Starting phenix.real_space_refine on Thu Aug 6 19:56:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wc_68033/08_2026/21wc_68033.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wc_68033/08_2026/21wc_68033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21wc_68033/08_2026/21wc_68033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wc_68033/08_2026/21wc_68033.map" model { file = "/net/cci-nas-00/data/ceres_data/21wc_68033/08_2026/21wc_68033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wc_68033/08_2026/21wc_68033.cif" } resolution = 3.9 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= 0.002 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: 8 Type Number sf(0) Gaussians P 276 5.49 5 Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 9751 2.51 5 N 3123 2.21 5 O 3645 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16838 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 4936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4936 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 19, 'TRANS': 583} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2791 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "Y" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2826 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.55, per 1000 atoms: 0.21 Number of scatterers: 16838 At special positions: 0 Unit cell: (110, 121, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 38 16.00 P 276 15.00 Mg 1 11.99 F 3 9.00 O 3645 8.00 N 3123 7.00 C 9751 6.00 Be 1 4.00 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: 1.26 Conformation dependent library (CDL) restraints added in 517.8 milliseconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 9 sheets defined 62.7% alpha, 4.0% beta 97 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.923A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 111 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.900A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.522A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.859A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.551A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.656A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.524A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.667A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 87 through 114 removed outlier: 3.523A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.516A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.762A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.874A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.932A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.552A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.641A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.624A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.763A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 573 removed outlier: 3.889A pdb=" N GLN I 555 " --> pdb=" O ALA I 551 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN I 556 " --> pdb=" O TYR I 552 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I 562 " --> pdb=" O ASP I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 736 removed outlier: 3.842A pdb=" N HIS I 736 " --> pdb=" O TYR I 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 732 through 736' Processing helix chain 'I' and resid 755 through 771 Processing helix chain 'I' and resid 786 through 799 Processing helix chain 'I' and resid 811 through 825 removed outlier: 4.505A pdb=" N SER I 816 " --> pdb=" O LEU I 812 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 837 through 843 Processing helix chain 'I' and resid 844 through 851 removed outlier: 3.628A pdb=" N GLY I 851 " --> pdb=" O GLN I 847 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 866 removed outlier: 3.615A pdb=" N ILE I 863 " --> pdb=" O THR I 859 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 864 " --> pdb=" O TYR I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 883 through 888 removed outlier: 4.123A pdb=" N ASN I 888 " --> pdb=" O ARG I 885 " (cutoff:3.500A) Processing helix chain 'I' and resid 891 through 900 Processing helix chain 'I' and resid 918 through 929 removed outlier: 3.811A pdb=" N TRP I 922 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing helix chain 'I' and resid 960 through 972 removed outlier: 3.646A pdb=" N LEU I 972 " --> pdb=" O LEU I 968 " (cutoff:3.500A) Processing helix chain 'I' and resid 973 through 976 removed outlier: 3.934A pdb=" N LEU I 976 " --> pdb=" O ARG I 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 973 through 976' Processing helix chain 'I' and resid 980 through 985 removed outlier: 3.584A pdb=" N VAL I 984 " --> pdb=" O LEU I 980 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1015 