Starting phenix.real_space_refine on Fri Aug 7 00:47:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubj_42090/08_2026/8ubj_42090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubj_42090/08_2026/8ubj_42090.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/8ubj_42090/08_2026/8ubj_42090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubj_42090/08_2026/8ubj_42090.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubj_42090/08_2026/8ubj_42090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubj_42090/08_2026/8ubj_42090.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= 0.000 sd= 0.003 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 33 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: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16288 At special positions: 0 Unit cell: (137.214, 139.755, 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=2.04 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: 1.23 Conformation dependent library (CDL) restraints added in 442.4 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, 21.3% beta 162 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.972A 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: 3.847A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.601A 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: 4.291A 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: 3.681A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.867A 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 removed outlier: 3.575A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) 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: 3.903A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.323A 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: 3.778A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.405A 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: 3.541A 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: 3.524A pdb=" N SER M 240 " --> pdb=" O SER M 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.647A 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: 6.887A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.220A 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 101 through 102 removed outlier: 6.642A 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: 6.912A 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: 7.272A 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: 3.791A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.897A 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: 6.618A 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: 3.791A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.919A pdb=" N GLU M 159 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR M 266 " --> pdb=" O GLU M 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 161 " --> 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: 4.444A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.949A 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: 3.919A pdb=" N GLU M 159 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR M 266 " --> pdb=" O GLU M 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 161 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.056A 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: 3.722A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 72 through 73 removed outlier: 6.470A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 72 through 73 removed outlier: 6.470A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (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: 4.474A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.940A 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: 4.043A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 412 hydrogen bonds 824 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.60 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: 3969 1.34 - 1.46: 4945 1.46 - 1.58: 7648 1.58 - 1.70: 646 1.70 - 1.82: 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 1.546 -0.078 1.40e-02 5.10e+03 3.14e+01 bond pdb=" C1' DC J 4 " pdb=" N1 DC J 4 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.14e+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 2.92e+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 2.87e+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 - 2.20: 23631 2.20 - 4.41: 998 4.41 - 6.61: 75 6.61 - 8.82: 5 8.82 - 11.02: 3 Bond angle restraints: 24712 Sorted by residual: angle pdb=" CB LYS H 34 " pdb=" CG LYS H 34 " pdb=" CD LYS H 34 " ideal model delta sigma weight residual 111.30 122.32 -11.02 2.30e+00 1.89e-01 2.30e+01 angle pdb=" O4' DC J 5 " pdb=" C1' DC J 5 " pdb=" N1 DC J 5 " ideal model delta sigma weight residual 108.00 111.10 -3.10 7.00e-01 2.04e+00 1.97e+01 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 1.93e+01 angle pdb=" N3 DT I 7 " pdb=" C4 DT I 7 " pdb=" O4 DT I 7 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O5' DC J 4 " pdb=" C5' DC J 4 " pdb=" C4' DC