Starting phenix.real_space_refine on Fri Jul 3 19:39:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfx_43193/07_2026/8vfx_43193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfx_43193/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vfx_43193/07_2026/8vfx_43193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfx_43193/07_2026/8vfx_43193.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfx_43193/07_2026/8vfx_43193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfx_43193/07_2026/8vfx_43193.cif" } 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-dev-6108/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: 2.69, per 1000 atoms: 0.17 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: 0.92 Conformation dependent library (CDL) restraints added in 428.2 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: 2.29 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: 2.75 Time building geometry restraints manager: 1.25 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: 21718 1.09 - 2.17: 1827 2.17 - 3.26: 734 3.26 - 4.34: 132 4.34 - 5.43: 17 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: 1.110 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.130 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:5.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 21.260 ------------------------------------------------------------------------------- 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 : 0.773 5.430 24436 Z= 0.664 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 0.77344 / 0.66 (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 : 0.298 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: 0.8006 (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: 0.8206 (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: 0.8306 (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: 0.8377 time to fit residues: 223.6931 Evaluate side-chains 174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.3738 r_free = 0.3738 target = 0.117422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078356 restraints weight = 23863.191| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.53 r_work: 0.2932 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1166 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= 0.157 Angle : 0.641 8.705 24436 Z= 0.376 Chirality : 0.045 0.233 2752 Planarity : 0.004 0.043 1988 Dihedral : 29.026 178.604 4892 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.45 % Allowed : 8.86 % 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: 2.18 (0.24), residues: 1198 helix: 2.60 (0.22), residues: 546 sheet: 1.07 (0.35), residues: 228 loop : 0.16 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 33 TYR 0.010 0.001 TYR G 57 PHE 0.008 0.001 PHE E 67 TRP 0.008 0.001 TRP M 259 HIS 0.007 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (17076) covalent geometry : angle 0.64145 / 0.38 (24428) SS BOND : bond 0.00571 / 0.29 ( 4) SS BOND : angle 0.71737 / 0.31 ( 8) hydrogen bonds : bond 0.04962 / 3.36 ( 939) hydrogen bonds : angle 3.79575 / 2.82 ( 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 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8706 (mtmt) REVERT: B 24 ASP cc_start: 0.7929 (t0) cc_final: 0.7645 (t0) REVERT: C 90 ASP cc_start: 0.9139 (t0) cc_final: 0.8915 (t70) REVERT: E 122 LYS cc_start: 0.9069 (pttt) cc_final: 0.8828 (pttt) REVERT: G 36 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8917 (mptt) REVERT: H 33 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8273 (mtt90) REVERT: H 34 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8305 (mttp) REVERT: H 36 SER cc_start: 0.9184 (p) cc_final: 0.8903 (p) REVERT: H 68 ASP cc_start: 0.9317 (t70) cc_final: 0.8751 (t0) REVERT: H 71 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: H 72 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8970 (mtm180) REVERT: M 33 SER cc_start: 0.8769 (m) cc_final: 0.8498 (p) REVERT: M 100 ASP cc_start: 0.9047 (p0) cc_final: 0.8812 (p0) REVERT: M 102 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9376 (t) REVERT: M 222 ASP cc_start: 0.8970 (t0) cc_final: 0.8468 (t0) REVERT: N 19 MET cc_start: 0.7268 (tpp) cc_final: 0.6850 (pmt) REVERT: N 20 ASP cc_start: 0.8823 (m-30) cc_final: 0.8590 (m-30) REVERT: N 31 HIS cc_start: 0.8454 (m-70) cc_final: 0.8227 (m-70) REVERT: N 49 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7819 (mtm-85) REVERT: N 152 GLN cc_start: 0.8925 (tt0) cc_final: 0.8667 (tt0) REVERT: N 191 ARG cc_start: 0.8737 (ttp-170) cc_final: 0.8499 (ttp80) REVERT: N 230 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7595 (tpt) outliers start: 15 outliers final: 5 residues processed: 