removed outlier: 3.846A pdb=" N LEU I1007 " --> pdb=" O LEU I1003 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG I1009 " --> pdb=" O ARG I1005 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS I1010 " --> pdb=" O VAL I1006 " (cutoff:3.500A) Processing helix chain 'I' and resid 1037 through 1048 Processing helix chain 'I' and resid 1049 through 1053 removed outlier: 3.571A pdb=" N PHE I1052 " --> pdb=" O PRO I1049 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN I1053 " --> pdb=" O TYR I1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1049 through 1053' Processing helix chain 'I' and resid 1054 through 1063 removed outlier: 3.732A pdb=" N SER I1058 " --> pdb=" O HIS I1054 " (cutoff:3.500A) Processing helix chain 'I' and resid 1072 through 1079 removed outlier: 4.315A pdb=" N TYR I1076 " --> pdb=" O GLY I1072 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER I1079 " --> pdb=" O LEU I1075 " (cutoff:3.500A) Processing helix chain 'I' and resid 1079 through 1095 Proline residue: I1090 - end of helix Processing helix chain 'I' and resid 1105 through 1120 removed outlier: 3.595A pdb=" N MET I1109 " --> pdb=" O MET I1105 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP I1114 " --> pdb=" O THR I1110 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR I1115 " --> pdb=" O ILE I1111 " (cutoff:3.500A) Processing helix chain 'I' and resid 1133 through 1144 removed outlier: 4.330A pdb=" N MET I1137 " --> pdb=" O GLU I1133 " (cutoff:3.500A) Processing helix chain 'I' and resid 1179 through 1188 removed outlier: 4.162A pdb=" N ASP I1183 " --> pdb=" O ASN I1179 " (cutoff:3.500A) Processing helix chain 'I' and resid 1189 through 1191 No H-bonds generated for 'chain 'I' and resid 1189 through 1191' Processing helix chain 'I' and resid 1209 through 1227 removed outlier: 3.910A pdb=" N LYS I1213 " --> pdb=" O SER I1209 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL I1224 " --> pdb=" O TYR I1220 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS I1227 " --> pdb=" O ASN I1223 " (cutoff:3.500A) Processing helix chain 'I' and resid 1241 through 1255 removed outlier: 3.555A pdb=" N ALA I1245 " --> pdb=" O HIS I1241 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA I1249 " --> pdb=" O ALA I1245 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE I1250 " --> pdb=" O PHE I1246 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU I1251 " --> pdb=" O LEU I1247 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU I1252 " --> pdb=" O GLN I1248 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU I1255 " --> pdb=" O LEU I1251 " (cutoff:3.500A) Processing helix chain 'I' and resid 1301 through 1307 Processing helix chain 'I' and resid 1309 through 1314 Processing helix chain 'I' and resid 1315 through 1318 Processing helix chain 'I' and resid 1319 through 1330 removed outlier: 3.850A pdb=" N ARG I1329 " --> pdb=" O ARG I1325 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN I1330 " --> pdb=" O GLU I1326 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 19 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.585A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.530A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.557A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.832A pdb=" N THR F 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 776 through 777 removed outlier: 6.551A pdb=" N ILE I 808 " --> pdb=" O THR I 858 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL I 832 " --> pdb=" O LEU I 857 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 992 through 996 removed outlier: 6.979A pdb=" N VAL I1171 " --> pdb=" O LEU I1202 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU I1204 " --> pdb=" O VAL I1171 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE I1173 " --> pdb=" O LEU I1204 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL I1099 " --> pdb=" O PHE I1152 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU I1154 " --> pdb=" O VAL I1099 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU I1101 " --> pdb=" O LEU I1154 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER I1155 " --> pdb=" O LEU I1126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 1016 through 1018 570 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 250 hydrogen bonds 488 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3928 1.33 - 1.45: 4716 1.45 - 1.57: 8434 1.57 - 1.69: 549 1.69 - 1.81: 68 Bond restraints: 17695 Sorted by residual: bond pdb=" C3' DA Y 60 " pdb=" C2' DA Y 60 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT Y 15 " pdb=" C2' DT Y 15 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC X 45 " pdb=" C2' DC X 45 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC Y 104 " pdb=" C2' DC