J 4 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 ... (remaining 24707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 8126 34.85 - 69.71: 1379 69.71 - 104.56: 39 104.56 - 139.42: 0 139.42 - 174.27: 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 45.73 174.27 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 70.20 149.80 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C ASP A 81 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 9543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2100 0.052 - 0.104: 341 0.104 - 0.156: 331 0.156 - 0.208: 8 0.208 - 0.259: 4 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE G 62 " pdb=" CA ILE G 62 " pdb=" CG1 ILE G 62 " pdb=" CG2 ILE G 62 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB VAL M 265 " pdb=" CA VAL M 265 " pdb=" CG1 VAL M 265 " pdb=" CG2 VAL M 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2781 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 73 " 0.029 2.00e-02 2.50e+03 1.47e-02 5.91e+00 pdb=" N9 DA J 73 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 73 " -0.001 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 " -0.009 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 2.25e-02 5.08e+00 pdb=" C ARG F 23 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.015 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 1.38e-02 4.28e+00 pdb=" N1 DC I 91 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DC I 91 " -0.006 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 " 0.001 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1362 2.74 - 3.28: 13761 3.28 - 3.82: 30193 3.82 - 4.36: 36518 4.36 - 4.90: 54822 Nonbonded interactions: 136656 Sorted by model distance: nonbonded pdb=" OD2 ASP M 222 " pdb=" OG SER M 225 " model vdw 2.206 3.040 nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.207 3.120 nonbonded pdb=" NH1 ARG C 11 " pdb=" O4' DA J 47 " model vdw 2.213 3.120 nonbonded pdb=" N GLU M 124 " pdb=" OE1 GLU M 124 " model vdw 2.263 3.120 nonbonded pdb=" OE1 GLN H 95 " pdb=" NH2 ARG H 99 " model vdw 2.296 3.120 ... (remaining 136651 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.078 17264 Z= 0.586 Angle : 0.895 11.024 24720 Z= 0.712 Chirality : 0.057 0.259 2784 Planarity : 0.005 0.061 1996 Dihedral : 25.563 174.272 7262 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.67 % Allowed : 15.99 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.24), residues: 1198 helix: 2.64 (0.22), residues: 538 sheet: 1.17 (0.35), residues: 218 loop : 0.09 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 191 TYR 0.021 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.007 0.001 TRP M 196 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.59 (17260) covalent geometry : angle 0.89515 / 0.71 (24712) SS BOND : bond 0.00383 / 0.19 ( 4) SS BOND : angle 0.55810 / 0.27 ( 8) hydrogen bonds : bond 0.13718 / 9.15 ( 959) hydrogen bonds : angle 4.76535 / 3.47 ( 2414) *********************** 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 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.435 Fit side-chains REVERT: E 115 LYS cc_start: 0.8590 (mtmp) cc_final: 0.8309 (mtmm) REVERT: E 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8491 (m-30) REVERT: H 52 THR cc_start: 0.9046 (m) cc_final: 0.8801 (m) REVERT: H 59 MET cc_start: 0.8635 (tpp) cc_final: 0.8379 (tpp) REVERT: H 85 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8648 (mmtt) REVERT: M 37 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7909 (mtp180) REVERT: M 265 VAL cc_start: 0.8208 (t) cc_final: 0.7899 (p) REVERT: N 152 GLN cc_start: 0.8427 (tt0) cc_final: 0.8080 (tt0) REVERT: N 230 MET cc_start: 0.8526 (tpt) cc_final: 0.8301 (tmm) REVERT: N 239 ASP cc_start: 0.7677 (m-30) cc_final: 0.7345 (m-30) outliers start: 7 outliers final: 1 residues processed: 229 average time/residue: 0.7489 time to fit residues: 185.4750 Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089544 restraints weight = 24912.142| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.89 r_work: 0.3127 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1266 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= 0.216 Angle : 0.690 7.604 24720 Z= 0.400 Chirality : 0.050 0.240 2784 Planarity : 0.005 0.043 1996 Dihedral : 28.675 177.493 4908 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.79 % Allowed : 15.32 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.24), residues: 1198 helix: 2.57 (0.22), residues: 546 sheet: 1.41 (0.37), residues: 206 loop : -0.15 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 191 TYR 0.018 0.002 TYR H 42 PHE 0.012 0.002 PHE C 25 TRP 0.012 0.002 TRP M 196 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (17260) covalent geometry : angle 0.68947 / 0.40 (24712) SS BOND : bond 0.00728 / 0.37 ( 4) SS BOND : angle 1.41050 / 0.68 ( 8) hydrogen bonds : bond 0.05706 / 3.89 ( 959) hydrogen bonds : angle 3.60138 / 2.63 ( 2414) *********************** 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 