Starting phenix.real_space_refine on Fri Sep 11 20:37:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pp_77743/09_2026/36pp_77743.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pp_77743/09_2026/36pp_77743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36pp_77743/09_2026/36pp_77743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pp_77743/09_2026/36pp_77743.map" model { file = "/net/cci-nas-00/data/ceres_data/36pp_77743/09_2026/36pp_77743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pp_77743/09_2026/36pp_77743.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 97 5.49 5 S 78 5.16 5 C 6833 2.51 5 N 1936 2.21 5 O 2381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11325 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1357 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 23, 'rna3p_pyr': 16} Link IDs: {'rna2p': 23, 'rna3p': 39} Chain: "C" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 481 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "I" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Time building chain proxies: 2.33, per 1000 atoms: 0.21 Number of scatterers: 11325 At special positions: 0 Unit cell: (95.76, 114, 144.78, 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 78 16.00 P 97 15.00 O 2381 8.00 N 1936 7.00 C 6833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.88 Conformation dependent library (CDL) restraints added in 447.4 milliseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 18 sheets defined 42.1% alpha, 36.4% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.744A pdb=" N ASP D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.574A pdb=" N ASP E 23 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 70 through 82 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.726A pdb=" N ASP E 91 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 120 removed outlier: 6.149A pdb=" N ASP E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'F' and resid 18 through 23 removed outlier: 4.439A pdb=" N LEU F 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP F 23 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 86 through 93 removed outlier: 3.549A pdb=" N ASP F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 117 through 120 removed outlier: 6.585A pdb=" N ASP F 120 " --> pdb=" O LYS F 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 117 through 120' Processing helix chain 'F' and resid 158 through 173 removed outlier: 3.903A pdb=" N MET F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 42 through 57 Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 86 through 93 removed outlier: 3.770A pdb=" N ARG G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 117 through 120 removed outlier: 6.592A pdb=" N ASP G 120 " --> pdb=" O LYS G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.639A pdb=" N MET G 164 " --> pdb=" O GLU G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.585A pdb=" N ASP H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.593A pdb=" N SER H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 70 through 83 removed outlier: 4.054A pdb=" N LEU H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 93 removed outlier: 4.154A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 120 removed outlier: 6.671A pdb=" N ASP H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 158 through 173 removed outlier: 3.732A pdb=" N MET H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 23 removed outlier: 4.609A pdb=" N LEU I 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP I 23 " --> pdb=" O THR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 42 through 57 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 86 through 93 removed outlier: 4.526A pdb=" N ARG I 92 " --> pdb=" O LYS I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 117 through 120 removed outlier: 6.412A pdb=" N ASP I 120 " --> pdb=" O LYS I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.330A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.330A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN D 5 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.831A pdb=" N ALA D 132 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.421A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.421A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN E 5 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.268A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.268A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN