Starting phenix.real_space_refine on Thu Feb 5 14:42:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubi_42089/02_2026/8ubi_42089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubi_42089/02_2026/8ubi_42089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubi_42089/02_2026/8ubi_42089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubi_42089/02_2026/8ubi_42089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubi_42089/02_2026/8ubi_42089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubi_42089/02_2026/8ubi_42089.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 324 5.49 5 S 32 5.16 5 C 9232 2.51 5 N 2970 2.21 5 O 3730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 3.27, per 1000 atoms: 0.20 Number of scatterers: 16288 At special positions: 0 Unit cell: (137.214, 138.484, 144.837, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 324 15.00 O 3730 8.00 N 2970 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.04 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 483.8 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 22 sheets defined 48.0% alpha, 21.4% beta 162 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.932A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.810A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.577A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.321A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.631A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.890A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.524A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.326A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.728A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.388A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.609A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 removed outlier: 3.515A pdb=" N SER M 240 " --> pdb=" O SER M 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.708A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 236 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.925A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.201A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.566A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.913A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.293A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.201A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.201A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR M 116 " --> pdb=" O GLN M 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.520A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.520A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.712A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.349A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N 32 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.349A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N 32 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.584A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 4.006A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 412 hydrogen bonds 824 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3784 1.34 - 1.46: 4894 1.46 - 1.57: 7884 1.57 - 1.69: 646 1.69 - 1.81: 52 Bond restraints: 17260 Sorted by residual: bond pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.75e+00 bond pdb=" C1' DC I 39 " pdb=" N1 DC I 39 " ideal model delta sigma weight residual 1.490 1.548 -0.058 3.00e-02 1.11e+03 3.71e+00 bond pdb=" C1' DC J 4 " pdb=" N1 DC J 4 " ideal model delta sigma weight residual 1.490 1.547 -0.057 3.00e-02 1.11e+03 3.65e+00 bond pdb=" C1' DC I 91 " pdb=" N1 DC I 91 " ideal model delta sigma weight residual 1.490 1.544 -0.054 3.00e-02 1.11e+03 3.28e+00 bond pdb=" N ALA G 10 " pdb=" CA ALA G 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 23321 1.45 - 2.90: 1181 2.90 - 4.35: 155 4.35 - 5.80: 44 5.80 - 7.25: 11 Bond angle restraints: 24712 Sorted by residual: angle pdb=" CA GLU M 162 " pdb=" CB GLU M 162 " pdb=" CG GLU M 162 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CB LYS B 77 " pdb=" CG LYS B 77 " pdb=" CD LYS B 77 " ideal model delta sigma weight residual 111.30 118.38 -7.08 2.30e+00 1.89e-01 9.47e+00 angle pdb=" C2' DC I 29 " pdb=" C1' DC I 29 " pdb=" N1 DC I 29 " ideal model delta sigma weight residual 113.50 118.11 -4.61 1.50e+00 4.44e-01 9.44e+00 angle pdb=" C2' DC I 39 " pdb=" C1' DC I 39 " pdb=" N1 DC I 39 " ideal model delta sigma weight residual 113.50 118.07 -4.57 1.50e+00 4.44e-01 9.27e+00 angle pdb=" CA GLN N 154 " pdb=" CB GLN N 154 " pdb=" CG GLN N 154 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.25e+00 ... (remaining 24707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 8147 34.86 - 69.73: 1361 69.73 - 104.59: 36 104.59 - 