239 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8125 (t0) cc_final: 0.7747 (t160) REVERT: D 76 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 116 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8147 (tttm) REVERT: E 41 TYR cc_start: 0.9031 (m-80) cc_final: 0.8707 (m-80) REVERT: E 56 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8118 (ttmm) REVERT: E 120 MET cc_start: 0.7630 (mmt) cc_final: 0.7130 (mpp) REVERT: E 123 ASP cc_start: 0.8723 (m-30) cc_final: 0.8308 (m-30) REVERT: F 27 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: F 84 MET cc_start: 0.8422 (mmp) cc_final: 0.8219 (mmt) REVERT: G 15 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7601 (pptt) REVERT: H 34 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8090 (mmmm) REVERT: H 59 MET cc_start: 0.8612 (tpp) cc_final: 0.8339 (tpp) REVERT: H 71 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: H 87 SER cc_start: 0.8233 (m) cc_final: 0.7849 (p) REVERT: M 37 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8571 (mtp180) REVERT: M 160 LEU cc_start: 0.8535 (mm) cc_final: 0.8308 (mm) REVERT: M 231 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8410 (mm-30) REVERT: M 238 GLU cc_start: 0.8956 (pt0) cc_final: 0.8474 (pm20) REVERT: N 36 GLU cc_start: 0.7346 (pm20) cc_final: 0.6848 (pm20) REVERT: N 52 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8916 (tp) REVERT: N 98 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7029 (mt-10) REVERT: N 152 GLN cc_start: 0.8483 (tt0) cc_final: 0.8117 (tt0) REVERT: N 195 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: N 208 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8404 (ttpp) REVERT: N 222 ASP cc_start: 0.7619 (t0) cc_final: 0.7397 (t0) REVERT: N 231 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7670 (mm-30) outliers start: 29 outliers final: 10 residues processed: 224 average time/residue: 0.8252 time to fit residues: 199.4061 Evaluate side-chains 206 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS 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: 8.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 119 optimal weight: 0.0970 chunk 140 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091884 restraints weight = 25122.649| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.90 r_work: 0.3166 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17264 Z= 0.132 Angle : 0.588 5.885 24720 Z= 0.350 Chirality : 0.044 0.249 2784 Planarity : 0.004 0.055 1996 Dihedral : 29.054 177.391 4906 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.12 % Allowed : 16.76 % 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: 2.38 (0.24), residues: 1198 helix: 2.91 (0.22), residues: 548 sheet: 1.28 (0.36), residues: 218 loop : -0.03 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.013 0.001 TYR H 42 PHE 0.007 0.001 PHE F 61 TRP 0.007 0.001 TRP M 185 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (17260) covalent geometry : angle 0.58791 / 0.35 (24712) SS BOND : bond 0.00421 / 0.22 ( 4) SS BOND : angle 0.75473 / 0.38 ( 8) hydrogen bonds : bond 0.04512 / 3.03 ( 959) hydrogen bonds : angle 3.28024 / 2.40 ( 2414) *********************** 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 229 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8220 (tttm) cc_final: 0.7925 (ttmp) REVERT: C 73 ASN cc_start: 0.8180 (t0) cc_final: 0.7664 (t160) REVERT: D 71 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: D 76 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 116 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8145 (tttm) REVERT: E 56 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8092 (ttmm) REVERT: E 120 MET cc_start: 0.7451 (mmt) cc_final: 0.6875 (mpp) REVERT: E 123 ASP cc_start: 0.8602 (m-30) cc_final: 0.8172 (m-30) REVERT: F 27 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8567 (mp10) REVERT: F 79 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8166 (mtpt) REVERT: F 84 MET cc_start: 0.8233 (mmp) cc_final: 0.8002 (mmt) REVERT: G 24 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8067 (mm-40) REVERT: G 51 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7868 (tp) REVERT: G 73 ASN cc_start: 0.8117 (t0) cc_final: 0.7696 (t0) REVERT: H 34 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8099 (mmmm) REVERT: H 59 MET cc_start: 0.8310 (tpp) cc_final: 0.7964 (tpp) REVERT: H 76 GLU cc_start: 0.8635 (tp30) cc_final: 0.8435 (mm-30) REVERT: H 91 SER cc_start: 0.8870 (p) cc_final: 0.8491 (m) REVERT: M 37 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8432 (mtp180) REVERT: M 113 SER cc_start: 0.7045 (OUTLIER) cc_final: 0.6743 (t) REVERT: M 231 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8311 (mm-30) REVERT: M 238 GLU cc_start: 0.8907 (pt0) cc_final: 0.8526 (pm20) REVERT: N 98 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7026 (mt-10) REVERT: N 152 GLN cc_start: 0.8369 (tt0) cc_final: 0.7986 (tt0) REVERT: N 159 GLU cc_start: 0.8446 (tt0) cc_final: 