193 average time/residue: 0.7353 time to fit residues: 152.6054 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 64 ASN M 46 GLN M 154 GLN N 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077323 restraints weight = 24187.691| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.53 r_work: 0.2911 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17080 Z= 0.169 Angle : 0.617 8.833 24436 Z= 0.358 Chirality : 0.044 0.247 2752 Planarity : 0.004 0.044 1988 Dihedral : 29.435 179.775 4892 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.64 % Allowed : 10.69 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1198 helix: 2.63 (0.22), residues: 546 sheet: 1.05 (0.34), residues: 228 loop : 0.15 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.011 0.001 TYR N 244 PHE 0.010 0.001 PHE E 67 TRP 0.009 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (17076) covalent geometry : angle 0.61700 / 0.36 (24428) SS BOND : bond 0.00440 / 0.22 ( 4) SS BOND : angle 0.95263 / 0.43 ( 8) hydrogen bonds : bond 0.04755 / 3.21 ( 939) hydrogen bonds : angle 3.54308 / 2.62 ( 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 197 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8058 (t0) cc_final: 0.7708 (t0) REVERT: B 88 TYR cc_start: 0.9128 (m-10) cc_final: 0.8915 (m-80) REVERT: C 91 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8756 (tp30) REVERT: C 94 ASN cc_start: 0.9345 (t0) cc_final: 0.9144 (t0) REVERT: E 122 LYS cc_start: 0.9056 (pttt) cc_final: 0.8829 (pttt) REVERT: G 36 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8906 (mptt) REVERT: H 34 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8313 (mttp) REVERT: H 36 SER cc_start: 0.9248 (p) cc_final: 0.8951 (p) REVERT: H 68 ASP cc_start: 0.9327 (t70) cc_final: 0.8758 (t0) REVERT: H 71 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: M 33 SER cc_start: 0.8781 (m) cc_final: 0.8513 (p) REVERT: M 100 ASP cc_start: 0.9028 (p0) cc_final: 0.8824 (p0) REVERT: M 102 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9294 (t) REVERT: M 222 ASP cc_start: 0.8960 (t0) cc_final: 0.8342 (t0) REVERT: N 19 MET cc_start: 0.7311 (tpp) cc_final: 0.6894 (pmt) REVERT: N 20 ASP cc_start: 0.8815 (m-30) cc_final: 0.8585 (m-30) REVERT: N 49 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7830 (mtm-85) REVERT: N 89 ASP cc_start: 0.8391 (m-30) cc_final: 0.8026 (p0) REVERT: N 191 ARG cc_start: 0.8723 (ttp-170) cc_final: 0.8511 (ttp80) outliers start: 17 outliers final: 5 residues processed: 186 average time/residue: 0.7611 time to fit residues: 151.9676 Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.117161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077815 restraints weight = 24063.306| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.52 r_work: 0.2920 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1623 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= 0.148 Angle : 0.605 8.481 24436 Z= 0.349 Chirality : 0.043 0.240 2752 Planarity : 0.004 0.036 1988 Dihedral : 29.555 179.941 4892 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.54 % Allowed : 12.04 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.24), residues: 1198 helix: 2.69 (0.22), residues: 546 sheet: 1.12 (0.35), residues: 228 loop : 0.13 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 37 TYR 0.010 0.001 TYR M 199 PHE 0.010 0.001 PHE E 67 TRP 0.008 0.001 TRP M 259 HIS 0.010 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (17076) covalent geometry : angle 0.60498 / 0.35 (24428) SS BOND : bond 0.00420 / 0.21 ( 4) SS BOND : angle 0.93005 / 0.41 ( 8) hydrogen bonds : bond 0.04340 / 2.92 ( 939) hydrogen bonds : angle 3.41860 / 2.52 ( 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 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.363 Fit side-chains REVERT: B 24 ASP cc_start: 0.8095 (t0) cc_final: 0.7837 (t0) REVERT: B 88 TYR cc_start: 0.9118 (m-10) cc_final: 0.8917 (m-80) REVERT: C 91 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8746 (tp30) REVERT: E 122 LYS cc_start: 0.9042 (pttt) cc_final: 0.8808 (pttt) REVERT: H 34 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8310 (mttp) REVERT: H 36 SER cc_start: 0.9274 (p) cc_final: 0.8983 (p) REVERT: H 68 ASP cc_start: 0.9326 (t70) cc_final: 0.8790 (t0) REVERT: H 71 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: M 37 ARG cc_start: 0.8824 (ttm-80) cc_final: 0.8603 (ttm-80) REVERT: M 102 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9321 (t) REVERT: M 222 ASP cc_start: 0.8880 (t0) cc_final: 0.8233 (t0) REVERT: N 19 MET cc_start: 0.7274 (tpp) cc_final: 0.6855 (pmt) REVERT: N 20 ASP cc_start: 0.8851 (m-30) cc_final: 0.8634 (m-30) REVERT: N 49 