F 5 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.169A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.169A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN G 5 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.174A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.174A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU H 3 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU H 192 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN H 5 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.120A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.120A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN I 5 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 14 through 15 509 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.21 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: 2091 1.33 - 1.45: 3175 1.45 - 1.57: 6152 1.57 - 1.69: 191 1.69 - 1.81: 132 Bond restraints: 11741 Sorted by residual: bond pdb=" C3' DA B 26 " pdb=" C2' DA B 26 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" P DT B 37 " pdb=" O5' DT B 37 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.03e+01 bond pdb=" C3' DT B 29 " pdb=" C2' DT B 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DA B 23 " pdb=" C2' DA B 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 bond pdb=" C3' DC C 37 " pdb=" C2' DC C 37 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 ... (remaining 11736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15568 1.58 - 3.16: 622 3.16 - 4.74: 64 4.74 - 6.32: 22 6.32 - 7.90: 11 Bond angle restraints: 16287 Sorted by residual: angle pdb=" C3' G A 78 " pdb=" O3' G A 78 " pdb=" P U A 79 " ideal model delta sigma weight residual 119.70 126.21 -6.51 1.20e+00 6.94e-01 2.94e+01 angle pdb=" N1 U A 55 " pdb=" C2 U A 55 " pdb=" O2 U A 55 " ideal model delta sigma weight residual 122.80 126.53 -3.73 7.00e-01 2.04e+00 2.84e+01 angle pdb=" O2 U A 55 " pdb=" C2 U A 55 " pdb=" N3 U A 55 " ideal model delta sigma weight residual 122.20 118.57 3.63 7.00e-01 2.04e+00 2.68e+01 angle pdb=" C1' U A 55 " pdb=" N1 U A 55 " pdb=" C2 U A 55 " ideal model delta sigma weight residual 117.70 123.88 -6.18 1.20e+00 6.94e-01 2.65e+01 angle pdb=" O5' G A 32 " pdb=" C5' G A 32 " pdb=" C4' G A 32 " ideal model delta sigma weight residual 109.40 113.36 -3.96 8.00e-01 1.56e+00 2.45e+01 ... (remaining 16282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 6855 35.98 - 71.96: 282 71.96 - 107.94: 11 107.94 - 143.92: 0 143.92 - 179.90: 5 Dihedral angle restraints: 7153 sinusoidal: 3757 harmonic: 3396 Sorted by residual: dihedral pdb=" O4' U A 30 " pdb=" C1' U A 30 " pdb=" N1 U A 30 " pdb=" C2 U A 30 " ideal model delta sinusoidal sigma weight residual 232.00 52.10 179.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 55 " pdb=" C1' U A 55 " pdb=" N1 U A 55 " pdb=" C2 U A 55 " ideal model delta sinusoidal sigma weight residual 232.00 70.47 161.53 1 1.70e+01 3.46e-03 6.47e+01 dihedral pdb=" O4' U A 80 " pdb=" C1' U A 80 " pdb=" N1 U A 80 " pdb=" C2 U A 80 " ideal model delta sinusoidal sigma weight residual -160.00 -78.06 -81.94 1 1.50e+01 4.44e-03 3.67e+01 ... (remaining 7150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1782 0.119 - 0.237: 85 0.237 - 0.356: 1 0.356 - 0.474: 0 0.474 - 0.593: 5 Chirality restraints: 1873 Sorted by residual: chirality pdb=" P DA B 16 " pdb=" OP1 DA B 16 " pdb=" OP2 DA B 16 " pdb=" O5' DA B 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" P DG C 32 " pdb=" OP1 DG C 32 " pdb=" OP2 DG C 32 " pdb=" O5' DG C 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" P DC C 34 " pdb=" OP1 DC C 34 " pdb=" OP2 DC C 34 " pdb=" O5' DC C 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 1870 not shown) Planarity restraints: 1717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 57 " 0.039 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 U A 57 " -0.044 2.00e-02 2.50e+03 pdb=" C2 U A 57 " -0.006 2.00e-02 2.50e+03 pdb=" O2 U A 57 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 57 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U A 57 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U A 57 " 0.014 2.00e-02 2.50e+03 pdb=" C5 U A 57 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 133 " 0.238 9.50e-02 1.11e+02 1.07e-01 7.00e+00 pdb=" NE ARG I 133 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG I 133 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 133 