Starting phenix.real_space_refine on Thu Aug 6 15:01:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfx_43193/08_2026/8vfx_43193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfx_43193/08_2026/8vfx_43193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vfx_43193/08_2026/8vfx_43193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfx_43193/08_2026/8vfx_43193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vfx_43193/08_2026/8vfx_43193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfx_43193/08_2026/8vfx_43193.map" } resolution = 2.65 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 316 5.49 5 S 32 5.16 5 C 9172 2.51 5 N 2922 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16124 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: "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 Chain: "I" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3239 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "J" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3239 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Time building chain proxies: 3.19, per 1000 atoms: 0.20 Number of scatterers: 16124 At special positions: 0 Unit cell: (133.65, 141.075, 128.7, 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 316 15.00 O 3682 8.00 N 2922 7.00 C 9172 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=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 338.1 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 48.1% alpha, 21.9% beta 158 base pairs and 285 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 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: 3.652A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 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: 4.264A 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 104 through 124 removed outlier: 3.640A 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 removed outlier: 3.557A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.974A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.678A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.619A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.260A 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 Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.668A 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 211 through 214 removed outlier: 3.592A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' 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: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.548A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.466A 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: 6.636A 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: 6.863A 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: 7.170A 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 removed outlier: 3.923A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.167A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.486A 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: 6.167A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.554A 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: 6.576A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.859A 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: 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: 3.664A 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: 3.707A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.466A 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: 3.707A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (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: 6.617A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.760A 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: 4.025A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 384 hydrogen bonds 768 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 285 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3477 1.33 - 1.45: 4881 1.45 - 1.57: 8036 1.57 - 1.69: 630 1.69 - 1.81: 52 Bond restraints: 17076 Sorted by residual: bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.45e+01 bond pdb=" C1' DT J 53 " pdb=" N1 DT J 53 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.45e+01 bond pdb=" C1' DC I 162 " pdb=" N1 DC I 162 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.17e+01 bond pdb=" C1' DC J 78 " pdb=" N1 DC J 78 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" C3' DT I 51 " pdb=" C2' DT I 51 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.81e+01 ... (remaining 17071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 21660 1.09 - 2.17: 1880 2.17 - 3.26: 739 3.26 - 4.34: 129 4.34 - 5.43: 20 Bond angle restraints: 24428 Sorted by residual: angle pdb=" N3 DT I 123 " pdb=" C4 DT I 123 " pdb=" O4 DT I 123 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4' DA I 79 " pdb=" C1' DA I 79 " pdb=" N9 DA I 79 " ideal model delta sigma weight residual 108.00 111.14 -3.14 7.00e-01 2.04e+00 2.01e+01 angle pdb=" N3 DT J 75 " pdb=" C4 DT J 75 " pdb=" O4 DT J 75 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J 121 " pdb=" C4 DT J 121 " pdb=" O4 DT J 121 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 163 " pdb=" C4 DT I 163 " pdb=" O4 DT I 163 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 ... (remaining 24423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 8130 34.85 - 69.71: 1385 69.71 - 104.56: 11 104.56 - 139.41: 0 139.41 - 174.27: 4 Dihedral angle restraints: 9530 sinusoidal: 5984 harmonic: 3546 Sorted by residual: dihedral pdb=" C4' DT J 126 " pdb=" C3' DT J 126 " pdb=" O3' DT J 126 " pdb=" P DG J 127 " ideal model delta sinusoidal sigma weight residual 220.00 45.73 174.27 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 92 " pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " pdb=" P DC J 93 " ideal model delta sinusoidal sigma weight residual 220.00 51.47 168.53 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA J 106 " pdb=" C3' DA J 106 " pdb=" O3' DA J 106 " pdb=" P DT J 107 " ideal model delta sinusoidal sigma weight residual 220.00 53.64 166.36 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 9527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2023 0.046 - 0.092: 349 0.092 - 0.138: 234 0.138 - 0.184: 144 0.184 - 0.230: 2 Chirality restraints: 2752 Sorted by residual: chirality pdb=" C3' DG I 122 " pdb=" C4' DG I 122 " pdb=" O3' DG I 122 " pdb=" C2' DG I 122 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' DA I 126 " pdb=" C4' DA I 126 " pdb=" O3' DA I 126 " pdb=" C2' DA I 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" C3' DT J 11 " pdb=" C4' DT J 11 " pdb=" O3' DT J 11 " pdb=" C2' DT J 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 2749 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 132 " 0.024 2.00e-02 2.50e+03 1.13e-02 3.52e+00 pdb=" N9 DA I 132 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 132 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 132 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 132 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 132 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 132 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 132 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 132 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 132 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 132 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 162 " -0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 DC I 162 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DC I 162 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 162 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 162 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 162 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 162 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 162 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DC I 162 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 89 " -0.024 2.00e-02 2.50e+03 1.18e-02 3.51e+00 pdb=" N1 DT I 89 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 89 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 89 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 89 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 89 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 89 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 89 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 89 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 89 " 0.002 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 161 2.63 - 3.20: 13135 3.20 - 3.77: 28189 3.77 - 4.33: 39477 4.33 - 4.90: 57714 Nonbonded interactions: 138676 Sorted by model distance: nonbonded pdb=" OG SER H 32 " pdb=" OP1 DC I 145 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.334 3.120 nonbonded pdb=" OE1 GLU G 91 " pdb=" OG SER N 180 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.395 3.040 nonbonded pdb=" NH2 ARG M 80 " pdb=" OD2 ASP M 101 " model vdw 2.395 3.120 ... (remaining 138671 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.260 Find NCS groups from input model: 0.140 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:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 17080 Z= 0.554 Angle : 0.780 5.430 24436 Z= 0.669 Chirality : 0.057 0.230 2752 Planarity : 0.004 0.035 1988 Dihedral : 24.467 174.268 7246 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.39 % Allowed : 1.64 % Favored : 97.98 % 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: 2.56 (0.22), residues: 536 sheet: 0.84 (0.33), residues: 248 loop : 0.11 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 49 TYR 0.012 0.001 TYR M 199 PHE 0.006 0.001 PHE E 84 TRP 0.009 0.001 TRP M 259 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.55 (17076) covalent geometry : angle 0.77957 / 0.67 (24428) SS BOND : bond 0.00288 / 0.15 ( 4) SS BOND : angle 0.62868 / 0.33 ( 8) hydrogen bonds : bond 0.12648 / 8.58 ( 939) hydrogen bonds : angle 4.82521 / 3.57 ( 2358) *********************** 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 251 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 0.391 Fit side-chains REVERT: A 64 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7577 (mtpt) REVERT: B 31 LYS cc_start: 0.8291 (tttt) cc_final: 0.7896 (tttm) REVERT: B 79 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8131 (mtpt) REVERT: C 99 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7855 (mmm160) REVERT: C 114 VAL cc_start: 0.8971 (t) cc_final: 0.8762 (p) REVERT: D 76 GLU cc_start: 0.8883 (tp30) cc_final: 0.8540 (tp30) REVERT: E 122 LYS cc_start: 0.8484 (pttt) cc_final: 0.8157 (pttt) REVERT: E 129 ARG cc_start: 0.8438 (tpt90) cc_final: 0.8180 (tpt-90) REVERT: F 79 LYS cc_start: 0.8437 (mttt) cc_final: 0.8188 (mtpm) REVERT: F 91 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8390 (tttp) REVERT: G 36 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8439 (mptt) REVERT: G 95 LYS cc_start: 0.8933 (tttm) cc_final: 0.8691 (tptp) REVERT: H 34 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7877 (mttp) REVERT: H 68 ASP cc_start: 0.9090 (t70) cc_final: 0.8192 (t0) REVERT: H 72 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8436 (mtm180) REVERT: H 87 SER cc_start: 0.8756 (m) cc_final: 0.8169 (p) REVERT: H 105 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8378 (mm-30) REVERT: H 116 LYS cc_start: 0.8511 (tttt) cc_final: 0.8307 (tttp) REVERT: H 120 LYS cc_start: 0.8610 (tttm) cc_final: 0.8112 (tttm) REVERT: M 30 MET cc_start: 0.8958 (ptp) cc_final: 0.8391 (ptm) REVERT: M 31 HIS cc_start: 0.8152 (m90) cc_final: 0.6894 (m-70) REVERT: M 33 SER cc_start: 0.8400 (m) cc_final: 0.7958 (p) REVERT: M 36 GLU cc_start: 0.8542 (pt0) cc_final: 0.8310 (pt0) REVERT: M 46 GLN cc_start: 0.7751 (tt0) cc_final: 0.7417 (mt0) REVERT: M 124 GLU cc_start: 0.8129 (pt0) cc_final: 0.7851 (pm20) REVERT: M 154 GLN cc_start: 0.8047 (tp40) cc_final: 0.7783 (mm110) REVERT: M 222 ASP cc_start: 0.8579 (t0) cc_final: 0.7879 (t0) REVERT: M 231 GLU cc_start: 0.8225 (tp30) cc_final: 0.7859 (tp30) REVERT: M 238 GLU cc_start: 0.8356 (pt0) cc_final: 0.7943 (pm20) REVERT: N 19 MET cc_start: 0.7012 (tpp) cc_final: 0.6723 (pmt) REVERT: N 30 MET cc_start: 0.8885 (ptp) cc_final: 0.7916 (ptp) REVERT: N 49 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7504 (mtm-85) REVERT: N 89 ASP cc_start: 0.8334 (m-30) cc_final: 0.7888 (p0) REVERT: N 112 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7542 (mm-30) REVERT: N 152 GLN cc_start: 0.8664 (tt0) cc_final: 0.8237 (tt0) REVERT: N 159 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8412 (mt-10) REVERT: N 191 ARG cc_start: 0.8824 (ttp-170) cc_final: 0.8482 (ttp80) outliers start: 4 outliers final: 1 residues processed: 250 average time/residue: 0.8003 time to fit residues: 214.0559 Evaluate side-chains 173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN D 63 ASN F 93 GLN H 63 ASN H 67 ASN N 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.117365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078484 restraints weight = 23869.611| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.47 r_work: 0.2939 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17080 Z= 0.155 Angle : 0.651 8.642 24436 Z= 0.379 Chirality : 0.045 0.252 2752 Planarity : 0.004 0.043 1988 Dihedral : 28.937 179.488 4892 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.35 % Allowed : 8.96 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1198 helix: 2.60 (0.22), residues: 546 sheet: 1.08 (0.35), residues: 228 loop : 0.18 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 33 TYR 0.010 0.001 TYR M 203 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP M 259 HIS 0.010 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (17076) covalent geometry : angle 0.65144 / 0.38 (24428) SS BOND : bond 0.00533 / 0.27 ( 4) SS BOND : angle 0.76354 / 0.33 ( 8) hydrogen bonds : bond 0.04958 / 3.35 ( 939) hydrogen bonds : angle 3.81289 / 2.83 ( 2358) *********************** 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 200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8677 (mtmt) REVERT: B 24 ASP cc_start: 0.7924 (t0) cc_final: 0.7643 (t0) REVERT: C 90 ASP cc_start: 0.9136 (t0) cc_final: 0.8914 (t70) REVERT: D 76 GLU cc_start: 0.8903 (tp30) cc_final: 0.8626 (tp30) REVERT: E 122 LYS cc_start: 0.9057 (pttt) cc_final: 0.8808 (pttt) REVERT: G 36 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8903 (mptt) REVERT: H 34 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8299 (mttp) REVERT: H 36 SER cc_start: 0.9185 (p) cc_final: 0.8897 (p) REVERT: H 68 ASP cc_start: 0.9342 (t70) cc_final: 0.8765 (t0) REVERT: H 71 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: H 72 ARG cc_start: 0.9161 (mtt180) cc_final: 0.8959 (mtm180) REVERT: M 33 SER cc_start: 0.8762 (m) cc_final: 0.8493 (p) REVERT: M 46 GLN cc_start: 0.7902 (tt0) cc_final: 0.7699 (mt0) REVERT: M 100 ASP cc_start: 0.9040 (p0) cc_final: 0.8807 (p0) REVERT: M 102 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9374 (t) REVERT: M 222 ASP cc_start: 0.8962 (t0) cc_final: 0.8472 (t0) REVERT: N 19 MET cc_start: 0.7245 (tpp) cc_final: 0.6817 (pmt) REVERT: N 20 ASP cc_start: 0.8822 (m-30) cc_final: 0.8463 (m-30) REVERT: N 31 HIS cc_start: 0.8428 (m-70) cc_final: 0.8216 (m-70) REVERT: N 49 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7764 (mtm-85) REVERT: N 152 GLN cc_start: 0.8921 (tt0) cc_final: 0.8672 (tt0) REVERT: N 191 ARG cc_start: 0.8720 (ttp-170) cc_final: 0.8482 (ttp80) REVERT: N 230 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7598 (tpt) outliers start: 14 outliers final: 5 residues processed: 192 average time/residue: 0.7437 time to fit residues: 153.6098 Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 265 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN B 64 ASN M 154 GLN N 152 GLN N 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.117585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078451 restraints weight = 24242.003| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.53 r_work: 0.2933 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17080 Z= 0.144 Angle : 0.615 9.378 24436 Z= 0.356 Chirality : 0.044 0.264 2752 Planarity : 0.004 0.037 1988 Dihedral : 29.263 178.374 4892 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.64 % Allowed : 10.79 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1198 helix: 2.75 (0.22), residues: 546 sheet: 1.11 (0.35), residues: 228 loop : 0.21 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 37 TYR 0.010 0.001 TYR M 199 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP M 259 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (17076) covalent geometry : angle 0.61446 / 0.36 (24428) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 0.81082 / 0.37 ( 8) hydrogen bonds : bond 0.04504 / 3.03 ( 939) hydrogen bonds : angle 3.51559 / 2.60 ( 2358) *********************** 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 196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.449 Fit side-chains REVERT: B 24 ASP cc_start: 0.8015 (t0) cc_final: 0.7659 (t0) REVERT: B 88 TYR cc_start: 0.9130 (m-10) cc_final: 0.8921 (m-80) REVERT: C 90 ASP cc_start: 0.9148 (t0) cc_final: 0.8946 (t70) REVERT: C 91 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8753 (tp30) REVERT: D 76 GLU cc_start: 0.8904 (tp30) cc_final: 0.8704 (tp30) REVERT: E 122 LYS cc_start: 0.9056 (pttt) cc_final: 0.8821 (pttt) REVERT: G 91 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: H 34 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8285 (mttp) REVERT: H 36 SER cc_start: 0.9232 (p) cc_final: 0.8949 (p) REVERT: H 68 ASP cc_start: 0.9330 (t70) cc_final: 0.8794 (t0) REVERT: H 71 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: M 33 SER cc_start: 0.8776 (m) cc_final: 0.8518 (p) REVERT: M 46 GLN cc_start: 0.7963 (tt0) cc_final: 0.7760 (mt0) REVERT: M 100 ASP cc_start: 0.9031 (p0) cc_final: 0.8828 (p0) REVERT: M 102 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9291 (t) REVERT: M 222 ASP cc_start: 0.8957 (t0) cc_final: 0.8345 (t0) REVERT: N 19 MET cc_start: 0.7280 (tpp) cc_final: 0.6881 (pmt) REVERT: N 20 ASP cc_start: 0.8830 (m-30) cc_final: 0.8600 (m-30) REVERT: N 89 ASP cc_start: 0.8384 (m-30) cc_final: 0.8019 (p0) REVERT: N 191 ARG cc_start: 0.8722 (ttp-170) cc_final: 0.8510 (ttp80) outliers start: 17 outliers final: 3 residues processed: 186 average time/residue: 0.7561 time to fit residues: 150.9999 Evaluate side-chains 175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 145 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076486 