Y 104 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC X 107 " pdb=" C2' DC X 107 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 ... (remaining 17690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 23182 1.28 - 2.57: 1641 2.57 - 3.85: 185 3.85 - 5.14: 28 5.14 - 6.42: 9 Bond angle restraints: 25045 Sorted by residual: angle pdb=" N ILE A 112 " pdb=" CA ILE A 112 " pdb=" C ILE A 112 " ideal model delta sigma weight residual 112.83 106.77 6.06 9.90e-01 1.02e+00 3.75e+01 angle pdb=" N3 DT X 77 " pdb=" C4 DT X 77 " pdb=" O4 DT X 77 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4' DA Y 44 " pdb=" C4' DA Y 44 " pdb=" C3' DA Y 44 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT X 108 " pdb=" C4 DT X 108 " pdb=" O4 DT X 108 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT X 87 " pdb=" C4 DT X 87 " pdb=" O4 DT X 87 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 25040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 8646 34.96 - 69.91: 1300 69.91 - 104.87: 42 104.87 - 139.83: 1 139.83 - 174.79: 3 Dihedral angle restraints: 9992 sinusoidal: 5940 harmonic: 4052 Sorted by residual: dihedral pdb=" O2A ADP I1802 " pdb=" O3A ADP I1802 " pdb=" PA ADP I1802 " pdb=" PB ADP I1802 " ideal model delta sinusoidal sigma weight residual -60.00 -155.68 95.68 1 2.00e+01 2.50e-03 2.64e+01 dihedral pdb=" C4' DT Y 15 " pdb=" C3' DT Y 15 " pdb=" O3' DT Y 15 " pdb=" P DC Y 16 " ideal model delta sinusoidal sigma weight residual 220.00 45.21 174.79 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG Y 94 " pdb=" C3' DG Y 94 " pdb=" O3' DG Y 94 " pdb=" P DG Y 95 " ideal model delta sinusoidal sigma weight residual 220.00 49.70 170.30 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1707 0.032 - 0.065: 738 0.065 - 0.097: 280 0.097 - 0.130: 99 0.130 - 0.162: 5 Chirality restraints: 2829 Sorted by residual: chirality pdb=" C3' DG Y 94 " pdb=" C4' DG Y 94 " pdb=" O3' DG Y 94 " pdb=" C2' DG Y 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA PRO I 913 " pdb=" N PRO I 913 " pdb=" C PRO I 913 " pdb=" CB PRO I 913 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" C3' DT Y 15 " pdb=" C4' DT Y 15 " pdb=" O3' DT Y 15 " pdb=" C2' DT Y 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2826 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 107 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ALA H 107 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA H 107 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS H 108 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA Y 91 " -0.023 2.00e-02 2.50e+03 1.14e-02 3.55e+00 pdb=" N9 DA Y 91 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA Y 91 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA Y 91 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA Y 91 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA Y 91 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA Y 91 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA Y 91 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA Y 91 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA Y 91 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA Y 91 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 131 " 0.023 2.00e-02 2.50e+03 9.60e-03 2.54e+00 pdb=" N9 DA X 131 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA X 131 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA X 131 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA X 131 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA X 131 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA X 131 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA X 131 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA X 131 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA X 131 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA X 131 " -0.001 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 143 2.60 - 3.17: 13836 3.17 - 3.75: 28862 3.75 - 4.32: 37208 4.32 - 4.90: 57046 Nonbonded interactions: 137095 Sorted by model distance: nonbonded pdb=" OD2 ASP I 881 " pdb="MG MG I1801 " model vdw 2.024 2.170 nonbonded pdb=" O2 DC X 95 " pdb=" N2 DG Y 53 " model vdw 2.074 2.496 nonbonded pdb=" N2 DG X 148 " pdb=" O2 DC Y 0 " model vdw 2.084 2.496 nonbonded pdb=" O2 DC X 143 " pdb=" N2 DG Y 5 " model vdw 2.086 2.496 nonbonded pdb=" O3B ADP I1802 " pdb=" F1 BEF I1803 " model vdw 2.139 2.990 ... (remaining 137090 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' and (resid 22 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 117) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } 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 group one per residue 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: 3.450 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.630 