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 133 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 47 " -0.034 2.00e-02 2.50e+03 1.71e-02 6.56e+00 pdb=" N1 U A 47 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U A 47 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U A 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A 47 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A 47 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 47 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U A 47 " 0.011 2.00e-02 2.50e+03 ... (remaining 1714 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 4111 2.93 - 3.42: 10266 3.42 - 3.91: 18607 3.91 - 4.41: 21239 4.41 - 4.90: 34929 Nonbonded interactions: 89152 Sorted by model distance: nonbonded pdb=" OP1 G A 73 " pdb=" NH2 ARG D 181 " model vdw 2.434 3.120 nonbonded pdb=" O3' DG C 32 " pdb=" C5' DG C 33 " model vdw 2.532 2.752 nonbonded pdb=" O4' A A 37 " pdb=" NH2 ARG I 133 " model vdw 2.540 3.120 nonbonded pdb=" O5' A A 81 " pdb=" O4' A A 81 " model vdw 2.570 2.432 nonbonded pdb=" N1 G A 31 " pdb=" C4 G A 31 " model vdw 2.591 2.672 ... (remaining 89147 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.080 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.810 Find NCS groups from input model: 0.170 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.004 0.041 11741 Z= 0.289 Angle : 0.718 7.902 16287 Z= 0.550 Chirality : 0.060 0.593 1873 Planarity : 0.005 0.107 1717 Dihedral : 17.004 179.905 4957 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.55 % Favored : 98.36 % Rotamer: Outliers : 0.10 % Allowed : 0.87 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.62 (0.23), residues: 1158 helix: 0.77 (0.25), residues: 414 sheet: 0.98 (0.32), residues: 258 loop : -0.08 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 133 TYR 0.010 0.001 TYR D 59 PHE 0.010 0.001 PHE D 14 TRP 0.005 0.001 TRP D 178 HIS 0.003 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.29 (11741) covalent geometry : angle 0.71760 / 0.55 (16287) hydrogen bonds : bond 0.15148 / 15.82 ( 517) hydrogen bonds : angle 7.66488 / 9.69 ( 1513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 9 THR cc_start: 0.7704 (m) cc_final: 0.7383 (p) REVERT: D 128 LYS cc_start: 0.7606 (ttmt) cc_final: 0.7350 (tptt) REVERT: D 181 ARG cc_start: 0.8161 (ttt90) cc_final: 0.7911 (ttt180) REVERT: E 117 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7647 (mmtm) REVERT: F 1 MET cc_start: 0.8522 (mtm) cc_final: 0.8321 (mtm) REVERT: F 85 LYS cc_start: 0.8662 (mttt) cc_final: 0.8300 (mtmm) REVERT: F 88 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8621 (mmmm) REVERT: F 164 MET cc_start: 0.8527 (ttp) cc_final: 0.8299 (tpt) REVERT: I 137 TYR cc_start: 0.6740 (m-80) cc_final: 0.6392 (m-80) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1202 time to fit residues: 40.8800 Evaluate side-chains 159 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123437 restraints weight = 12644.825| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.71 r_work: 0.2917 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11741 Z= 0.181 Angle : 0.607 6.946 16287 Z= 0.343 Chirality : 0.048 0.361 1873 Planarity : 0.005 0.036 1717 Dihedral : 20.465 178.733 2611 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.13 % Allowed : 6.59 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.88 (0.24), residues: 1158 helix: 1.22 (0.25), residues: 438 sheet: 0.91 (0.32), residues: 258 loop : -0.11 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 133 TYR 0.018 0.002 TYR D 60 PHE 0.016 0.002 PHE D 152 TRP 0.004 0.001 TRP E 144 HIS 0.008 0.002 HIS F 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (11741) covalent geometry : angle 0.60745 / 0.34 (16287) hydrogen bonds : bond 0.04309 / 4.55 ( 517) hydrogen bonds : angle 5.74831 / 7.43 ( 1513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASN cc_start: 0.8446 (p0) cc_final: 0.8074 (p0) REVERT: D 128 LYS cc_start: 0.7349 (ttmt) cc_final: 0.6724 (tptt) REVERT: D 181 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7481 (mtp180) REVERT: E 117 LYS cc_start: 0.7429 (mtmm) cc_final: 0.7110 (mmtm) REVERT: E 153 ASP cc_start: 0.8314 (t0) cc_final: 0.8102 (t70) REVERT: F 85 LYS cc_start: 0.8218 (mttt) cc_final: 0.7755 (mtmm) REVERT: F 88 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8516 (mmmm) REVERT: F 164 MET cc_start: 0.7972 (ttp) cc_final: 0.7755 (tpt) REVERT: G 95 MET cc_start: 0.8621 (ptm) cc_final: 0.8399 (ptm) REVERT: H 103 MET cc_start: 0.8762 (ttt) cc_final: 0.8514 (ttt) REVERT: H 143 ASP cc_start: 0.8489 (t0) cc_final: 0.8096 (t0) REVERT: I 114 GLU cc_start: 0.6282 (tp30) cc_final: 0.6038 (mt-10) REVERT: I 115 LEU cc_start: 0.7422 (tt) cc_final: 0.7208 (tt) REVERT: I 135 MET cc_start: 0.8401 (mmm) cc_final: 0.8164 (mmt) REVERT: I 137 TYR cc_start: 0.6264 (m-80) cc_final: 0.6013 (m-80) outliers start: 22 outliers final: 10 residues processed: 186 average time/residue: 0.0963 time to fit residues: 25.7423 Evaluate side-chains 169 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122189 restraints weight = 12621.739| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.65 r_work: 0.3055 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11741 Z= 0.163 Angle : 0.561 6.496 16287 Z= 0.318 Chirality : 0.047 0.377 1873 Planarity : 0.004 0.040 1717 Dihedral : 20.442 178.463 2611 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.94 % Allowed : 8.72 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.95 (0.24), residues: 1158 helix: 1.38 (0.25), residues: 438 sheet: 0.79 (0.33), residues: 258 loop : -0.09 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 133 TYR 0.025 0.002 TYR D 60 PHE 0.014 0.002 PHE D 14 TRP 0.004 0.001 TRP D 144 HIS 0.004 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (11741) covalent geometry : angle 0.56108 / 0.32 (16287) hydrogen bonds : bond 0.03655 / 3.86 ( 517) hydrogen bonds : angle 5.30913 / 6.91 ( 1513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 111 ASN cc_start: 0.8415 (p0) cc_final: 0.8104 (p0) REVERT: D 128 LYS cc_start: 0.7433 (ttmt) cc_final: 0.6791 (tptt) REVERT: D 181 ARG cc_start: 0.8208 (ttt90) cc_final: 0.7614 (mtp180) REVERT: E 117 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7250 (mmtm) REVERT: E 153 ASP cc_start: 0.8421 (t0) cc_final: 0.7882 (t0) REVERT: E 181 ARG cc_start: 0.8728 (ttt90) cc_final: 0.8432 (ttt180) REVERT: F 85 LYS cc_start: 0.8326 (mttt) cc_final: 0.7912 (mtmm) REVERT: F 88 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8579 (mmmm) REVERT: H 143 ASP cc_start: 0.8626 (t0) cc_final: 0.8252 (t0) REVERT: I 114 GLU cc_start: 0.6342 (tp30) cc_final: 0.5940 (mt-10) REVERT: I 135 MET cc_start: 0.8505 (mmm) cc_final: 0.8231 (mmt) REVERT: I 137 TYR cc_start: 0.6328 (m-80) cc_final: 0.6118 (m-80) outliers start: 20 outliers final: 18 residues processed: 172 average time/residue: 0.1018 time to fit residues: 24.8816 Evaluate side-chains 175 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.171352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121389 restraints weight = 12634.264| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.70 r_work: 0.2966 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11741 Z= 0.156 Angle : 0.547 6.377 16287 Z= 0.309 Chirality : 0.046 0.382 1873 Planarity : 0.004 0.042 1717 Dihedral : 20.476 178.323 2611 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.23 % Allowed : 9.69 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1158 helix: 1.79 (0.26), residues: 402 sheet: 0.65 (0.33), residues: 258 loop : 0.17 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 142 TYR 0.027 0.002 TYR D 60 PHE 0.014 0.002 PHE D 14 TRP 0.004 0.001 TRP D 144 HIS 0.004 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (11741) covalent geometry : angle 0.54682 / 0.31 (16287) hydrogen bonds : bond 0.03357 / 3.55 ( 517) hydrogen bonds : angle 5.04115 / 6.55 ( 1513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 111 ASN cc_start: 0.8297 (p0) cc_final: 0.7974 (p0) REVERT: D 128 LYS cc_start: 0.7286 (ttmt) cc_final: 0.6525 (tptm) REVERT: D 181 ARG cc_start: 0.8208 (ttt90) cc_final: 0.7695 (mtp180) REVERT: D 190 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6269 (ttp) REVERT: E 117 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7256 (mmtm) REVERT: F 85 LYS cc_start: 0.8330 (mttt) cc_final: 0.7913 (mtmm) REVERT: F 88 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8527 (mmmm) REVERT: H 143 ASP cc_start: 0.8643 (t0) cc_final: 0.8283 (t0) REVERT: I 44 GLU cc_start: 0.6320 (pm20) cc_final: 0.5818 (tp30) REVERT: I 114 GLU cc_start: 0.6481 (tp30) cc_final: 0.6000 (mt-10) REVERT: I 137 TYR cc_start: 0.6277 (m-80) cc_final: 0.6062 (m-80) outliers start: 23 outliers final: 16 residues processed: 169 average time/residue: 0.1004 time to fit residues: 24.2217 Evaluate side-chains 169 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123929 restraints weight = 