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7921 (mtm-85) REVERT: N 89 ASP cc_start: 0.8366 (m-30) cc_final: 0.8022 (p0) REVERT: N 191 ARG cc_start: 0.8718 (ttp-170) cc_final: 0.8492 (ttp80) outliers start: 16 outliers final: 5 residues processed: 179 average time/residue: 0.7618 time to fit residues: 146.4032 Evaluate side-chains 174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 126 optimal weight: 9.9990 chunk 81 optimal weight: 0.0070 chunk 97 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN N 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079151 restraints weight = 24110.403| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.49 r_work: 0.2948 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17080 Z= 0.129 Angle : 0.584 9.247 24436 Z= 0.338 Chirality : 0.042 0.237 2752 Planarity : 0.004 0.041 1988 Dihedral : 29.578 179.692 4892 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.93 % Allowed : 12.14 % Favored : 85.93 % 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: 2.42 (0.24), residues: 1198 helix: 2.82 (0.22), residues: 546 sheet: 1.05 (0.34), residues: 240 loop : 0.30 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 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 0.00233 / 0.13 (17076) covalent geometry : angle 0.58383 / 0.34 (24428) SS BOND : bond 0.00361 / 0.18 ( 4) SS BOND : angle 0.77365 / 0.35 ( 8) hydrogen bonds : bond 0.04021 / 2.69 ( 939) hydrogen bonds : angle 3.28126 / 2.42 ( 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 198 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8992 (mttt) REVERT: B 24 ASP cc_start: 0.8097 (t0) cc_final: 0.7848 (t0) REVERT: E 122 LYS cc_start: 0.9027 (pttt) cc_final: 0.8781 (pttt) REVERT: G 36 LYS cc_start: 0.8899 (mptt) cc_final: 0.8679 (mptt) REVERT: G 74 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8737 (mtpp) REVERT: G 91 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: H 34 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8291 (mttp) REVERT: H 36 SER cc_start: 0.9254 (p) cc_final: 0.8966 (p) REVERT: H 68 ASP cc_start: 0.9309 (t70) cc_final: 0.8826 (t0) REVERT: H 71 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: H 86 ARG cc_start: 0.8558 (mtt90) cc_final: 0.8087 (mtp-110) REVERT: M 33 SER cc_start: 0.8765 (m) cc_final: 0.8520 (p) REVERT: M 102 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9247 (t) REVERT: M 222 ASP cc_start: 0.8851 (t0) cc_final: 0.8220 (t0) REVERT: N 19 MET cc_start: 0.7278 (tpp) cc_final: 0.7016 (pmt) REVERT: N 20 ASP cc_start: 0.8843 (m-30) cc_final: 0.8632 (m-30) REVERT: N 89 ASP cc_start: 0.8361 (m-30) cc_final: 0.8036 (p0) REVERT: N 191 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.8501 (ttp80) REVERT: N 230 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7514 (tpp) outliers start: 20 outliers final: 5 residues processed: 185 average time/residue: 0.7708 time to fit residues: 153.0127 Evaluate side-chains 175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 110 ASN Chi-restraints excluded: chain G residue 74 LYS 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 N residue 22 LYS Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.2980 chunk 135 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN F 93 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 = 0.3744 r_free = 0.3744 target = 0.117774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.078749 restraints weight = 24047.264| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.51 r_work: 0.2938 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1877 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= 0.135 Angle : 0.586 9.364 24436 Z= 0.337 Chirality : 0.042 0.239 2752 Planarity : 0.004 0.042 1988 Dihedral : 29.609 179.887 4892 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 2.43 (0.24), residues: 1198 helix: 2.82 (0.22), residues: 546 sheet: 1.04 (0.34), residues: 240 loop : 0.33 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 49 TYR 0.011 0.001 TYR M 199 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 0.00254 / 0.14 (17076) covalent geometry : angle 0.58606 / 0.34 (24428) SS BOND : bond 0.00376 / 0.19 ( 4) SS BOND : angle 0.84767 / 0.38 ( 8) hydrogen bonds : bond 0.04003 / 2.67 ( 939) hydrogen bonds : angle 3.23415 / 2.38 ( 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 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.325 Fit side-chains REVERT: A 115 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8975 (mttt) REVERT: B 24 ASP cc_start: 0.8141 (t0) cc_final: 0.7893 (t0) REVERT: C 91 GLU cc_start: 0.9032 (tp30) cc_final: 0.8780 (tp30) REVERT: E 122 LYS cc_start: 0.9015 (pttt) cc_final: 0.8778 (pttt) REVERT: G 91 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: H 34 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8277 (mttp) REVERT: H 36 SER cc_start: 0.9262 (p) cc_final: 0.8965 (p) REVERT: H 68 ASP cc_start: 0.9333 (t70) cc_final: 0.8828 (t0) REVERT: H 71 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: H 86 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8075 (mtp-110) REVERT: M 23 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8203 (mmm) REVERT: M 102 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9271 (t) REVERT: M 222 ASP cc_start: 0.8864 (t0) cc_final: 0.8231 (t0) REVERT: N 19 MET cc_start: 0.7288 (tpp) cc_final: 0.7030 (pmt) REVERT: N 20 ASP cc_start: 0.8816 (m-30) cc_final: 0.8578 (m-30) REVERT: N 89 ASP cc_start: 0.8330 (m-30) cc_final: 0.7944 (p0) REVERT: N 191 ARG cc_start: 0.8770 (ttp-170) cc_final: 0.8546 (ttp80) REVERT: N 230 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7515 (tpp) outliers start: 21 outliers final: 9 residues processed: 174 average time/residue: 0.7620 time to fit residues: 142.2439 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 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 38 VAL Chi-restraints excluded: chain N residue 230 MET 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: 0.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078854 restraints weight = 23954.889| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.54 r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17080 Z= 0.132 Angle : 0.583 10.356 24436 Z= 0.335 Chirality : 0.042 0.238 2752 Planarity : 0.004 0.036 1988 Dihedral : 29.622 179.854 4892 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.45 % Allowed : 12.91 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.24), residues: 1198 helix: 2.83 (0.22), residues: 546 sheet: 1.36 (0.35), residues: 214 loop : 0.21 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 49 TYR 0.011 0.001 TYR M 199 PHE 0.009 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 0.00245 / 0.13 (17076) covalent geometry : angle 0.58259 / 0.33 (24428) SS BOND : bond 0.00382 / 0.19 ( 4) SS BOND : angle 0.82304 / 0.37 ( 8) hydrogen bonds : bond 0.03921 / 2.61 ( 939) hydrogen bonds : angle 3.20983 / 2.36 ( 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 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.387 Fit side-chains REVERT: A 115 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8960 (mttt) REVERT: B 24 ASP cc_start: 0.8152 (t0) cc_final: 0.7909 (t0) REVERT: C 91 GLU cc_start: 0.9031 (tp30) cc_final: 0.8775 (tp30) REVERT: E 122 LYS cc_start: 0.9013 (pttt) cc_final: 0.8751 (pttt) REVERT: G 91 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: H 34 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8280 (mttp) REVERT: H 36 SER cc_start: 0.9266 (p) cc_final: 0.8968 (p) REVERT: H 68 ASP cc_start: 0.9327 (t70) cc_final: 0.8821 (t0) REVERT: H 71 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: H 86 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8073 (mtp-110) REVERT: M 23 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: M 102 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9270 (t) REVERT: M 222 ASP cc_start: 0.8869 (t0) cc_final: 0.8226 (t0) REVERT: N 19 MET cc_start: 0.7284 (tpp) cc_final: 0.7032 (pmt) REVERT: N 20 ASP cc_start: 0.8808 (m-30) cc_final: 0.8563 (m-30) REVERT: N 89 ASP cc_start: 0.8322 (m-30) cc_final: 0.7947 (p0) REVERT: N 191 ARG cc_start: 0.8777 (ttp-170) cc_final: 0.8559 (ttp80) REVERT: N 230 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7516 (tpp) outliers start: 15 outliers final: 6 residues processed: 174 average time/residue: 0.7703 time to fit residues: 143.5307 Evaluate side-chains 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain G residue 91 GLU 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 221 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN M 31 HIS M 152 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078738 restraints weight = 24092.356| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.51 r_work: 0.2937 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1957 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= 0.138 Angle : 0.587 11.083 24436 Z= 0.335 Chirality : 0.042 0.239 2752 Planarity : 0.004 0.036 1988 Dihedral : 29.639 179.921 4890 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.93 % Allowed : 12.62 % 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: 2.42 (0.24), residues: 1198 helix: 2.82 (0.22), residues: 546 sheet: 1.34 (0.36), residues: 214 loop : 0.20 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.011 0.001 TYR M 199 PHE 0.009 