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17695 Z= 0.428 Angle : 0.701 6.422 25045 Z= 0.577 Chirality : 0.043 0.162 2829 Planarity : 0.004 0.036 2220 Dihedral : 24.565 174.787 7370 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.93 % Allowed : 11.02 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1362 helix: 1.15 (0.19), residues: 789 sheet: -0.73 (0.66), residues: 64 loop : -1.73 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1005 TYR 0.020 0.001 TYR I 560 PHE 0.019 0.001 PHE I 822 TRP 0.013 0.001 TRP I 825 HIS 0.003 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.43 (17695) covalent geometry : angle 0.70090 / 0.58 (25045) hydrogen bonds : bond 0.11375 / 7.30 ( 820) hydrogen bonds : angle 4.61362 / 3.23 ( 2174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (t) REVERT: F 84 MET cc_start: 0.8781 (tpt) cc_final: 0.8505 (tpt) REVERT: F 91 LYS cc_start: 0.8958 (ttpp) cc_final: 0.8710 (ttmt) REVERT: H 42 TYR cc_start: 0.7766 (t80) cc_final: 0.7404 (t80) REVERT: H 76 GLU cc_start: 0.8970 (tp30) cc_final: 0.8341 (mm-30) REVERT: I 1005 ARG cc_start: 0.7305 (mmm160) cc_final: 0.6873 (mmm160) REVERT: I 1051 MET cc_start: 0.8524 (ptp) cc_final: 0.7888 (ptp) REVERT: I 1116 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7352 (m-80) outliers start: 23 outliers final: 10 residues processed: 205 average time/residue: 0.1535 time to fit residues: 44.2660 Evaluate side-chains 177 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 overall best weight: 0.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 125 GLN B 25 ASN D 49 HIS D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 85 GLN H 49 HIS H 82 HIS ** I 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 941 GLN I1010 HIS ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1104 GLN I1185 GLN I1253 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134327 restraints weight = 21766.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132513 restraints weight = 39229.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133212 restraints weight = 36513.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132342 restraints weight = 30393.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132566 restraints weight = 27649.669| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17695 Z= 0.138 Angle : 0.596 6.696 25045 Z= 0.341 Chirality : 0.042 0.296 2829 Planarity : 0.004 0.045 2220 Dihedral : 28.433 176.630 4571 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.78 % Allowed : 13.62 % Favored : 83.60 % 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: 0.31 (0.23), residues: 1362 helix: 1.42 (0.19), residues: 799 sheet: -0.70 (0.66), residues: 67 loop : -1.73 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1200 TYR 0.019 0.001 TYR I 560 PHE 0.018 0.001 PHE I 927 TRP 0.012 0.001 TRP I 922 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (17695) covalent geometry : angle 0.59552 / 0.34 (25045) hydrogen bonds : bond 0.05620 / 3.76 ( 820) hydrogen bonds : angle 3.70245 / 2.61 ( 2174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 LYS cc_start: 0.7241 (mptt) cc_final: 0.7018 (mptt) REVERT: F 91 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8742 (ttmt) REVERT: G 34 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8954 (mp) REVERT: H 42 TYR cc_start: 0.7659 (t80) cc_final: 0.7459 (t80) REVERT: H 76 GLU cc_start: 0.8925 (tp30) cc_final: 0.8285 (mm-30) REVERT: I 864 ILE cc_start: 0.9192 (mm) cc_final: 0.8913 (mt) REVERT: I 1051 MET cc_start: 0.8597 (ptp) cc_final: 0.7952 (ptp) REVERT: I 1116 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7248 (m-10) outliers start: 33 outliers final: 19 residues processed: 197 average time/residue: 0.1628 time to fit residues: 45.5940 Evaluate side-chains 184 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1321 LEU Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 17 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS H 82 HIS H 109 HIS I 770 ASN I1164 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119681 restraints weight = 22471.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117494 restraints weight = 48094.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118105 restraints weight = 50452.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119216 restraints weight = 33424.