139.46: 0 139.46 - 174.32: 2 Dihedral angle restraints: 9546 sinusoidal: 6000 harmonic: 3546 Sorted by residual: dihedral pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " pdb=" P DG J 144 " ideal model delta sinusoidal sigma weight residual 220.00 45.68 174.32 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 109 " pdb=" C3' DT J 109 " pdb=" O3' DT J 109 " pdb=" P DG J 110 " ideal model delta sinusoidal sigma weight residual 220.00 70.17 149.83 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA ASP D 51 " pdb=" CB ASP D 51 " pdb=" CG ASP D 51 " pdb=" OD1 ASP D 51 " ideal model delta sinusoidal sigma weight residual -30.00 -87.31 57.31 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1760 0.032 - 0.063: 748 0.063 - 0.095: 196 0.095 - 0.126: 63 0.126 - 0.158: 17 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA LYS E 115 " pdb=" N LYS E 115 " pdb=" C LYS E 115 " pdb=" CB LYS E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA SER M 113 " pdb=" N SER M 113 " pdb=" C SER M 113 " pdb=" CB SER M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 2781 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 73 " 0.027 2.00e-02 2.50e+03 1.37e-02 5.16e+00 pdb=" N9 DA J 73 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 73 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 73 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 73 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA J 73 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 73 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DA J 73 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 73 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 23 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ARG F 23 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP F 24 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 91 " -0.025 2.00e-02 2.50e+03 1.37e-02 4.24e+00 pdb=" N1 DC I 91 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DC I 91 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC I 91 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC I 91 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 91 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 91 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC I 91 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 91 " -0.000 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2183 2.77 - 3.30: 13586 3.30 - 3.83: 30358 3.83 - 4.37: 36507 4.37 - 4.90: 54357 Nonbonded interactions: 136991 Sorted by model distance: nonbonded pdb=" OD2 ASP M 222 " pdb=" OG SER M 225 " model vdw 2.234 3.040 nonbonded pdb=" N GLU M 124 " pdb=" OE1 GLU M 124 " model vdw 2.249 3.120 nonbonded pdb=" N GLU N 124 " pdb=" OE1 GLU N 124 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLU G 91 " pdb=" OG SER N 180 " model vdw 2.262 3.040 nonbonded pdb=" O GLU M 162 " pdb=" OG1 THR M 165 " model vdw 2.407 3.040 ... (remaining 136986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.270 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17264 Z= 0.215 Angle : 0.729 7.251 24720 Z= 0.431 Chirality : 0.039 0.158 2784 Planarity : 0.005 0.067 1996 Dihedral : 25.375 174.322 7262 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.48 % Allowed : 11.46 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.24), residues: 1198 helix: 2.72 (0.22), residues: 532 sheet: 1.46 (0.34), residues: 226 loop : -0.13 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 86 TYR 0.021 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP M 196 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00521 (17260) covalent geometry : angle 0.72855 (24712) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.76345 ( 8) hydrogen bonds : bond 0.13506 ( 958) hydrogen bonds : angle 4.71220 ( 2387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.485 Fit side-chains REVERT: A 73 GLU cc_start: 0.6218 (tt0) cc_final: 0.6016 (tt0) REVERT: A 112 ILE cc_start: 0.6529 (mt) cc_final: 0.6325 (mp) REVERT: B 79 LYS cc_start: 0.7240 (mtmm) cc_final: 0.7016 (mttp) REVERT: B 91 LYS cc_start: 0.7413 (ttpm) cc_final: 0.7185 (ttpp) REVERT: B 93 GLN cc_start: 0.7455 (mt0) cc_final: 0.7242 (mt0) REVERT: C 24 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7237 (mm-40) REVERT: C 73 ASN cc_start: 0.6831 (m-40) cc_final: 0.6097 (t160) REVERT: M 30 MET cc_start: 0.7482 (ptp) cc_final: 0.7235 (ptm) REVERT: N 228 VAL cc_start: 0.9216 (t) cc_final: 0.8943 (t) outliers start: 5 outliers final: 0 residues processed: 202 average time/residue: 0.8111 time to fit residues: 176.1578 Evaluate side-chains 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 89 ASN D 84 ASN F 75 HIS F 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102087 restraints weight = 