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 0.00265 / 0.14 (17076) covalent geometry : angle 0.58649 / 0.34 (24428) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 0.96098 / 0.43 ( 8) hydrogen bonds : bond 0.03947 / 2.62 ( 939) hydrogen bonds : angle 3.20236 / 2.36 ( 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 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.310 Fit side-chains REVERT: A 115 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8953 (mttt) REVERT: B 24 ASP cc_start: 0.8165 (t0) cc_final: 0.7927 (t0) REVERT: C 91 GLU cc_start: 0.9040 (tp30) cc_final: 0.8796 (tp30) REVERT: E 122 LYS cc_start: 0.9030 (pttt) cc_final: 0.8768 (pttt) REVERT: G 91 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: H 34 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8305 (mttp) REVERT: H 36 SER cc_start: 0.9277 (p) cc_final: 0.8982 (p) REVERT: H 68 ASP cc_start: 0.9330 (t70) cc_final: 0.8826 (t0) REVERT: H 71 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: H 86 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8062 (mtp-110) REVERT: M 23 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8314 (mmm) REVERT: M 102 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9282 (t) REVERT: M 222 ASP cc_start: 0.8865 (t0) cc_final: 0.8229 (t0) REVERT: N 19 MET cc_start: 0.7256 (tpp) cc_final: 0.6985 (pmt) REVERT: N 20 ASP cc_start: 0.8802 (m-30) cc_final: 0.8562 (m-30) REVERT: N 89 ASP cc_start: 0.8334 (m-30) cc_final: 0.7956 (p0) REVERT: N 191 ARG cc_start: 0.8752 (ttp-170) cc_final: 0.8542 (ttp80) REVERT: N 230 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.7517 (tpp) outliers start: 20 outliers final: 7 residues processed: 172 average time/residue: 0.7760 time to fit residues: 143.1329 Evaluate side-chains 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 79 LYS 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 23 MET 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 38 VAL Chi-restraints excluded: chain N residue 222 ASP 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: 0.8980 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN M 31 HIS M 152 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.117228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077819 restraints weight = 24031.853| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.53 r_work: 0.2921 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17080 Z= 0.153 Angle : 0.591 11.119 24436 Z= 0.337 Chirality : 0.042 0.241 2752 Planarity : 0.004 0.036 1988 Dihedral : 29.683 179.766 4890 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.64 % Allowed : 13.20 % 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: 2.37 (0.24), residues: 1198 helix: 2.77 (0.22), residues: 546 sheet: 1.31 (0.36), residues: 214 loop : 0.17 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.014 0.001 TYR M 199 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (17076) covalent geometry : angle 0.59064 / 0.34 (24428) SS BOND : bond 0.00430 / 0.22 ( 4) SS BOND : angle 1.00269 / 0.46 ( 8) hydrogen bonds : bond 0.04052 / 2.69 ( 939) hydrogen bonds : angle 3.21788 / 2.37 ( 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 182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.360 Fit side-chains REVERT: A 115 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8962 (mttt) REVERT: B 24 ASP cc_start: 0.8169 (t0) cc_final: 0.7939 (t0) REVERT: C 91 GLU cc_start: 0.9027 (tp30) cc_final: 0.8764 (tp30) REVERT: C 110 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.9048 (t0) REVERT: E 122 LYS cc_start: 0.9037 (pttt) cc_final: 0.8802 (pttt) REVERT: G 91 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: H 33 ARG cc_start: 0.8509 (mtt90) cc_final: 0.8295 (mtt90) REVERT: H 34 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8325 (mttp) REVERT: H 36 SER cc_start: 0.9290 (p) cc_final: 0.8997 (p) REVERT: H 68 ASP cc_start: 0.9313 (t70) cc_final: 0.8818 (t0) REVERT: H 71 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8394 (mt-10) REVERT: H 86 ARG cc_start: 0.8547 (mtt90) cc_final: 0.8100 (mtp-110) REVERT: M 102 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9264 (t) REVERT: M 222 ASP cc_start: 0.8882 (t0) cc_final: 0.8257 (t0) REVERT: N 19 MET cc_start: 0.7293 (tpp) cc_final: 0.7001 (pmt) REVERT: N 20 ASP cc_start: 0.8766 (m-30) cc_final: 0.8511 (m-30) REVERT: N 89 ASP cc_start: 0.8356 (m-30) cc_final: 0.8003 (p0) REVERT: N 191 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8550 (ttp80) REVERT: N 230 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7551 (tpp) outliers start: 17 outliers final: 6 residues processed: 170 average time/residue: 0.7815 time to fit residues: 142.5412 