12458.667| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.63 r_work: 0.3055 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11741 Z= 0.136 Angle : 0.519 7.270 16287 Z= 0.295 Chirality : 0.045 0.386 1873 Planarity : 0.004 0.039 1717 Dihedral : 20.461 178.170 2611 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.52 % Allowed : 10.47 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1158 helix: 1.60 (0.25), residues: 438 sheet: 0.59 (0.33), residues: 258 loop : -0.00 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 133 TYR 0.022 0.001 TYR D 60 PHE 0.029 0.002 PHE D 185 TRP 0.006 0.001 TRP D 144 HIS 0.004 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11741) covalent geometry : angle 0.51916 / 0.29 (16287) hydrogen bonds : bond 0.03087 / 3.28 ( 517) hydrogen bonds : angle 4.87066 / 6.34 ( 1513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 111 ASN cc_start: 0.8378 (p0) cc_final: 0.8093 (p0) REVERT: D 128 LYS cc_start: 0.7281 (ttmt) cc_final: 0.6653 (tppt) REVERT: D 181 ARG cc_start: 0.8133 (ttt90) cc_final: 0.7612 (mtp180) REVERT: D 190 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6351 (ttp) REVERT: E 117 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7230 (mmtm) REVERT: F 85 LYS cc_start: 0.8423 (mttt) cc_final: 0.8038 (mtmm) REVERT: F 88 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8538 (mmmm) REVERT: H 143 ASP cc_start: 0.8636 (t0) cc_final: 0.8295 (t0) REVERT: I 114 GLU cc_start: 0.6489 (tp30) cc_final: 0.6024 (mt-10) REVERT: I 137 TYR cc_start: 0.6275 (m-80) cc_final: 0.6062 (m-80) outliers start: 26 outliers final: 19 residues processed: 164 average time/residue: 0.0956 time to fit residues: 22.5477 Evaluate side-chains 168 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 chunk 118 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122343 restraints weight = 12638.350| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.58 r_work: 0.2910 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11741 Z= 0.142 Angle : 0.520 6.056 16287 Z= 0.294 Chirality : 0.044 0.390 1873 Planarity : 0.004 0.039 1717 Dihedral : 20.499 178.153 2611 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.52 % Allowed : 11.24 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1158 helix: 1.98 (0.26), residues: 402 sheet: 0.50 (0.33), residues: 258 loop : 0.24 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 142 TYR 0.020 0.001 TYR D 60 PHE 0.013 0.002 PHE D 185 TRP 0.003 0.001 TRP I 144 HIS 0.004 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11741) covalent geometry : angle 0.52024 / 0.29 (16287) hydrogen bonds : bond 0.03150 / 3.37 ( 517) hydrogen bonds : angle 4.79999 / 6.28 ( 1513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: D 111 ASN cc_start: 0.8403 (p0) cc_final: 0.8088 (p0) REVERT: D 128 LYS cc_start: 0.7120 (ttmt) cc_final: 0.6419 (tppt) REVERT: D 150 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7210 (tp) REVERT: D 181 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7520 (mtp180) REVERT: D 190 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6313 (ttp) REVERT: E 117 LYS cc_start: 0.7552 (mtmm) cc_final: 0.7152 (mmtm) REVERT: F 85 LYS cc_start: 0.8355 (mttt) cc_final: 0.7932 (mtmm) REVERT: F 88 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8476 (mmmm) REVERT: H 143 ASP cc_start: 0.8550 (t0) cc_final: 0.8197 (t0) REVERT: I 44 GLU cc_start: 0.6388 (pm20) cc_final: 0.5653 (tp30) REVERT: I 114 GLU cc_start: 0.6447 (tp30) cc_final: 0.5942 (mt-10) REVERT: I 137 TYR cc_start: 0.6192 (m-80) cc_final: 0.5966 (m-80) outliers start: 26 outliers final: 22 residues processed: 165 average time/residue: 0.1151 time to fit residues: 27.0908 Evaluate side-chains 176 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 157 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.169919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120906 restraints weight = 12688.184| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.70 r_work: 0.2886 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11741 Z= 0.152 Angle : 0.534 7.983 16287 Z= 0.300 Chirality : 0.045 0.393 1873 Planarity : 0.004 0.038 1717 Dihedral : 20.529 178.274 2611 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.33 % Allowed : 12.40 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.99 (0.24), residues: 1158 helix: 1.69 (0.25), residues: 438 sheet: 0.41 (0.33), residues: 258 loop : -0.10 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 133 