19201.461| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.69 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17264 Z= 0.261 Angle : 0.626 5.826 24720 Z= 0.366 Chirality : 0.040 0.149 2784 Planarity : 0.005 0.047 1996 Dihedral : 29.494 177.677 4906 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.24 % Allowed : 12.72 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.24), residues: 1198 helix: 2.34 (0.22), residues: 548 sheet: 1.45 (0.34), residues: 240 loop : -0.14 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 86 TYR 0.019 0.002 TYR H 42 PHE 0.014 0.002 PHE C 25 TRP 0.012 0.002 TRP M 185 HIS 0.006 0.002 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00613 (17260) covalent geometry : angle 0.62535 (24712) SS BOND : bond 0.00830 ( 4) SS BOND : angle 1.36541 ( 8) hydrogen bonds : bond 0.05557 ( 958) hydrogen bonds : angle 3.46439 ( 2387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.490 Fit side-chains REVERT: A 73 GLU cc_start: 0.8014 (tt0) cc_final: 0.7787 (tt0) REVERT: A 79 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8231 (tttp) REVERT: B 59 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8225 (tttp) REVERT: C 73 ASN cc_start: 0.7592 (m-40) cc_final: 0.6756 (t160) REVERT: D 47 GLN cc_start: 0.8423 (tt0) cc_final: 0.8062 (mt0) REVERT: E 120 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7323 (mmm) REVERT: F 84 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7638 (mmt) REVERT: G 15 LYS cc_start: 0.7280 (pttm) cc_final: 0.6588 (pmtt) REVERT: G 20 ARG cc_start: 0.8328 (ttm170) cc_final: 0.7991 (ttm170) REVERT: G 73 ASN cc_start: 0.7477 (t160) cc_final: 0.7257 (t0) REVERT: G 99 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7827 (mtm110) REVERT: H 62 MET cc_start: 0.8846 (mmm) cc_final: 0.8533 (mmm) REVERT: H 71 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: M 30 MET cc_start: 0.8073 (ptp) cc_final: 0.7870 (ptp) REVERT: M 52 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8439 (tp) REVERT: M 80 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7685 (mtp180) REVERT: M 98 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: M 102 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.8006 (t) REVERT: M 124 GLU cc_start: 0.8277 (pm20) cc_final: 0.8047 (pm20) REVERT: M 230 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.6581 (tpt) REVERT: N 231 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6640 (mm-30) outliers start: 44 outliers final: 17 residues processed: 195 average time/residue: 0.8720 time to fit residues: 182.4208 Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103915 restraints weight = 19358.927| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.69 r_work: 0.3104 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17264 Z= 0.191 Angle : 0.555 5.373 24720 Z= 0.330 Chirality : 0.036 0.137 2784 Planarity : 0.004 0.043 1996 Dihedral : 29.239 177.617 4906 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.56 % Allowed : 15.13 % Favored : 81.31 % 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: 2.50 (0.22), residues: 548 sheet: 1.37 (0.34), residues: 240 loop : -0.15 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.017 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.011 0.002 TRP M 60 HIS 0.005 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00439 (17260) covalent geometry : angle 0.55459 (24712) SS BOND : bond 0.00624 ( 4) SS BOND : angle 1.07215 ( 8) hydrogen bonds : bond 0.04504 ( 958) hydrogen bonds : angle 3.25071 ( 2387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.317 Fit side-chains REVERT: A 79 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8194 (tttp) REVERT: A 133 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: D 47 GLN cc_start: 0.8232 (tt0) cc_final: 0.7838 (mt0) REVERT: E 133 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: G 51 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7669 (tp) REVERT: G 73 ASN cc_start: 0.7434 (t0) cc_final: 0.7195 (t0) REVERT: G 99 ARG cc_start: 0.8368 (mpp-170) cc_final: 0.7898 (mtm110) REVERT: H 62 MET cc_start: 0.8833 (mmm) cc_final: 0.8537 (mmm) REVERT: M 30 MET cc_start: 0.8249 (ptp) cc_final: 0.7787 (ptp) REVERT: M 52 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8476 (tp) REVERT: M 98 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: M 102 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7905 (t) REVERT: M 124 GLU cc_start: 0.8343 (pm20) cc_final: 0.7899 (pm20) REVERT: M 230 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.6619 (tpt) REVERT: N 231 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6525 (mm-30) outliers start: 37 outliers final: 17 residues processed: 185 average time/residue: 0.7928 time to fit residues: 157.9283 