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119093 restraints weight = 28699.175| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.110 17695 Z= 0.487 Angle : 0.979 11.933 25045 Z= 0.516 Chirality : 0.059 0.450 2829 Planarity : 0.007 0.062 2220 Dihedral : 29.368 176.351 4567 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.22 % Allowed : 16.48 % Favored : 77.29 % 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: -0.98 (0.22), residues: 1362 helix: 0.29 (0.18), residues: 814 sheet: -1.88 (0.61), residues: 65 loop : -2.06 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 55 TYR 0.044 0.004 TYR D 83 PHE 0.017 0.003 PHE H 70 TRP 0.016 0.003 TRP I 922 HIS 0.009 0.002 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.01112 / 0.49 (17695) covalent geometry : angle 0.97887 / 0.52 (25045) hydrogen bonds : bond 0.08587 / 5.86 ( 820) hydrogen bonds : angle 4.58829 / 3.30 ( 2174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 175 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 107 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8803 (t) REVERT: B 25 ASN cc_start: 0.8217 (t160) cc_final: 0.7787 (t0) REVERT: B 47 SER cc_start: 0.9425 (t) cc_final: 0.9098 (p) REVERT: E 69 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8524 (mtp180) REVERT: F 91 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8692 (ttmt) REVERT: I 749 MET cc_start: 0.4884 (ptt) cc_final: 0.4580 (ptt) REVERT: I 864 ILE cc_start: 0.9384 (mm) cc_final: 0.9023 (mt) REVERT: I 1116 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7729 (m-10) REVERT: I 1200 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7744 (mtt-85) REVERT: I 1234 PHE cc_start: 0.7086 (m-80) cc_final: 0.6262 (m-80) REVERT: I 1235 ASP cc_start: 0.7850 (p0) cc_final: 0.6517 (t0) outliers start: 74 outliers final: 44 residues processed: 234 average time/residue: 0.1477 time to fit residues: 49.6244 Evaluate side-chains 212 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 828 SER Chi-restraints excluded: chain I residue 848 LEU Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1112 MET Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1151 ILE Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.167630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125492 restraints weight = 22008.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123461 restraints weight = 45627.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124217 restraints weight = 42694.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124113 restraints weight = 31507.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124136 restraints weight = 31914.448| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17695 Z= 0.170 Angle : 0.668 9.773 25045 Z= 0.367 Chirality : 0.045 0.351 2829 Planarity : 0.005 0.056 2220 Dihedral : 29.005 178.610 4567 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.29 % Allowed : 18.92 % Favored : 76.79 % 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: -0.14 (0.23), residues: 1362 helix: 1.08 (0.19), residues: 810 sheet: -1.62 (0.63), residues: 65 loop : -1.91 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1200 TYR 0.018 0.002 TYR I 560 PHE 0.009 0.001 PHE F 100 TRP 0.007 0.001 TRP I 922 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (17695) covalent geometry : angle 0.66774 / 0.37 (25045) hydrogen bonds : bond 0.05911 / 3.96 ( 820) hydrogen bonds : angle 3.77325 / 2.69 ( 2174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7610 (pt0) cc_final: 0.7347 (pt0) REVERT: F 91 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8877 (ttmt) REVERT: I 749 MET cc_start: 0.4788 (ptt) cc_final: 0.4550 (ptt) REVERT: I 864 ILE cc_start: 0.9344 (mm) cc_final: 0.9008 (mt) REVERT: I 1116 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7494 (m-10) REVERT: I 1187 GLN cc_start: 0.7479 (pt0) cc_final: 0.7104 (pt0) REVERT: I 1234 PHE cc_start: 0.7013 (m-80) cc_final: 0.6346 (m-80) REVERT: I 1235 ASP cc_start: 0.7789 (p0) cc_final: 0.6451 (t0) REVERT: I 1366 MET cc_start: 0.6916 (pmm) cc_final: 0.6598 (pmm) outliers start: 51 outliers final: 31 residues processed: 211 average time/residue: 0.1405 time to fit residues: 42.7801 Evaluate side-chains 195 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 89 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS H 82 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127108 restraints weight = 21968.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124981 restraints weight = 37463.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124932 restraints weight = 38576.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123808 restraints weight = 32346.