restraints weight = 24013.790| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.50 r_work: 0.2897 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17080 Z= 0.189 Angle : 0.641 8.867 24436 Z= 0.361 Chirality : 0.045 0.266 2752 Planarity : 0.004 0.037 1988 Dihedral : 29.575 179.494 4892 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 11.37 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1198 helix: 2.61 (0.22), residues: 548 sheet: 0.95 (0.33), residues: 240 loop : 0.21 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 37 TYR 0.012 0.002 TYR M 199 PHE 0.009 0.001 PHE A 67 TRP 0.010 0.001 TRP M 259 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17076) covalent geometry : angle 0.64053 / 0.36 (24428) SS BOND : bond 0.00466 / 0.24 ( 4) SS BOND : angle 0.92998 / 0.44 ( 8) hydrogen bonds : bond 0.04791 / 3.22 ( 939) hydrogen bonds : angle 3.45631 / 2.55 ( 2358) *********************** 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 190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.450 Fit side-chains REVERT: B 24 ASP cc_start: 0.8151 (t0) cc_final: 0.7892 (t0) REVERT: C 91 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (tp30) REVERT: D 33 ARG cc_start: 0.8555 (ptp-170) cc_final: 0.8044 (ptm-80) REVERT: D 76 GLU cc_start: 0.8948 (tp30) cc_final: 0.8687 (tp30) REVERT: E 122 LYS cc_start: 0.9039 (pttt) cc_final: 0.8802 (pttt) REVERT: G 36 LYS cc_start: 0.8883 (mptt) cc_final: 0.8657 (mptt) REVERT: G 74 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8853 (mtpp) REVERT: G 91 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: H 34 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8288 (mttp) REVERT: H 36 SER cc_start: 0.9277 (p) cc_final: 0.8979 (p) REVERT: H 68 ASP cc_start: 0.9330 (t70) cc_final: 0.8753 (t0) REVERT: H 71 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: M 37 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8609 (ttm-80) REVERT: M 46 GLN cc_start: 0.8055 (tt0) cc_final: 0.7851 (mt0) REVERT: M 102 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9312 (t) REVERT: M 222 ASP cc_start: 0.8870 (t0) cc_final: 0.8220 (t0) REVERT: N 19 MET cc_start: 0.7253 (tpp) cc_final: 0.6856 (pmt) REVERT: N 20 ASP cc_start: 0.8812 (m-30) cc_final: 0.8575 (m-30) REVERT: N 37 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8269 (ttm-80) REVERT: N 191 ARG cc_start: 0.8742 (ttp-170) cc_final: 0.8502 (ttp80) outliers start: 21 outliers final: 6 residues processed: 177 average time/residue: 0.8001 time to fit residues: 151.6971 Evaluate side-chains 173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.077464 restraints weight = 23987.191| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.50 r_work: 0.2912 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17080 Z= 0.146 Angle : 0.630 10.999 24436 Z= 0.355 Chirality : 0.044 0.262 2752 Planarity : 0.004 0.046 1988 Dihedral : 29.592 179.531 4892 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.93 % Allowed : 11.75 % Favored : 86.32 % 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: 2.25 (0.24), residues: 1198 helix: 2.65 (0.22), residues: 548 sheet: 0.97 (0.34), residues: 240 loop : 0.27 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 191 TYR 0.012 0.001 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP M 259 HIS 0.005 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (17076) covalent geometry : angle 0.63019 / 0.36 (24428) SS BOND : bond 0.00482 / 0.24 ( 4) SS BOND : angle 0.93545 / 0.42 ( 8) hydrogen bonds : bond 0.04463 / 2.99 ( 939) hydrogen bonds : angle 3.41472 / 2.51 ( 2358) *********************** 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 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.292 Fit side-chains REVERT: A 79 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8718 (ttmt) REVERT: A 115 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9003 (mttt) REVERT: B 24 ASP cc_start: 0.8122 (t0) cc_final: 0.7869 (t0) REVERT: B 88 TYR cc_start: 0.9126 (m-10) cc_final: 0.8855 (m-80) REVERT: C 91 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8736 (tp30) REVERT: E 122 LYS cc_start: 0.9029 (pttt) cc_final: 0.8791 (pttt) REVERT: G 74 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8853 (mtpp) REVERT: G 91 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: H 34 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8273 (mttp) REVERT: H 36 SER cc_start: 0.9299 (p) cc_final: 0.8998 (p) REVERT: H 68 ASP cc_start: 0.9321 (t70) cc_final: 0.8749 (t0) REVERT: H 71 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: M 102 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9329 (t) REVERT: M 222 ASP cc_start: 0.8863 (t0) cc_final: 0.8214 (t0) REVERT: N 19 MET cc_start: 0.7242 (tpp) cc_final: 0.6852 (pmt) REVERT: N 20 ASP cc_start: 0.8822 (m-30) cc_final: 0.8599 (m-30) REVERT: N 37 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8255 (ttm-80) REVERT: N 191 ARG cc_start: 0.8742 (ttp-170) cc_final: 0.8522 (ttp80) outliers start: 20 outliers final: 9 residues processed: 179 average time/residue: 0.7476 time to fit residues: 143.8060 Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 125 GLN M 46 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.115463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.076529 restraints weight = 23963.539| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.46 r_work: 0.2895 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17080 Z= 0.181 Angle : 0.635 8.590 24436 Z= 0.356 Chirality : 0.045 0.264 2752 Planarity : 0.004 0.042 1988 Dihedral : 29.726 179.984 4892 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 12.14 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1198 helix: 2.59 (0.22), residues: 548 sheet: 0.96 (0.34), residues: 240 loop : 0.25 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 191 TYR 0.011 0.001 TYR M 199 PHE 0.009 0.001 PHE A 67 TRP 0.010 0.001 TRP M 259 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (17076) covalent geometry : angle 0.63519 / 0.36 (24428) SS BOND : bond 0.00443 / 0.23 ( 4) SS BOND : angle 0.96108 / 0.44 ( 8) hydrogen bonds : bond 0.04514 / 3.02 ( 939) hydrogen bonds : angle 3.36926 / 2.48 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.446 Fit side-chains REVERT: A 79 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8742 (ttmt) REVERT: A 115 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8990 (mttt) REVERT: B 24 ASP cc_start: 0.8207 (t0) cc_final: 0.7953 (t0) REVERT: C 91 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8754 (tp30) REVERT: D 33 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8077 (ptp-170) REVERT: E 122 LYS cc_start: 0.9040 (pttt) cc_final: 0.8800 (pttt) REVERT: G 36 LYS cc_start: 0.8862 (mptt) cc_final: 0.8647 (mptt) REVERT: G 74 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8835 (mtpp) REVERT: G 91 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: H 34 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8295 (mttp) REVERT: H 36 SER cc_start: 0.9310 (p) cc_final: 0.9015 (p) REVERT: H 68 ASP cc_start: 0.9317 (t70) cc_final: 0.8700 (t0) REVERT: H 71 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: M 37 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8483 (ttm-80) REVERT: M 102 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9280 (t) REVERT: M 222 ASP cc_start: 0.8874 (t0) cc_final: 0.8245 (t0) REVERT: N 19 MET cc_start: 0.7263 (tpp) cc_final: 0.7002 (pmt) REVERT: N 37 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8325 (ttm-80) REVERT: N 222 ASP cc_start: 0.8435 (t0) cc_final: 0.8224 (t70) outliers start: 21 outliers final: 7 residues processed: 178 average time/residue: 0.7203 time to fit residues: 137.7391 Evaluate side-chains 177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 103 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN M 31 HIS M 152 GLN N 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.116149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.076995 restraints weight = 23860.824| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.49 r_work: 0.2904 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17080 Z= 0.145 Angle : 0.623 11.815 24436 Z= 0.350 Chirality : 0.044 0.261 2752 Planarity : 0.004 0.090 1988 Dihedral : 29.729 179.980 4890 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 12.14 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.24), residues: 1198 helix: 2.64 (0.22), residues: 548 sheet: 0.95 (0.34), residues: 240 loop : 0.28 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.011 0.001 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (17076) covalent geometry : angle 0.62317 / 0.35 (24428) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 1.02523 / 0.46 ( 8) hydrogen bonds : bond 0.04263 / 2.85 ( 939) hydrogen bonds : angle 3.33841 / 2.45 ( 2358) *********************** 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 188 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.426 Fit side-chains REVERT: A 115 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8989 (mttt) REVERT: B 24 ASP cc_start: 0.8195 (t0) cc_final: 0.7945 (t0) REVERT: C 91 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8748 (tp30) REVERT: E 122 LYS cc_start: 0.9013 (pttt) cc_final: 