TYR 0.019 0.001 TYR D 60 PHE 0.016 0.002 PHE D 185 TRP 0.004 0.001 TRP D 144 HIS 0.004 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11741) covalent geometry : angle 0.53410 / 0.30 (16287) hydrogen bonds : bond 0.03234 / 3.45 ( 517) hydrogen bonds : angle 4.74549 / 6.20 ( 1513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: D 85 LYS cc_start: 0.7733 (mttt) cc_final: 0.7378 (mmmt) REVERT: D 111 ASN cc_start: 0.8373 (p0) cc_final: 0.8033 (p0) REVERT: D 128 LYS cc_start: 0.7075 (ttmt) cc_final: 0.6105 (mttt) REVERT: D 150 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7123 (tp) REVERT: D 181 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7416 (mtp180) REVERT: D 190 MET cc_start: 0.6714 (ttt) cc_final: 0.6352 (ttp) REVERT: E 117 LYS cc_start: 0.7514 (mtmm) cc_final: 0.7075 (mmtm) REVERT: F 85 LYS cc_start: 0.8259 (mttt) cc_final: 0.7819 (mtmm) REVERT: F 88 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8415 (mmmm) REVERT: G 95 MET cc_start: 0.8551 (ptm) cc_final: 0.8329 (ptm) REVERT: H 143 ASP cc_start: 0.8510 (t0) cc_final: 0.8133 (t0) REVERT: I 114 GLU cc_start: 0.6404 (tp30) cc_final: 0.5839 (mt-10) REVERT: I 137 TYR cc_start: 0.6158 (m-80) cc_final: 0.5942 (m-80) outliers start: 24 outliers final: 21 residues processed: 162 average time/residue: 0.1118 time to fit residues: 25.9016 Evaluate side-chains 171 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121889 restraints weight = 12538.630| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.57 r_work: 0.2906 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11741 Z= 0.139 Angle : 0.525 9.611 16287 Z= 0.294 Chirality : 0.044 0.393 1873 Planarity : 0.004 0.039 1717 Dihedral : 20.531 178.253 2611 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.52 % Allowed : 12.50 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1158 helix: 2.03 (0.26), residues: 402 sheet: 0.38 (0.33), residues: 258 loop : 0.16 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 133 TYR 0.018 0.001 TYR D 60 PHE 0.014 0.002 PHE D 185 TRP 0.005 0.001 TRP I 144 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11741) covalent geometry : angle 0.52549 / 0.29 (16287) hydrogen bonds : bond 0.03085 / 3.29 ( 517) hydrogen bonds : angle 4.70643 / 6.17 ( 1513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: D 85 LYS cc_start: 0.7738 (mttt) cc_final: 0.7386 (mmmt) REVERT: D 111 ASN cc_start: 0.8375 (p0) cc_final: 0.8038 (p0) REVERT: D 128 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6406 (tppt) REVERT: D 150 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7094 (tp) REVERT: D 164 MET cc_start: 0.6949 (ttp) cc_final: 0.6694 (tmm) REVERT: D 181 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7405 (mtp180) REVERT: D 190 MET cc_start: 0.6696 (ttt) cc_final: 0.6338 (ttp) REVERT: E 117 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7087 (mmtm) REVERT: F 85 LYS cc_start: 0.8270 (mttt) cc_final: 0.7830 (mtmm) REVERT: F 88 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8438 (mmmm) REVERT: G 95 MET cc_start: 0.8500 (ptm) cc_final: 0.8280 (ptm) REVERT: H 23 ASP cc_start: 0.6686 (t0) cc_final: 0.5838 (t0) REVERT: H 143 ASP cc_start: 0.8500 (t0) cc_final: 0.8116 (t0) REVERT: I 44 GLU cc_start: 0.6596 (pm20) cc_final: 0.5833 (tp30) REVERT: I 114 GLU cc_start: 0.6418 (tp30) cc_final: 0.5855 (mt-10) REVERT: I 137 TYR cc_start: 0.6170 (m-80) cc_final: 0.5909 (m-80) outliers start: 26 outliers final: 22 residues processed: 168 average time/residue: 0.1098 time to fit residues: 26.4756 Evaluate side-chains 176 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 171 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.169720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121723 restraints weight = 12454.836| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.53 r_work: 0.2896 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11741 Z= 0.156 Angle : 0.543 8.728 16287 Z= 0.302 Chirality : 0.045 0.394 1873 Planarity : 0.004 0.038 1717 Dihedral : 20.569 178.000 2611 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.23 % Allowed : 13.18 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1158 helix: 2.02 (0.26), residues: 402 sheet: 0.30 (0.33), residues: 258 loop : 0.11 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 133 TYR 0.017 0.001 TYR D 31 PHE 0.014 0.002 PHE D 14 TRP 0.004 0.001 TRP D 144 HIS 0.004 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11741) covalent geometry : angle 