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124412 restraints weight = 30637.424| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17695 Z= 0.154 Angle : 0.630 8.620 25045 Z= 0.348 Chirality : 0.043 0.339 2829 Planarity : 0.004 0.072 2220 Dihedral : 28.854 178.369 4566 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.71 % Allowed : 19.26 % Favored : 76.03 % 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: 0.10 (0.23), residues: 1362 helix: 1.32 (0.19), residues: 813 sheet: -1.53 (0.64), residues: 65 loop : -1.93 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1200 TYR 0.019 0.001 TYR H 83 PHE 0.012 0.001 PHE I1367 TRP 0.008 0.001 TRP I 818 HIS 0.010 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (17695) covalent geometry : angle 0.63036 / 0.35 (25045) hydrogen bonds : bond 0.05464 / 3.65 ( 820) hydrogen bonds : angle 3.60446 / 2.57 ( 2174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7648 (pt0) cc_final: 0.7379 (pt0) REVERT: F 91 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8781 (ttmt) REVERT: H 44 VAL cc_start: 0.9568 (OUTLIER) cc_final: 0.9345 (t) REVERT: H 59 MET cc_start: 0.9070 (tpp) cc_final: 0.8479 (tpp) REVERT: I 749 MET cc_start: 0.4706 (ptt) cc_final: 0.4500 (ptt) REVERT: I 864 ILE cc_start: 0.9285 (mm) cc_final: 0.8973 (mt) REVERT: I 1084 LEU cc_start: 0.8026 (pp) cc_final: 0.7745 (pp) REVERT: I 1187 GLN cc_start: 0.7448 (pt0) cc_final: 0.7019 (pt0) REVERT: I 1234 PHE cc_start: 0.6898 (m-80) cc_final: 0.6245 (m-80) REVERT: I 1235 ASP cc_start: 0.7812 (p0) cc_final: 0.6531 (t0) outliers start: 56 outliers final: 36 residues processed: 210 average time/residue: 0.1525 time to fit residues: 46.3374 Evaluate side-chains 197 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1011 MET Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 110 optimal weight: 0.3980 chunk 154 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 99 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS H 82 HIS H 109 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129280 restraints weight = 21950.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127932 restraints weight = 31223.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127388 restraints weight = 34124.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126500 restraints weight = 30044.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126960 restraints weight = 28434.650| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17695 Z= 0.137 Angle : 0.607 8.652 25045 Z= 0.336 Chirality : 0.042 0.332 2829 Planarity : 0.004 0.052 2220 Dihedral : 28.712 178.901 4566 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.21 % Allowed : 20.52 % Favored : 75.27 % 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: 0.33 (0.23), residues: 1362 helix: 1.54 (0.19), residues: 813 sheet: -1.31 (0.66), residues: 65 loop : -1.91 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1200 TYR 0.017 0.001 TYR I 560 PHE 0.015 0.001 PHE I1367 TRP 0.007 0.001 TRP I 922 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (17695) covalent geometry : angle 0.60700 / 0.34 (25045) hydrogen bonds : bond 0.05189 / 3.43 ( 820) hydrogen bonds : angle 3.48474 / 2.49 ( 2174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 104 GLN cc_start: 0.7684 (pt0) cc_final: 0.7409 (pt0) REVERT: F 91 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8691 (ttmt) REVERT: H 44 VAL cc_start: 0.9588 (OUTLIER) cc_final: 0.9364 (t) REVERT: H 59 MET cc_start: 0.9050 (tpp) cc_final: 0.8539 (tpp) REVERT: I 756 GLN cc_start: 0.7840 (pm20) cc_final: 0.7589 (tm-30) REVERT: I 864 ILE cc_start: 0.9254 (mm) cc_final: 0.8935 (mt) REVERT: I 1084 LEU cc_start: 0.8034 (pp) cc_final: 0.7738 (pp) REVERT: I 1111 ILE cc_start: 0.8743 (tt) cc_final: 0.8502 (mt) REVERT: I 1187 GLN cc_start: 0.7477 (pt0) cc_final: 0.7036 (pt0) REVERT: I 1234 PHE cc_start: 0.7010 (m-80) cc_final: 0.6450 (m-80) REVERT: I 1235 ASP cc_start: 0.7807 (p0) cc_final: 0.6562 (t0) outliers start: 50 outliers final: 36 residues processed: 206 average time/residue: 0.1305 time to fit residues: 38.9763 Evaluate side-chains 195 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1321 LEU Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 139 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125273 restraints weight = 21931.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122904 restraints weight = 44033.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123680 restraints weight = 44142.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123436 restraints weight = 30276.