0.8161 (mt-10) REVERT: N 195 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: N 208 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: N 222 ASP cc_start: 0.7597 (t0) cc_final: 0.7049 (t0) REVERT: N 231 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7582 (mm-30) outliers start: 22 outliers final: 6 residues processed: 220 average time/residue: 0.8060 time to fit residues: 191.6463 Evaluate side-chains 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN G 38 ASN N 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089905 restraints weight = 24922.899| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.88 r_work: 0.3138 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17264 Z= 0.156 Angle : 0.593 6.437 24720 Z= 0.347 Chirality : 0.044 0.241 2784 Planarity : 0.004 0.046 1996 Dihedral : 29.356 175.830 4906 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.89 % Allowed : 16.76 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1198 helix: 2.93 (0.22), residues: 548 sheet: 1.30 (0.36), residues: 218 loop : -0.08 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 191 TYR 0.014 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.010 0.001 TRP M 185 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (17260) covalent geometry : angle 0.59300 / 0.35 (24712) SS BOND : bond 0.00599 / 0.31 ( 4) SS BOND : angle 1.09736 / 0.54 ( 8) hydrogen bonds : bond 0.04698 / 3.17 ( 959) hydrogen bonds : angle 3.17296 / 2.33 ( 2414) *********************** 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 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8282 (tttm) cc_final: 0.7993 (ttmp) REVERT: A 59 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: C 73 ASN cc_start: 0.8341 (t0) cc_final: 0.7787 (t160) REVERT: D 71 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: D 76 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8106 (mm-30) REVERT: D 116 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8218 (tttm) REVERT: E 56 LYS cc_start: 0.8347 (mtpt) cc_final: 0.8114 (ttmm) REVERT: E 123 ASP cc_start: 0.8756 (m-30) cc_final: 0.8323 (m-30) REVERT: E 133 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: F 79 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8147 (mtpt) REVERT: F 84 MET cc_start: 0.8491 (mmp) cc_final: 0.8282 (mmt) REVERT: G 24 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8064 (mm-40) REVERT: G 73 ASN cc_start: 0.8169 (t0) cc_final: 0.7774 (t0) REVERT: H 34 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8096 (mmmm) REVERT: H 86 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7885 (mtt90) REVERT: H 91 SER cc_start: 0.8987 (p) cc_final: 0.8618 (m) REVERT: M 113 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6937 (t) REVERT: M 230 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7922 (tpp) REVERT: M 231 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8211 (mm-30) REVERT: M 238 GLU cc_start: 0.8961 (pt0) cc_final: 0.8453 (pm20) REVERT: N 152 GLN cc_start: 0.8471 (tt0) cc_final: 0.8091 (tt0) REVERT: N 159 GLU cc_start: 0.8422 (tt0) cc_final: 0.8209 (mt-10) REVERT: N 195 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: N 208 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8267 (mtpp) REVERT: N 222 ASP cc_start: 0.7772 (t0) cc_final: 0.7105 (t0) REVERT: N 231 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7657 (mm-30) outliers start: 30 outliers final: 13 residues processed: 217 average time/residue: 0.8067 time to fit residues: 188.9689 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 SER 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 77 VAL Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 93 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 68 GLN G 38 ASN N 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090035 restraints weight = 24930.099| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.88 r_work: 0.3138 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17264 Z= 0.146 Angle : 0.584 5.856 24720 Z= 0.340 Chirality : 0.043 0.245 2784 Planarity : 0.004 0.045 1996 Dihedral : 29.451 175.613 4906 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.08 % Allowed : 17.24 % Favored : 79.67 % 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: 2.38 (0.24), residues: 1198 helix: 2.98 (0.22), residues: 548 sheet: 1.58 (0.37), residues: 192 loop : -0.19 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 191 TYR 0.015 0.001 TYR H 42 PHE 0.007 0.001 PHE C 25 TRP 0.008 0.001 TRP M 185 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (17260) covalent geometry : angle 0.58407 / 0.34 (24712) SS BOND : bond 0.00537 / 0.28 ( 4) SS BOND : angle 1.01087 / 0.51 ( 8) hydrogen bonds : bond 0.04330 / 2.91 ( 959) hydrogen bonds : angle 3.09490 / 2.27 ( 2414) *********************** 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 238 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.275 Fit side-chains REVERT: A 56 LYS cc_start: 0.8284 (tttm) cc_final: 0.7998 (ttmp) REVERT: A 59 