Evaluate side-chains 173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105130 restraints weight = 19173.034| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.68 r_work: 0.3124 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17264 Z= 0.155 Angle : 0.535 5.260 24720 Z= 0.321 Chirality : 0.035 0.137 2784 Planarity : 0.004 0.058 1996 Dihedral : 29.226 177.543 4906 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.70 % Allowed : 16.67 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.24), residues: 1198 helix: 2.66 (0.22), residues: 550 sheet: 1.35 (0.34), residues: 240 loop : -0.14 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.016 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.010 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00346 (17260) covalent geometry : angle 0.53439 (24712) SS BOND : bond 0.00544 ( 4) SS BOND : angle 0.93928 ( 8) hydrogen bonds : bond 0.04066 ( 958) hydrogen bonds : angle 3.15772 ( 2387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.579 Fit side-chains REVERT: A 79 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8202 (tttp) REVERT: B 59 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8181 (tttp) REVERT: D 47 GLN cc_start: 0.8404 (tt0) cc_final: 0.8059 (mt0) REVERT: E 115 LYS cc_start: 0.8456 (mtmp) cc_final: 0.8179 (mttp) REVERT: E 133 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: F 84 MET cc_start: 0.7854 (mmp) cc_final: 0.7430 (mmt) REVERT: G 51 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7732 (tp) REVERT: G 73 ASN cc_start: 0.7428 (t0) cc_final: 0.7176 (t0) REVERT: G 90 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7893 (t70) REVERT: G 99 ARG cc_start: 0.8366 (mpp-170) cc_final: 0.7913 (mtm110) REVERT: H 62 MET cc_start: 0.8832 (mmm) cc_final: 0.8608 (mmm) REVERT: M 30 MET cc_start: 0.8283 (ptp) cc_final: 0.7811 (ptp) REVERT: M 52 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8446 (tp) REVERT: M 98 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: M 102 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7916 (t) REVERT: M 124 GLU cc_start: 0.8261 (pm20) cc_final: 0.7789 (pm20) REVERT: N 231 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6517 (mm-30) outliers start: 28 outliers final: 10 residues processed: 177 average time/residue: 0.8187 time to fit residues: 156.2421 Evaluate side-chains 185 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102655 restraints weight = 19190.597| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.69 r_work: 0.3090 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17264 Z= 0.215 Angle : 0.566 5.216 24720 Z= 0.336 Chirality : 0.037 0.145 2784 Planarity : 0.004 0.045 1996 Dihedral : 29.300 177.148 4906 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.14 % Allowed : 15.80 % Favored : 80.06 % 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: 2.02 (0.24), residues: 1198 helix: 2.56 (0.22), residues: 546 sheet: 1.18 (0.33), residues: 240 loop : -0.23 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 60 HIS 0.007 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00500 (17260) covalent geometry : angle 0.56544 (24712) SS BOND : bond 0.00679 ( 4) SS BOND : angle 1.33441 ( 8) hydrogen bonds : bond 0.04832 ( 958) hydrogen bonds : angle 3.21541 ( 2387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.463 Fit side-chains REVERT: A 79 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8064 (tttp) REVERT: A 133 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: B 59 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (tttp) REVERT: C 73 ASN cc_start: 0.7552 (m-40) cc_final: 0.6803 (t160) REVERT: D 47 GLN cc_start: 0.8425 (tt0) cc_final: 0.8090 (mt0) REVERT: E 115 LYS cc_start: 0.8467 (mtmp) cc_final: 0.8203 (mttp) REVERT: E 133 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: F 79 LYS cc_start: 0.8284 (mtpt) cc_final: 0.8050 (mtpt) REVERT: F 84 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7474 (mmt) REVERT: G 73 ASN cc_start: 0.7509 (t0) cc_final: 0.7265 (t0) REVERT: G 90 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.7912 (t70) REVERT: G 99 ARG cc_start: 0.8239 (mpp-170) cc_final: 0.7909 (mtm110) REVERT: H 62 MET cc_start: 0.8804 (mmm) cc_final: 0.8590 (mmm) REVERT: M 30 MET cc_start: 0.8310 (ptp) cc_final: 0.7703 (ptp) REVERT: M 52 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8457 (tp) REVERT: M 98 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: M 102 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7914 (t) REVERT: M 124 GLU cc_start: 0.8213 (pm20) cc_final: 0.7660 (pm20) REVERT: M 230 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.6800 (tpt) REVERT: N 124 GLU cc_start: 0.7866 (pm20) cc_final: 0.7645 (pm20) REVERT: N 231 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6618 (mm-30) outliers start: 43 outliers final: 24 residues processed: 193 average time/residue: 0.8115 time to fit residues: 168.5249 Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102652 restraints weight = 18879.017| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.64 r_work: 0.3059 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17264 Z= 0.229 Angle : 0.577 5.248 24720 Z= 0.341 Chirality : 0.038 0.144 2784 Planarity : 0.004 0.048 1996 Dihedral : 29.433 176.124 4906 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.82 % Allowed : 15.