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 : 0.445 ------------------------------------------------------------------------------- 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 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 23 MET 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 38 VAL 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: 0.8980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN M 31 HIS M 152 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078152 restraints weight = 23959.082| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.53 r_work: 0.2926 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2003 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= 0.138 Angle : 0.590 12.022 24436 Z= 0.336 Chirality : 0.042 0.239 2752 Planarity : 0.004 0.049 1988 Dihedral : 29.684 179.724 4890 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.35 % Allowed : 13.68 % Favored : 84.97 % 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: 2.39 (0.24), residues: 1198 helix: 2.79 (0.22), residues: 546 sheet: 1.32 (0.36), residues: 214 loop : 0.18 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 37 TYR 0.014 0.001 TYR B 88 PHE 0.009 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 0.00264 / 0.14 (17076) covalent geometry : angle 0.59037 / 0.34 (24428) SS BOND : bond 0.00394 / 0.20 ( 4) SS BOND : angle 0.74221 / 0.35 ( 8) hydrogen bonds : bond 0.03985 / 2.64 ( 939) hydrogen bonds : angle 3.20297 / 2.35 ( 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: 14 poor density : 165 time to evaluate : 0.283 Fit side-chains REVERT: A 115 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8959 (mttt) REVERT: B 24 ASP cc_start: 0.8194 (t0) cc_final: 0.7967 (t0) REVERT: C 91 GLU cc_start: 0.9024 (tp30) cc_final: 0.8760 (tp30) REVERT: C 110 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.9045 (t0) REVERT: E 122 LYS cc_start: 0.9022 (pttt) cc_final: 0.8786 (pttt) REVERT: G 91 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: H 33 ARG cc_start: 0.8504 (mtt90) cc_final: 0.8251 (mtt90) REVERT: H 34 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8316 (mttp) REVERT: H 36 SER cc_start: 0.9287 (p) cc_final: 0.8993 (p) REVERT: H 68 ASP cc_start: 0.9314 (t70) cc_final: 0.8820 (t0) REVERT: H 71 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: H 86 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8094 (mtp-110) REVERT: M 102 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9261 (t) REVERT: M 222 ASP cc_start: 0.8876 (t0) cc_final: 0.8254 (t0) REVERT: N 19 MET cc_start: 0.7284 (tpp) cc_final: 0.7013 (pmt) REVERT: N 20 ASP cc_start: 0.8761 (m-30) cc_final: 0.8526 (m-30) REVERT: N 89 ASP cc_start: 0.8357 (m-30) cc_final: 0.8001 (p0) REVERT: N 191 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8533 (ttp80) REVERT: N 230 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7525 (tpp) outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 0.7607 time to fit residues: 137.7273 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 : 0.336 ------------------------------------------------------------------------------- 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 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 23 MET 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 38 VAL Chi-restraints excluded: chain N residue 222 ASP 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: 0.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN M 31 HIS M 152 GLN N 31 HIS N 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078185 restraints weight = 23957.555| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.52 r_work: 0.2928 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2025 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= 0.138 Angle : 0.587 11.106 24436 Z= 0.335 Chirality : 0.042 0.238 2752 Planarity : 0.004 0.067 1988 Dihedral : 29.685 179.741 4890 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.45 % Allowed : 13.68 % Favored : 84.87 % 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: 2.41 (0.24), residues: 1198 helix: 2.81 (0.22), residues: 546 sheet: 1.37 (0.36), residues: 214 loop : 0.17 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 49 TYR 0.017 0.001 TYR B 88 PHE 0.009 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 0.00266 / 0.14 (17076) covalent geometry : angle 0.58681 / 0.34 (24428) SS BOND : bond 0.00395 / 0.20 ( 4) SS BOND : angle 0.68550 / 0.33 ( 8) hydrogen bonds : bond 0.03936 / 2.60 ( 939) hydrogen bonds : angle 3.19430 / 2.34 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.40 seconds wall clock time: 102 minutes 6.95 seconds (6126.95 seconds total)