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: B 77 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8373 (ttmm) REVERT: C 73 ASN cc_start: 0.8447 (t0) cc_final: 0.7839 (t160) REVERT: D 76 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8131 (mm-30) REVERT: D 116 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8364 (ttmm) REVERT: E 56 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8127 (ttmm) REVERT: E 133 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: F 79 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8133 (mtpt) REVERT: F 84 MET cc_start: 0.8503 (mmp) cc_final: 0.8283 (mmt) REVERT: H 34 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8147 (mmmm) REVERT: H 79 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7691 (mtp180) REVERT: H 86 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7865 (mtt90) REVERT: H 91 SER cc_start: 0.8969 (p) cc_final: 0.8624 (m) REVERT: M 37 ARG cc_start: 0.8935 (mtp85) cc_final: 0.8629 (mtp180) REVERT: M 89 ASP cc_start: 0.8148 (t0) cc_final: 0.7748 (p0) REVERT: M 113 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6968 (t) REVERT: M 122 LYS cc_start: 0.7804 (tptp) cc_final: 0.7409 (mtpp) REVERT: M 230 MET cc_start: 0.8756 (tpp) cc_final: 0.7633 (tpp) REVERT: M 231 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8135 (mm-30) REVERT: M 238 GLU cc_start: 0.8948 (pt0) cc_final: 0.8463 (pm20) REVERT: N 36 GLU cc_start: 0.7206 (pm20) cc_final: 0.6646 (pm20) REVERT: N 152 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: N 159 GLU cc_start: 0.8408 (tt0) cc_final: 0.8184 (mt-10) REVERT: N 195 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: N 222 ASP cc_start: 0.7853 (t0) cc_final: 0.7111 (t0) REVERT: N 231 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7534 (mm-30) outliers start: 32 outliers final: 14 residues processed: 222 average time/residue: 0.7180 time to fit residues: 171.9954 Evaluate side-chains 223 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 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: 3.9990 chunk 103 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 126 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088687 restraints weight = 24817.922| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.88 r_work: 0.3115 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2038 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= 0.173 Angle : 0.605 6.464 24720 Z= 0.349 Chirality : 0.044 0.247 2784 Planarity : 0.004 0.051 1996 Dihedral : 29.554 174.992 4906 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.28 % Allowed : 17.53 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.24), residues: 1198 helix: 2.91 (0.22), residues: 548 sheet: 1.49 (0.37), residues: 192 loop : -0.26 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 191 TYR 0.017 0.001 TYR H 42 PHE 0.010 0.001 PHE C 25 TRP 0.009 0.001 TRP M 185 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (17260) covalent geometry : angle 0.60498 / 0.35 (24712) SS BOND : bond 0.00646 / 0.33 ( 4) SS BOND : angle 1.28507 / 0.64 ( 8) hydrogen bonds : bond 0.04718 / 3.18 ( 959) hydrogen bonds : angle 3.12002 / 2.29 ( 2414) *********************** 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 237 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.473 Fit side-chains REVERT: A 56 LYS cc_start: 0.8207 (tttm) cc_final: 0.7915 (ttmp) REVERT: A 59 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: B 77 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8273 (ttmm) REVERT: C 73 ASN cc_start: 0.8428 (t0) cc_final: 0.7800 (t160) REVERT: C 91 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: D 76 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: D 86 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7859 (mpt-90) REVERT: D 116 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8200 (ttmm) REVERT: E 56 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8101 (ttmm) REVERT: E 133 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: F 79 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8011 (mtpt) REVERT: F 84 MET cc_start: 0.8386 (mmp) cc_final: 0.8182 (mmt) REVERT: G 15 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7198 (pptt) REVERT: G 20 ARG cc_start: 0.8314 (ttm170) cc_final: 0.7999 (ttm170) REVERT: H 34 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8135 (mmmm) REVERT: H 86 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7821 (mtt90) REVERT: H 91 SER cc_start: 0.8948 (p) cc_final: 0.8587 (m) REVERT: M 89 ASP cc_start: 0.8117 (t0) cc_final: 0.7701 (p0) REVERT: M 113 SER cc_start: 0.7279 (OUTLIER) cc_final: 0.7050 (t) REVERT: M 122 LYS cc_start: 0.7692 (tptp) cc_final: 0.7293 (mtpp) REVERT: M 230 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7691 (tpp) REVERT: M 231 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8018 (mm-30) REVERT: M 238 GLU cc_start: 0.8978 (pt0) cc_final: 0.8456 (pm20) REVERT: N 36 GLU cc_start: 0.7160 (pm20) cc_final: 0.6580 (pm20) REVERT: N 152 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: N 159 GLU cc_start: 0.8392 (tt0) cc_final: 0.8166 (mt-10) REVERT: N 195 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: N 222 ASP cc_start: 0.7733 (t0) cc_final: 0.6956 (t0) outliers start: 34 outliers final: 17 residues processed: 218 average time/residue: 0.7487 time to fit residues: 176.0306 Evaluate side-chains 227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087735 restraints weight = 24917.489| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.88 r_work: 0.3101 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17264 Z= 0.188 Angle : 0.628 7.445 24720 Z= 0.357 Chirality : 0.044 0.249 2784 Planarity : 0.004 0.059 1996 Dihedral : 29.667 174.416 4906 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.66 % Allowed : 18.21 % Favored : 78.13 % 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: 2.19 (0.24), residues: 1198 helix: 2.84 (0.22), residues: 546 sheet: 1.48 (0.37), residues: 192 loop : -0.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 37 TYR 0.020 0.002 TYR H 42 PHE 0.010 0.002 PHE C 25 TRP 0.010 0.001 TRP M 185 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (17260) covalent geometry : angle 0.62719 / 0.36 (24712) SS BOND : bond 0.00677 / 0.35 ( 4) SS BOND : angle 1.33203 / 0.66 ( 8) hydrogen bonds : bond 0.04837 / 3.26 ( 959) hydrogen bonds : angle 3.14807 / 2.30 ( 2414) *********************** 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 242 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.396 Fit side-chains REVERT: A 56 LYS cc_start: 0.8287 (tttm) cc_final: 0.7994 (ttmp) REVERT: A 59 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: B 77 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: C 73 ASN cc_start: 0.8550 (t0) cc_final: 0.7832 (t0) REVERT: C 91 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: D 76 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: D 116 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8314 (ttmm) REVERT: E 56 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8160 (ttmm) REVERT: E 115 LYS cc_start: 0.9023 (mtmp) cc_final: 0.8668 (mptp) REVERT: E 133 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: F 79 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8062 (mtpt) REVERT: G 15 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7227 (pptt) REVERT: G 20 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8087 (ttm170) REVERT: H 34 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8165 (mmmm) REVERT: H 79 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7625 (mtp180) REVERT: H 86 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7880 (mtt90) REVERT: H 91 SER cc_start: 0.9023 (p) cc_final: 0.8622 (m) REVERT: M 89 ASP cc_start: 0.8188 (t0) cc_final: 0.7876 (p0) REVERT: M 122 LYS cc_start: 0.7764 (tptp) cc_final: 0.7370 (mtpp) REVERT: M 230 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7813 (tpp) REVERT: M 231 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8009 (mm-30) REVERT: M 238 GLU cc_start: 0.8956 (pt0) cc_final: 0.8480 (pm20) REVERT: N 36 GLU cc_start: 0.7165 (pm20) cc_final: 0.6877 (pm20) REVERT: N 113 SER cc_start: 0.8625 (t) cc_final: 0.8248 (p) REVERT: N 152 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: N 159 GLU cc_start: 0.8417 (tt0) cc_final: 0.8210 (mt-10) REVERT: N 195 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: N 222 ASP cc_start: 0.7898 (t0) cc_final: 0.7145 (t0) outliers start: 38 outliers final: 19 residues processed: 220 average time/residue: 0.7189 time to fit residues: 170.9064 Evaluate side-chains 229 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 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: 3.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 30.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088364 restraints weight = 24862.434| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.87 r_work: 0.3106 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17264 Z= 0.163 Angle : 0.617 9.873 24720 Z= 0.351 Chirality : 0.044 0.248 2784 Planarity : 0.004 0.065 1996 Dihedral : 29.665 174.475 4906 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.18 % Allowed : 19.27 % Favored : 77.55 % 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: 2.22 (0.24), residues: 1198 helix: 2.87 (0.22), residues: 546 sheet: 1.47 (0.37), residues: 192 loop : -0.29 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 191 TYR 0.016 0.001 TYR H 42 PHE 0.008 0.001 PHE E 104 TRP 0.008 0.001 TRP M 185 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (17260) covalent geometry : angle 0.61714 / 0.35 (24712) SS BOND : bond 0.00623 / 0.32 ( 4) SS BOND : angle 1.22420 / 0.62 ( 8) hydrogen bonds : bond 0.04612 / 3.10 ( 959) hydrogen bonds : angle 3.12650 / 2.28 ( 2414) *********************** 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 231 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.438 Fit side-chains REVERT: A 56 LYS cc_start: 0.8204 (tttm) cc_final: 0.7911 (ttmp) REVERT: A 59 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7021 (pp20) REVERT: B 77 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8267 (ttmm) REVERT: C 73 ASN cc_start: 0.8525 (t0) cc_final: 0.7841 (t0) REVERT: C 91 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7875 (tp30) REVERT: D 76 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: D 116 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8220 (ttmm) REVERT: E 56 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8094 (ttmm) REVERT: E 115 LYS cc_start: 0.8976 (mtmp) cc_final: 0.8632 (mptp) REVERT: E 133 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6573 (mt-10) REVERT: F 79 LYS cc_start: 0.8505 (mtpp) cc_final: 0.7966 (mtpt) REVERT: G 15 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7137 (pptt) REVERT: G 20 ARG cc_start: 0.8332 (ttm170) cc_final: 0.8036 (ttm170) REVERT: H 34 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8147 (mmmm) REVERT: H 79 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7495 (mtp180) REVERT: H 86 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7797 (mtt90) REVERT: H 91 SER cc_start: 0.8975 (p) cc_final: 0.8571 (m) REVERT: M 37 ARG cc_start: 0.9020 (mtp85) cc_final: 0.8676 (mtp180) REVERT: M 46 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7019 (mt0) REVERT: M 89 ASP cc_start: 0.8143 (t0) cc_final: 0.7816 (p0) REVERT: M 122 LYS cc_start: 0.7694 (tptp) cc_final: 0.7316 (mtpp) REVERT: M 230 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7744 (tpp) REVERT: M 231 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7952 (mm-30) REVERT: M 238 GLU cc_start: 0.8975 (pt0) cc_final: 0.8465 (pm20) REVERT: N 36 GLU cc_start: 0.7137 (pm20) cc_final: 0.6564 (pm20) REVERT: N 113 SER cc_start: 0.8603 (t) cc_final: 0.8227 (p) REVERT: N 152 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: N 159 GLU cc_start: 0.8427 (tt0) cc_final: 0.8214 (mt-10) REVERT: N 195 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: N 222 ASP cc_start: 0.7811 (t0) cc_final: 0.7040 (t0) outliers start: 33 outliers final: 15 residues processed: 211 average time/residue: 0.6916 time to fit residues: 157.5104 Evaluate side-chains 224 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088990 restraints weight = 24884.714| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.88 r_work: 0.3119 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17264 Z= 0.135 Angle : 0.605 9.488 24720 Z= 0.347 Chirality : 0.043 0.244 2784 Planarity : 0.004 0.073 1996 Dihedral : 29.645 174.636 4906 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.18 % Allowed : 19.27 % Favored : 77.55 % 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: 2.29 (0.24), residues: 1198 helix: 2.95 (0.22), residues: 546 sheet: 1.49 (0.37), residues: 192 loop : -0.28 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.015 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.007 0.001 TRP M 185 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (17260) covalent geometry : angle 0.60516 / 0.35 (24712) SS BOND : bond 0.00560 / 0.29 ( 4) SS BOND : angle 1.00576 / 0.51 ( 8) hydrogen bonds : bond 0.04333 / 2.91 ( 959) hydrogen bonds : angle 3.08998 / 2.26 ( 2414) *********************** 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 235 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.468 Fit side-chains REVERT: A 56 LYS cc_start: 0.8198 (tttm) cc_final: 0.7907 (ttmp) REVERT: A 59 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7001 (pp20) REVERT: B 77 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8261 (ttmm) REVERT: C 73 ASN cc_start: 0.8407 (t0) cc_final: 0.7735 (t0) REVERT: C 91 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: D 76 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: D 116 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8210 (ttmm) REVERT: E 56 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8082 (ttmm) REVERT: E 115 LYS cc_start: 0.8968 (mtmp) cc_final: 0.8631 (mptp) REVERT: E 120 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6773 (mtp) REVERT: E 133 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: F 79 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7948 (mtpt) REVERT: G 15 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7134 (pptt) REVERT: G 20 ARG cc_start: 0.8334 (ttm170) cc_final: 0.8032 (ttm170) REVERT: H 34 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8111 (mmmm) REVERT: H 79 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7483 (mtp180) REVERT: H 86 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7751 (mtt90) REVERT: H 91 SER cc_start: 0.8958 (p) cc_final: 0.8569 (m) REVERT: M 37 ARG cc_start: 0.9022 (mtp85) cc_final: 0.8688 (mtp180) REVERT: M 89 ASP cc_start: 0.8126 (t0) cc_final: 0.7806 (p0) REVERT: M 122 LYS cc_start: 0.7684 (tptp) cc_final: 0.7322 (mtpp) REVERT: M 230 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7713 (tpp) REVERT: M 231 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7941 (mm-30) REVERT: M 238 GLU cc_start: 0.8962 (pt0) cc_final: 0.8480 (pm20) REVERT: M 239 ASP cc_start: 0.8406 (m-30) cc_final: 0.8157 (m-30) REVERT: N 36 GLU cc_start: 0.7143 (pm20) cc_final: 0.6564 (pm20) REVERT: N 113 SER cc_start: 0.8591 (t) cc_final: 0.8215 (p) REVERT: N 152 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: N 159 GLU cc_start: 0.8415 (tt0) cc_final: 0.8213 (mt-10) REVERT: N 195 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: N 222 ASP cc_start: 0.7802 (t0) cc_final: 0.7024 (t0) outliers start: 33 outliers final: 19 residues processed: 214 average time/residue: 0.7135 time to fit residues: 164.7996 Evaluate side-chains 233 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089645 restraints weight = 24847.775| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.87 r_work: 0.3132 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17264 Z= 0.142 Angle : 0.597 8.336 24720 Z= 0.343 Chirality : 0.042 0.243 2784 Planarity : 0.004 0.067 1996 Dihedral : 29.604 175.016 4906 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.70 % Allowed : 19.85 % 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: 2.30 (0.24), residues: 1198 helix: 2.97 (0.22), residues: 546 sheet: 1.48 (0.37), residues: 192 loop : -0.28 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 191 TYR 0.016 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 0.00280 / 0.14 (17260) covalent geometry : angle 0.59709 / 0.34 (24712) SS BOND : bond 0.00538 / 0.28 ( 4) SS BOND : angle 1.02646 / 0.52 ( 8) hydrogen bonds : bond 0.04207 / 2.83 ( 959) hydrogen bonds : angle 3.02616 / 2.22 ( 2414) ********************** 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 231 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.311 Fit side-chains REVERT: A 56 LYS cc_start: 0.8295 (tttm) cc_final: 0.8009 (ttmp) REVERT: A 59 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: B 77 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: C 73 ASN cc_start: 0.8458 (t0) cc_final: 0.7732 (t0) REVERT: C 91 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: D 76 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: D 116 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8317 (ttmm) REVERT: E 56 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8158 (ttmm) REVERT: E 115 LYS cc_start: 0.9026 (mtmp) cc_final: 0.8721 (mptp) REVERT: F 79 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8058 (mtpt) REVERT: G 15 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7256 (pptt) REVERT: G 20 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8113 (ttm170) REVERT: H 34 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8196 (mmmm) REVERT: H 79 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.7595 (mtp180) REVERT: H 86 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7814 (mtt90) REVERT: H 91 SER cc_start: 0.9014 (p) cc_final: 0.8649 (m) REVERT: M 37 ARG cc_start: 0.9014 (mtp85) cc_final: 0.8670 (mtp180) REVERT: M 89 ASP cc_start: 0.8165 (t0) cc_final: 0.7893 (p0) REVERT: M 122 LYS cc_start: 0.7735 (tptp) cc_final: 0.7371 (mtpp) REVERT: M 230 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7774 (tpp) REVERT: M 231 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7999 (mm-30) REVERT: M 238 GLU cc_start: 0.8906 (pt0) cc_final: 0.8355 (pm20) REVERT: N 36 GLU cc_start: 0.7171 (pm20) cc_final: 0.6872 (pm20) REVERT: N 113 SER cc_start: 0.8610 (t) cc_final: 0.8230 (p) REVERT: N 152 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: N 195 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: N 222 ASP cc_start: 0.7915 (t0) cc_final: 0.7143 (t0) outliers start: 28 outliers final: 15 residues processed: 215 average time/residue: 0.7043 time to fit residues: 163.1878 Evaluate side-chains 225 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 109 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.131136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089912 restraints weight = 24808.845| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.88 r_work: 0.3136 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17264 Z= 0.132 Angle : 0.594 9.476 24720 Z= 0.342 Chirality : 0.042 0.241 2784 Planarity : 0.004 0.068 1996 Dihedral : 29.592 175.115 4906 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.60 % Allowed : 20.52 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1198 helix: 3.00 (0.22), residues: 546 sheet: 1.49 (0.37), residues: 192 loop : -0.25 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.013 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP M 196 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (17260) covalent geometry : angle 0.59418 / 0.34 (24712) SS BOND : bond 0.00506 / 0.26 ( 4) SS BOND : angle 0.92462 / 0.47 ( 8) hydrogen bonds : bond 0.04094 / 2.75 ( 959) hydrogen bonds : angle 3.01671 / 2.21 ( 2414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5949.58 seconds wall clock time: 101 minutes 36.74 seconds (6096.74 seconds total)