0.8775 (pttt) REVERT: G 74 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8839 (mtpp) REVERT: H 34 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8284 (mttp) REVERT: H 36 SER cc_start: 0.9299 (p) cc_final: 0.9008 (p) REVERT: H 68 ASP cc_start: 0.9317 (t70) cc_final: 0.8757 (t0) REVERT: H 71 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: M 102 THR cc_start: 0.9532 (OUTLIER) cc_final: 0.9290 (t) REVERT: M 222 ASP cc_start: 0.8867 (t0) cc_final: 0.8235 (t0) REVERT: N 19 MET cc_start: 0.7262 (tpp) cc_final: 0.7002 (pmt) REVERT: N 95 ASN cc_start: 0.8754 (m-40) cc_final: 0.8481 (m-40) REVERT: N 222 ASP cc_start: 0.8409 (t0) cc_final: 0.8197 (t70) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.7323 time to fit residues: 138.6557 Evaluate side-chains 177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 40 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN M 31 HIS M 152 GLN N 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077311 restraints weight = 24031.789| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.50 r_work: 0.2910 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17080 Z= 0.137 Angle : 0.625 12.421 24436 Z= 0.350 Chirality : 0.044 0.260 2752 Planarity : 0.004 0.060 1988 Dihedral : 29.716 179.868 4890 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 12.43 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.24), residues: 1198 helix: 2.67 (0.22), residues: 548 sheet: 0.93 (0.34), residues: 240 loop : 0.28 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.014 0.001 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (17076) covalent geometry : angle 0.62453 / 0.35 (24428) SS BOND : bond 0.00410 / 0.21 ( 4) SS BOND : angle 1.06168 / 0.47 ( 8) hydrogen bonds : bond 0.04147 / 2.77 ( 939) hydrogen bonds : angle 3.31441 / 2.44 ( 2358) *********************** 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 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.336 Fit side-chains REVERT: A 115 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8978 (mttt) REVERT: B 24 ASP cc_start: 0.8193 (t0) cc_final: 0.7944 (t0) REVERT: C 91 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8737 (tp30) REVERT: C 110 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.9042 (t0) REVERT: E 122 LYS cc_start: 0.9013 (pttt) cc_final: 0.8776 (pttt) REVERT: G 74 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8838 (mtpp) REVERT: H 34 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8277 (mttp) REVERT: H 36 SER cc_start: 0.9291 (p) cc_final: 0.9003 (p) REVERT: H 68 ASP cc_start: 0.9317 (t70) cc_final: 0.8797 (t0) REVERT: H 71 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: M 102 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9275 (t) REVERT: M 222 ASP cc_start: 0.8868 (t0) cc_final: 0.8231 (t0) REVERT: N 19 MET cc_start: 0.7266 (tpp) cc_final: 0.7003 (pmt) REVERT: N 222 ASP cc_start: 0.8417 (t0) cc_final: 0.8203 (t70) REVERT: N 230 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.7531 (tpp) outliers start: 18 outliers final: 9 residues processed: 171 average time/residue: 0.7693 time to fit residues: 140.7987 Evaluate side-chains 177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN F 93 GLN M 31 HIS M 152 GLN N 31 HIS N 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077305 restraints weight = 23994.268| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.53 r_work: 0.2910 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 17080 Z= 0.131 Angle : 0.623 13.599 24436 Z= 0.349 Chirality : 0.043 0.259 2752 Planarity : 0.004 0.037 1988 Dihedral : 29.701 179.771 4890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 13.01 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.24), residues: 1198 helix: 2.69 (0.22), residues: 548 sheet: 0.92 (0.34), residues: 240 loop : 0.31 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.021 0.001 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.006 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (17076) covalent geometry : angle 0.62245 / 0.35 (24428) SS BOND : bond 0.00352 / 0.18 ( 4) SS BOND : angle 1.22361 / 0.53 ( 8) hydrogen bonds : bond 0.04078 / 2.72 ( 939) hydrogen bonds : angle 3.29869 / 2.42 ( 2358) *********************** 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 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.438 Fit side-chains REVERT: A 115 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8972 (mttt) REVERT: B 24 ASP cc_start: 0.8192 (t0) cc_final: 0.7943 (t0) REVERT: B 88 TYR cc_start: 0.9244 (m-10) cc_final: 0.8878 (m-80) REVERT: C 91 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8754 (tp30) REVERT: C 110 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.9049 (t0) REVERT: E 122 LYS cc_start: 0.9008 (pttt) cc_final: 0.8768 (pttt) REVERT: G 74 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8849 (mtpp) REVERT: H 34 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8275 (mttp) REVERT: H 36 SER cc_start: 0.9289 (p) cc_final: 0.8998 (p) REVERT: H 68 ASP cc_start: 0.9328 (t70) cc_final: 0.8756 (t0) REVERT: H 71 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: M 102 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.9275 (t) REVERT: M 222 ASP cc_start: 0.8876 (t0) cc_final: 0.8222 (t0) REVERT: N 19 MET cc_start: 0.7267 (tpp) cc_final: 0.6998 (pmt) REVERT: N 222 ASP cc_start: 0.8411 (t0) cc_final: 0.8189 (t70) REVERT: N 230 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.7541 (tpp) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.7512 time to fit residues: 138.9251 Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN M 31 HIS M 152 GLN N 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077612 restraints weight = 23922.092| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.53 r_work: 0.2918 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17080 Z= 0.127 Angle : 0.616 12.925 24436 Z= 0.346 Chirality : 0.043 0.258 2752 Planarity : 0.004 0.064 1988 Dihedral : 29.677 179.643 4890 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 13.29 % Favored : 85.45 % 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: 2.31 (0.24), residues: 1198 helix: 2.73 (0.22), residues: 548 sheet: 0.90 (0.34), residues: 240 loop : 0.33 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 191 TYR 0.009 0.001 TYR N 244 PHE 0.010 0.001 PHE E 67 TRP 0.006 0.001 TRP M 259 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (17076) covalent geometry : angle 0.61588 / 0.35 (24428) SS BOND : bond 0.00380 / 0.19 ( 4) SS BOND : angle 1.31015 / 0.56 ( 8) hydrogen bonds : bond 0.04011 / 2.67 ( 939) hydrogen bonds : angle 3.27410 / 2.41 ( 2358) ********************** 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 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.379 Fit side-chains REVERT: A 115 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8982 (mttt) REVERT: B 24 ASP cc_start: 0.8177 (t0) cc_final: 0.7937 (t0) REVERT: B 88 TYR cc_start: 0.9253 (m-10) cc_final: 0.8881 (m-80) REVERT: C 91 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (tp30) REVERT: E 122 LYS cc_start: 0.9027 (pttt) cc_final: 0.8793 (pttt) REVERT: G 74 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8840 (mtpp) REVERT: H 34 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8306 (mttp) REVERT: H 36 SER cc_start: 0.9285 (p) cc_final: 0.9008 (p) REVERT: H 68 ASP cc_start: 0.9307 (t70) cc_final: 0.8777 (t0) REVERT: H 71 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: M 102 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9268 (t) REVERT: M 222 ASP cc_start: 0.8874 (t0) cc_final: 0.8264 (t0) REVERT: N 19 MET cc_start: 0.7277 (tpp) cc_final: 0.7011 (pmt) REVERT: N 20 ASP cc_start: 0.8781 (m-30) cc_final: 0.8547 (m-30) REVERT: N 222 ASP cc_start: 0.8395 (t0) cc_final: 0.8194 (t70) REVERT: N 230 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7538 (tpp) outliers start: 13 outliers final: 7 residues processed: 171 average time/residue: 0.7929 time to fit residues: 145.7070 Evaluate side-chains 175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN M 31 HIS M 152 GLN N 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.117451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078099 restraints weight = 23962.547| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.53 r_work: 0.2930 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17080 Z= 0.131 Angle : 0.604 12.226 24436 Z= 0.341 Chirality : 0.042 0.257 2752 Planarity : 0.004 0.039 1988 Dihedral : 29.593 179.396 4890 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.45 % Allowed : 13.39 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1198 helix: 2.77 (0.22), residues: 548 sheet: 1.18 (0.35), residues: 214 loop : 0.18 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 191 TYR 0.009 0.001 TYR M 199 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP M 259 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (17076) covalent geometry : angle 0.60433 / 0.34 (24428) SS BOND : bond 0.00308 / 0.16 ( 4) SS BOND : angle 0.84858 / 0.38 ( 8) hydrogen bonds : bond 0.03916 / 2.59 ( 939) hydrogen bonds : angle 3.21378 / 2.36 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5794.85 seconds wall clock time: 98 minutes 57.64 seconds (5937.64 seconds total)