: 0.8045 (pm20) REVERT: M 98 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: M 102 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7875 (t) REVERT: M 124 GLU cc_start: 0.8131 (pm20) cc_final: 0.7706 (pm20) REVERT: M 219 LEU cc_start: 0.8218 (mm) cc_final: 0.7740 (mm) REVERT: M 230 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.6714 (tpt) REVERT: N 19 MET cc_start: 0.7685 (tpp) cc_final: 0.7347 (tpp) REVERT: N 208 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8150 (ttmt) REVERT: N 231 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6534 (mm-30) outliers start: 20 outliers final: 7 residues processed: 189 average time/residue: 0.7669 time to fit residues: 156.5040 Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 131 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.159675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107377 restraints weight = 19113.232| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.69 r_work: 0.3158 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2279 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= 0.126 Angle : 0.566 6.769 24720 Z= 0.330 Chirality : 0.042 0.236 2784 Planarity : 0.004 0.045 1996 Dihedral : 29.552 174.664 4906 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.45 % Allowed : 21.29 % Favored : 77.26 % 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: 2.34 (0.25), residues: 1198 helix: 2.91 (0.22), residues: 548 sheet: 1.28 (0.35), residues: 240 loop : -0.19 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.018 0.001 TYR H 42 PHE 0.007 0.001 PHE F 61 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 0.00234 / 0.13 (17260) covalent geometry : angle 0.56626 / 0.33 (24712) SS BOND : bond 0.00474 / 0.24 ( 4) SS BOND : angle 0.88933 / 0.43 ( 8) hydrogen bonds : bond 0.03861 / 2.54 ( 958) hydrogen bonds : angle 2.98764 / 2.18 ( 2387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6332.03 seconds wall clock time: 108 minutes 6.07 seconds (6486.07 seconds total)