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1198 helix: 2.43 (0.22), residues: 546 sheet: 1.06 (0.33), residues: 238 loop : -0.35 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 191 TYR 0.014 0.002 TYR H 40 PHE 0.012 0.002 PHE C 25 TRP 0.017 0.002 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00535 (17260) covalent geometry : angle 0.57697 (24712) SS BOND : bond 0.00701 ( 4) SS BOND : angle 1.41534 ( 8) hydrogen bonds : bond 0.04842 ( 958) hydrogen bonds : angle 3.25445 ( 2387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.467 Fit side-chains REVERT: A 79 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8430 (tttp) REVERT: A 133 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: B 59 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8290 (tttp) REVERT: C 90 ASP cc_start: 0.8723 (t70) cc_final: 0.8372 (t0) REVERT: D 47 GLN cc_start: 0.8475 (tt0) cc_final: 0.8105 (mt0) REVERT: E 115 LYS cc_start: 0.8431 (mtmp) cc_final: 0.8186 (mttp) REVERT: E 133 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: G 73 ASN cc_start: 0.7584 (t0) cc_final: 0.7357 (t0) REVERT: G 90 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.7989 (t70) REVERT: G 99 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7999 (mtm110) REVERT: H 62 MET cc_start: 0.8800 (mmm) cc_final: 0.8599 (mmm) REVERT: M 52 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8560 (tp) REVERT: M 98 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: M 102 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7969 (t) REVERT: M 230 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.6820 (tpt) REVERT: N 124 GLU cc_start: 0.7872 (pm20) cc_final: 0.7632 (pm20) REVERT: N 230 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.6408 (tpp) REVERT: N 231 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6821 (mm-30) outliers start: 50 outliers final: 27 residues processed: 185 average time/residue: 0.7242 time to fit residues: 144.7028 Evaluate side-chains 204 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103832 restraints weight = 18930.999| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.63 r_work: 0.3074 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17264 Z= 0.186 Angle : 0.556 5.791 24720 Z= 0.331 Chirality : 0.036 0.146 2784 Planarity : 0.004 0.052 1996 Dihedral : 29.383 176.728 4906 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.85 % Allowed : 17.15 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.24), residues: 1198 helix: 2.58 (0.22), residues: 546 sheet: 1.05 (0.34), residues: 238 loop : -0.33 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 191 TYR 0.018 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.014 0.001 TRP M 60 HIS 0.005 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00429 (17260) covalent geometry : angle 0.55584 (24712) SS BOND : bond 0.00616 ( 4) SS BOND : angle 1.15741 ( 8) hydrogen bonds : bond 0.04403 ( 958) hydrogen bonds : angle 3.17580 ( 2387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.390 Fit side-chains REVERT: A 79 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8345 (tttp) REVERT: A 133 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: B 59 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8283 (tttp) REVERT: D 47 GLN cc_start: 0.8315 (tt0) cc_final: 0.7978 (mt0) REVERT: D 86 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7428 (mpt-90) REVERT: E 115 LYS cc_start: 0.8423 (mtmp) cc_final: 0.8182 (mttp) REVERT: E 133 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: G 51 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7730 (tt) REVERT: G 73 ASN cc_start: 0.7626 (t0) cc_final: 0.7387 (t0) REVERT: G 90 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.7947 (t70) REVERT: G 99 ARG cc_start: 0.8279 (mpp-170) cc_final: 0.7926 (mtm110) REVERT: H 62 MET cc_start: 0.8779 (mmm) cc_final: 0.8543 (mmm) REVERT: H 71 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: M 52 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8519 (tp) REVERT: M 89 ASP cc_start: 0.8116 (t70) cc_final: 0.7586 (m-30) REVERT: M 98 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: M 102 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7937 (t) REVERT: M 124 GLU cc_start: 0.8114 (pm20) cc_final: 0.7561 (pm20) REVERT: M 191 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8397 (ttp80) REVERT: N 124 GLU cc_start: 0.7874 (pm20) cc_final: 0.7481 (pm20) REVERT: N 230 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.6438 (tpp) REVERT: N 231 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6745 (mm-30) outliers start: 40 outliers final: 21 residues processed: 187 average time/residue: 0.7467 time to fit residues: 150.2283 Evaluate side-chains 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104425 restraints weight = 18887.094| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.63 r_work: 0.3082 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17264 Z= 0.161 Angle : 0.554 8.817 24720 Z= 0.330 Chirality : 0.035 0.146 2784 Planarity : 0.004 0.044 1996 Dihedral : 29.369 176.989 4906 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.28 % Allowed : 17.15 % Favored : 79.58 % 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: 2.04 (0.24), residues: 1198 helix: 2.66 (0.22), residues: 548 sheet: 1.07 (0.34), residues: 238 loop : -0.28 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.015 0.001 TYR H 42 PHE 0.008 0.001 PHE C 25 TRP 0.013 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00361 (17260) covalent geometry : angle 0.55351 (24712) SS BOND : bond 0.00570 ( 4) SS BOND : angle 1.00820 ( 8) hydrogen bonds : bond 0.04201 ( 958) hydrogen bonds : angle 3.14863 ( 2387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.450 Fit side-chains REVERT: A 79 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8348 (tttp) REVERT: A 133 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: B 59 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8279 (tttp) REVERT: D 47 GLN cc_start: 0.8312 (tt0) cc_final: 0.7964 (mt0) REVERT: E 115 LYS cc_start: 0.8407 (mtmp) cc_final: 0.8172 (mttp) REVERT: E 133 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: G 51 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7742 (tt) REVERT: G 73 ASN cc_start: 0.7600 (t0) cc_final: 0.7365 (t0) REVERT: G 90 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.7945 (t70) REVERT: G 99 ARG cc_start: 0.8283 (mpp-170) cc_final: 0.7936 (mtm110) REVERT: H 62 MET cc_start: 0.8810 (mmm) cc_final: 0.8574 (mmm) REVERT: H 71 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: M 52 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8508 (tp) REVERT: M 89 ASP cc_start: 0.8033 (t70) cc_final: 0.7532 (m-30) REVERT: M 98 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: M 102 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7928 (t) REVERT: M 230 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.6728 (tpt) REVERT: N 124 GLU cc_start: 0.7865 (pm20) cc_final: 0.7601 (pm20) REVERT: N 231 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6747 (mm-30) outliers start: 34 outliers final: 18 residues processed: 171 average time/residue: 0.7908 time to fit residues: 145.9419 Evaluate side-chains 188 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 92 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105023 restraints weight = 18953.152| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.63 r_work: 0.3094 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17264 Z= 0.163 Angle : 0.540 6.093 24720 Z= 0.323 Chirality : 0.035 0.138 2784 Planarity : 0.004 0.060 1996 Dihedral : 29.291 177.379 4906 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.37 % Allowed : 17.53 % Favored : 79.09 % 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: 2.69 (0.22), residues: 550 sheet: 1.10 (0.34), residues: 238 loop : -0.28 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.016 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.017 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00369 (17260) covalent geometry : angle 0.53945 (24712) SS BOND : bond 0.00541 ( 4) SS BOND : angle 0.97135 ( 8) hydrogen bonds : bond 0.04048 ( 958) hydrogen bonds : angle 3.08946 ( 2387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.404 Fit side-chains REVERT: A 68 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: A 79 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8337 (tttp) REVERT: A 133 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: B 59 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8308 (tttp) REVERT: D 47 GLN cc_start: 0.8312 (tt0) cc_final: 0.7951 (mt0) REVERT: E 115 LYS cc_start: 0.8400 (mtmp) cc_final: 0.8171 (mttp) REVERT: E 133 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: G 51 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7797 (tt) REVERT: G 90 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.7892 (t70) REVERT: H 62 MET cc_start: 0.8820 (mmm) cc_final: 0.8605 (mmm) REVERT: H 71 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: M 52 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8493 (tp) REVERT: M 98 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: M 102 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7919 (t) REVERT: M 124 GLU cc_start: 0.8156 (pm20) cc_final: 0.7618 (pm20) REVERT: M 191 ARG cc_start: 0.8693 (ttp-110) cc_final: 0.8412 (ttp80) REVERT: M 230 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.6857 (tpt) REVERT: N 124 GLU cc_start: 0.7879 (pm20) cc_final: 0.7611 (pm20) REVERT: N 231 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6763 (mm-30) outliers start: 35 outliers final: 16 residues processed: 180 average time/residue: 0.8272 time to fit residues: 159.8960 Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 108 optimal weight: 0.0070 chunk 141 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105681 restraints weight = 18926.165| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.63 r_work: 0.3100 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17264 Z= 0.145 Angle : 0.541 9.778 24720 Z= 0.323 Chirality : 0.034 0.137 2784 Planarity : 0.004 0.059 1996 Dihedral : 29.278 177.552 4906 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.99 % Allowed : 18.30 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1198 helix: 2.77 (0.22), residues: 550 sheet: 1.12 (0.34), residues: 238 loop : -0.26 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 191 TYR 0.016 0.001 TYR M 203 PHE 0.007 0.001 PHE A 67 TRP 0.016 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00320 (17260) covalent geometry : angle 0.54081 (24712) SS BOND : bond 0.00517 ( 4) SS BOND : angle 0.87368 ( 8) hydrogen bonds : bond 0.03885 ( 958) hydrogen bonds : angle 3.07016 ( 2387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.488 Fit side-chains REVERT: A 68 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: A 79 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8342 (tttp) REVERT: A 133 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: B 59 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (tttp) REVERT: D 47 GLN cc_start: 0.8301 (tt0) cc_final: 0.7931 (mt0) REVERT: E 115 LYS cc_start: 0.8387 (mtmp) cc_final: 0.8161 (mttp) REVERT: E 123 ASP cc_start: 0.8583 (m-30) cc_final: 0.8332 (m-30) REVERT: E 133 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: G 51 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7800 (tt) REVERT: G 90 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.7880 (t70) REVERT: H 62 MET cc_start: 0.8814 (mmm) cc_final: 0.8598 (mmm) REVERT: H 71 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: M 52 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8488 (tp) REVERT: M 89 ASP cc_start: 0.8019 (t70) cc_final: 0.7522 (m-30) REVERT: M 98 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: M 102 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7902 (t) REVERT: M 191 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8343 (ttp80) REVERT: M 230 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.6905 (tpt) REVERT: N 124 GLU cc_start: 0.7877 (pm20) cc_final: 0.7608 (pm20) REVERT: N 231 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6758 (mm-30) outliers start: 31 outliers final: 14 residues processed: 171 average time/residue: 0.7762 time to fit residues: 143.0618 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 23 MET Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 231 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.158891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106050 restraints weight = 18880.114| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.64 r_work: 0.3108 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17264 Z= 0.151 Angle : 0.532 6.354 24720 Z= 0.319 Chirality : 0.034 0.137 2784 Planarity : 0.004 0.059 1996 Dihedral : 29.211 177.655 4906 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.70 % Allowed : 18.50 % Favored : 78.81 % 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: 2.23 (0.25), residues: 1198 helix: 2.79 (0.22), residues: 550 sheet: 1.17 (0.34), residues: 240 loop : -0.18 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 191 TYR 0.019 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.019 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00338 (17260) covalent geometry : angle 0.53233 (24712) SS BOND : bond 0.00495 ( 4) SS BOND : angle 0.88874 ( 8) hydrogen bonds : bond 0.03826 ( 958) hydrogen bonds : angle 3.02951 ( 2387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6464.07 seconds wall clock time: 110 minutes 24.40 seconds (6624.40 seconds total)