0.54310 / 0.30 (16287) hydrogen bonds : bond 0.03274 / 3.50 ( 517) hydrogen bonds : angle 4.72131 / 6.17 ( 1513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: D 85 LYS cc_start: 0.7752 (mttt) cc_final: 0.7398 (mmmt) REVERT: D 111 ASN cc_start: 0.8397 (p0) cc_final: 0.8070 (p0) REVERT: D 128 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6137 (mttt) REVERT: D 150 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7115 (tp) REVERT: D 181 ARG cc_start: 0.7888 (ttt90) cc_final: 0.7410 (mtp180) REVERT: D 190 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6280 (ttp) REVERT: E 117 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7124 (mmtm) REVERT: F 85 LYS cc_start: 0.8294 (mttt) cc_final: 0.7851 (mtmm) REVERT: F 88 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8520 (mmmm) REVERT: G 95 MET cc_start: 0.8525 (ptm) cc_final: 0.8302 (ptm) REVERT: I 114 GLU cc_start: 0.6418 (tp30) cc_final: 0.5848 (mt-10) REVERT: I 137 TYR cc_start: 0.6195 (m-80) cc_final: 0.5958 (m-80) outliers start: 23 outliers final: 20 residues processed: 157 average time/residue: 0.1148 time to fit residues: 25.7207 Evaluate side-chains 168 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 3 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 17 HIS F 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.174114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125636 restraints weight = 12569.597| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.50 r_work: 0.2935 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11741 Z= 0.124 Angle : 0.516 8.931 16287 Z= 0.289 Chirality : 0.043 0.394 1873 Planarity : 0.004 0.039 1717 Dihedral : 20.530 177.955 2611 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.55 % Allowed : 13.95 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1158 helix: 2.09 (0.26), residues: 402 sheet: 0.36 (0.33), residues: 258 loop : 0.17 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 142 TYR 0.017 0.001 TYR D 31 PHE 0.019 0.002 PHE I 101 TRP 0.004 0.001 TRP E 144 HIS 0.003 0.001 HIS H 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11741) covalent geometry : angle 0.51614 / 0.29 (16287) hydrogen bonds : bond 0.02930 / 3.11 ( 517) hydrogen bonds : angle 4.64104 / 6.10 ( 1513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: D 85 LYS cc_start: 0.7803 (mttt) cc_final: 0.7455 (mmmt) REVERT: D 111 ASN cc_start: 0.8397 (p0) cc_final: 0.8072 (p0) REVERT: D 128 LYS cc_start: 0.7153 (ttmt) cc_final: 0.6438 (tppt) REVERT: D 150 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7290 (tp) REVERT: D 181 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7364 (mtp180) REVERT: D 190 MET cc_start: 0.6586 (ttt) cc_final: 0.6263 (ttp) REVERT: E 114 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8076 (tm-30) REVERT: E 117 LYS cc_start: 0.7590 (mtmm) cc_final: 0.7211 (mmtm) REVERT: F 85 LYS cc_start: 0.8377 (mttt) cc_final: 0.7947 (mtmm) REVERT: F 88 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8601 (mmmm) REVERT: I 114 GLU cc_start: 0.6493 (tp30) cc_final: 0.5957 (mt-10) REVERT: I 137 TYR cc_start: 0.6189 (m-80) cc_final: 0.5926 (m-80) outliers start: 16 outliers final: 13 residues processed: 158 average time/residue: 0.1145 time to fit residues: 25.5457 Evaluate side-chains 161 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 27 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.4261 > 50:) chunk 106 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124710 restraints weight = 12524.941| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.53 r_work: 0.2926 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11741 Z= 0.120 Angle : 0.511 8.794 16287 Z= 0.286 Chirality : 0.044 0.394 1873 Planarity : 0.004 0.039 1717 Dihedral : 20.529 177.796 2611 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.65 % Allowed : 14.24 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1158 helix: 2.15 (0.26), residues: 402 sheet: 0.37 (0.32), residues: 276 loop : 0.26 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 142 TYR 0.017 0.001 TYR D 31 PHE 0.014 0.001 PHE D 185 TRP 0.005 0.001 TRP I 144 HIS 0.003 0.001 HIS H 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11741) covalent geometry : angle 0.51095 / 0.29 (16287) hydrogen bonds : bond 0.02960 / 3.15 ( 517) hydrogen bonds : angle 4.60250 / 6.05 ( 1513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2576.03 seconds wall clock time: 44 minutes 59.01 seconds (2699.01 seconds total)