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123596 restraints weight = 29701.034| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17695 Z= 0.186 Angle : 0.644 9.591 25045 Z= 0.351 Chirality : 0.043 0.360 2829 Planarity : 0.004 0.051 2220 Dihedral : 28.804 178.534 4564 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.29 % Allowed : 21.45 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1362 helix: 1.44 (0.19), residues: 814 sheet: -1.40 (0.65), residues: 65 loop : -1.97 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1200 TYR 0.024 0.002 TYR H 83 PHE 0.013 0.001 PHE I1367 TRP 0.010 0.001 TRP I 922 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (17695) covalent geometry : angle 0.64373 / 0.35 (25045) hydrogen bonds : bond 0.05573 / 3.72 ( 820) hydrogen bonds : angle 3.59612 / 2.56 ( 2174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7718 (pt0) cc_final: 0.7416 (pt0) REVERT: F 91 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8726 (ttmt) REVERT: H 59 MET cc_start: 0.9033 (tpp) cc_final: 0.8539 (tpp) REVERT: I 864 ILE cc_start: 0.9293 (mm) cc_final: 0.8963 (mt) REVERT: I 1084 LEU cc_start: 0.8056 (pp) cc_final: 0.7758 (pp) REVERT: I 1111 ILE cc_start: 0.8772 (tt) cc_final: 0.8554 (mt) REVERT: I 1187 GLN cc_start: 0.7642 (pt0) cc_final: 0.7138 (pt0) REVERT: I 1234 PHE cc_start: 0.6923 (m-80) cc_final: 0.6316 (m-80) REVERT: I 1235 ASP cc_start: 0.7823 (p0) cc_final: 0.6691 (t0) outliers start: 51 outliers final: 41 residues processed: 205 average time/residue: 0.1388 time to fit residues: 41.1046 Evaluate side-chains 202 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 1011 MET Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1112 MET Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1321 LEU Chi-restraints excluded: chain I residue 1377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 138 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 109 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129131 restraints weight = 22183.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126924 restraints weight = 36169.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127152 restraints weight = 38618.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126780 restraints weight = 27506.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126819 restraints weight = 27776.024| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17695 Z= 0.152 Angle : 0.621 10.702 25045 Z= 0.341 Chirality : 0.042 0.345 2829 Planarity : 0.004 0.049 2220 Dihedral : 28.727 178.824 4564 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.78 % Allowed : 22.37 % Favored : 73.84 % 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: 0.34 (0.23), residues: 1362 helix: 1.54 (0.19), residues: 813 sheet: -1.33 (0.66), residues: 65 loop : -1.92 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1200 TYR 0.021 0.001 TYR H 83 PHE 0.014 0.001 PHE I1367 TRP 0.009 0.001 TRP I 922 HIS 0.012 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (17695) covalent geometry : angle 0.62092 / 0.34 (25045) hydrogen bonds : bond 0.05298 / 3.52 ( 820) hydrogen bonds : angle 3.52910 / 2.51 ( 2174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7708 (pt0) cc_final: 0.7407 (pt0) REVERT: F 91 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8678 (ttmt) REVERT: H 59 MET cc_start: 0.9035 (tpp) cc_final: 0.8534 (tpp) REVERT: I 756 GLN cc_start: 0.7776 (pm20) cc_final: 0.7572 (tm-30) REVERT: I 864 ILE cc_start: 0.9288 (mm) cc_final: 0.8957 (mt) REVERT: I 1084 LEU cc_start: 0.8019 (pp) cc_final: 0.7747 (pp) REVERT: I 1111 ILE cc_start: 0.8734 (tt) cc_final: 0.8517 (mt) REVERT: I 1187 GLN cc_start: 0.7565 (pt0) cc_final: 0.7083 (pt0) REVERT: I 1234 PHE cc_start: 0.6954 (m-80) cc_final: 0.6397 (m-80) REVERT: I 1235 ASP cc_start: 0.7874 (p0) cc_final: 0.6720 (t0) REVERT: I 1319 MET cc_start: 0.4743 (pmm) cc_final: 0.4378 (pmm) outliers start: 45 outliers final: 40 residues processed: 198 average time/residue: 0.1525 time to fit residues: 44.0789 Evaluate side-chains 204 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 1011 MET Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 98 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128467 restraints weight = 22048.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126511 restraints weight = 41382.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127029 restraints weight = 38104.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126724 restraints weight = 26427.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126832 restraints weight = 26640.386| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17695 Z= 0.143 Angle : 0.620 11.326 25045 Z= 0.340 Chirality : 0.042 0.342 2829 Planarity : 0.004 0.049 2220 Dihedral : 28.684 178.711 4563 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.87 % Allowed : 22.62 % Favored : 73.51 % 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: 0.34 (0.23), residues: 1362 helix: 1.55 (0.19), residues: 813 sheet: -1.32 (0.67), residues: 65 loop : -1.92 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I1324 TYR 0.020 0.001 TYR H 83 PHE 0.013 0.001 PHE I1367 TRP 0.008 0.001 TRP I 922 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (17695) covalent geometry : angle 0.62002 / 0.34 (25045) hydrogen bonds : bond 0.05223 / 3.46 ( 820) hydrogen bonds : angle 3.49799 / 2.49 ( 2174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7716 (pt0) cc_final: 0.7418 (pt0) REVERT: F 91 LYS cc_start: 0.8995 (ttpp) cc_final: 0.8684 (ttmt) REVERT: H 59 MET cc_start: 0.9018 (tpp) cc_final: 0.8560 (tpp) REVERT: I 756 GLN cc_start: 0.7879 (pm20) cc_final: 0.7614 (tm-30) REVERT: I 864 ILE cc_start: 0.9295 (mm) cc_final: 0.8979 (mt) REVERT: I 920 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6755 (pt0) REVERT: I 1084 LEU cc_start: 0.8022 (pp) cc_final: 0.7759 (pp) REVERT: I 1111 ILE cc_start: 0.8691 (tt) cc_final: 0.8484 (mt) REVERT: I 1187 GLN cc_start: 0.7574 (pt0) cc_final: 0.6925 (pt0) REVERT: I 1234 PHE cc_start: 0.7029 (m-80) cc_final: 0.6242 (m-80) REVERT: I 1235 ASP cc_start: 0.7880 (p0) cc_final: 0.6763 (t0) REVERT: I 1319 MET cc_start: 0.4940 (pmm) cc_final: 0.4612 (pmm) outliers start: 46 outliers final: 41 residues processed: 202 average time/residue: 0.1465 time to fit residues: 43.0444 Evaluate side-chains 207 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 920 GLU Chi-restraints excluded: chain I residue 1011 MET Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126506 restraints weight = 22012.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124451 restraints weight = 48054.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125372 restraints weight = 44189.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125289 restraints weight = 30619.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125472 restraints weight = 29225.341| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17695 Z= 0.152 Angle : 0.621 11.323 25045 Z= 0.339 Chirality : 0.042 0.349 2829 Planarity : 0.004 0.049 2220 Dihedral : 28.687 178.622 4563 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.87 % Allowed : 22.46 % Favored : 73.68 % 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: 0.34 (0.23), residues: 1362 helix: 1.54 (0.19), residues: 814 sheet: -1.33 (0.66), residues: 65 loop : -1.91 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I1324 TYR 0.018 0.001 TYR H 83 PHE 0.014 0.001 PHE I1367 TRP 0.008 0.001 TRP I 922 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (17695) covalent geometry : angle 0.62121 / 0.34 (25045) hydrogen bonds : bond 0.05261 / 3.49 ( 820) hydrogen bonds : angle 3.51812 / 2.50 ( 2174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7733 (pt0) cc_final: 0.7473 (pt0) REVERT: F 91 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8699 (ttmt) REVERT: H 59 MET cc_start: 0.9003 (tpp) cc_final: 0.8562 (tpp) REVERT: I 756 GLN cc_start: 0.7890 (pm20) cc_final: 0.7640 (tm-30) REVERT: I 864 ILE cc_start: 0.9292 (mm) cc_final: 0.8973 (mt) REVERT: I 920 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: I 1084 LEU cc_start: 0.8072 (pp) cc_final: 0.7779 (pp) REVERT: I 1111 ILE cc_start: 0.8727 (tt) cc_final: 0.8513 (mt) REVERT: I 1187 GLN cc_start: 0.7579 (pt0) cc_final: 0.6923 (pt0) REVERT: I 1234 PHE cc_start: 0.7058 (m-80) cc_final: 0.6433 (m-80) REVERT: I 1235 ASP cc_start: 0.7872 (p0) cc_final: 0.6749 (t0) outliers start: 46 outliers final: 42 residues processed: 203 average time/residue: 0.1541 time to fit residues: 45.2844 Evaluate side-chains 210 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 877 TYR Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 920 GLU Chi-restraints excluded: chain I residue 1011 MET Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1137 MET Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 0.0470 chunk 75 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131047 restraints weight = 22040.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129026 restraints weight = 39462.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128944 restraints weight = 37788.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127376 restraints weight = 33078.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127916 restraints weight = 30353.622| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17695 Z= 0.146 Angle : 0.618 11.246 25045 Z= 0.339 Chirality : 0.042 0.348 2829 Planarity : 0.004 0.050 2220 Dihedral : 28.659 178.615 4563 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.78 % Allowed : 22.88 % Favored : 73.34 % 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: 0.39 (0.23), residues: 1362 helix: 1.56 (0.19), residues: 814 sheet: -1.29 (0.67), residues: 65 loop : -1.87 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I1324 TYR 0.018 0.001 TYR H 83 PHE 0.014 0.001 PHE I1367 TRP 0.008 0.001 TRP I 922 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (17695) covalent geometry : angle 0.61837 / 0.34 (25045) hydrogen bonds : bond 0.05202 / 3.45 ( 820) hydrogen bonds : angle 3.50683 / 2.50 ( 2174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.88 seconds wall clock time: 38 minutes 8.38 seconds (2288.38 seconds total)