Starting phenix.real_space_refine on Fri Jun 5 01:46:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wc_68033/06_2026/21wc_68033.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wc_68033/06_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_68033/06_2026/21wc_68033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wc_68033/06_2026/21wc_68033.map" model { file = "/net/cci-nas-00/data/ceres_data/21wc_68033/06_2026/21wc_68033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wc_68033/06_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-dev-6079/lib/python3.9/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: 3.91, per 1000 atoms: 0.23 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: 1.36 Conformation dependent library (CDL) restraints added in 609.5 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: 2.24 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: 3.79 Time building geometry restraints manager: 1.86 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' DT Y 15 " pdb=" O3' DT Y 15 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" C3' DG Y 94 " pdb=" O3' DG Y 94 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CD GLU I1310 " pdb=" OE2 GLU I1310 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.19e+00 bond pdb=" C3' DC Y 126 " pdb=" O3' DC Y 126 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" C4 ADP I1802 " pdb=" C5 ADP I1802 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 17690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 24047 1.28 - 2.57: 856 2.57 - 3.85: 106 3.85 - 5.14: 27 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=" N PHE F 100 " pdb=" CA PHE F 100 " pdb=" C PHE F 100 " ideal model delta sigma weight residual 114.62 110.80 3.82 1.14e+00 7.69e-01 1.12e+01 angle pdb=" N ASP I1169 " pdb=" CA ASP I1169 " pdb=" C ASP I1169 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.56e+00 angle pdb=" CA ILE C 79 " pdb=" C ILE C 79 " pdb=" N PRO C 80 " ideal model delta sigma weight residual 117.33 120.02 -2.69 1.01e+00 9.80e-01 7.10e+00 angle pdb=" C LEU I 928 " pdb=" N LEU I 929 " pdb=" CA LEU I 929 " ideal model delta sigma weight residual 122.26 125.18 -2.92 1.10e+00 8.26e-01 7.03e+00 ... (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 - 0.031: 1948 0.031 - 0.062: 653 0.062 - 0.092: 145 0.092 - 0.123: 76 0.123 - 0.154: 7 Chirality restraints: 2829 Sorted by residual: 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=" CA ILE I 776 " pdb=" N ILE I 776 " pdb=" C ILE I 776 " pdb=" CB ILE I 776 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-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: 3.990 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.003 0.041 17695 Z= 0.156 Angle : 0.576 6.422 25045 Z= 0.341 Chirality : 0.035 0.154 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 0.00335 / 0.16 (17695) covalent geometry : angle 0.57576 / 0.34 (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 : 0.543 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: 0.1755 time to fit residues: 49.6255 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 : 0.506 ------------------------------------------------------------------------------- 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: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 125 GLN B 25 ASN D 49 HIS D 82 HIS D 95 GLN E 39 HIS E 85 GLN G 84 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 I1048 HIS I1185 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134967 restraints weight = 21867.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133426 restraints weight = 34977.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133474 restraints weight = 34717.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132914 restraints weight = 29277.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132986 restraints weight = 26309.377| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1073 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= 0.134 Angle : 0.545 6.179 25045 Z= 0.308 Chirality : 0.035 0.135 2829 Planarity : 0.004 0.044 2220 Dihedral : 28.170 175.417 4571 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.61 % Allowed : 14.13 % Favored : 83.26 % 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: 0.32 (0.23), residues: 1362 helix: 1.40 (0.19), residues: 813 sheet: -0.59 (0.68), residues: 65 loop : -1.78 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 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 0.00285 / 0.13 (17695) covalent geometry : angle 0.54494 / 0.31 (25045) hydrogen bonds : bond 0.04713 / 3.09 ( 820) hydrogen bonds : angle 3.50518 / 2.48 ( 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 212 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7806 (t0) REVERT: E 92 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9021 (mt) REVERT: F 91 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8733 (ttmt) REVERT: G 34 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8905 (mp) REVERT: H 42 TYR cc_start: 0.7716 (t80) cc_final: 0.7503 (t80) REVERT: I 864 ILE cc_start: 0.9155 (mm) cc_final: 0.8913 (mt) REVERT: I 1051 MET cc_start: 0.8575 (ptp) cc_final: 0.8356 (ptm) outliers start: 31 outliers final: 16 residues processed: 204 average time/residue: 0.1701 time to fit residues: 48.8374 Evaluate side-chains 186 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 25 ASN 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 G residue 104 GLN Chi-restraints excluded: chain I residue 759 ILE Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 928 LEU 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 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: 1.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS D 95 GLN H 82 HIS H 109 HIS I1104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124361 restraints weight = 22223.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122262 restraints weight = 43877.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123079 restraints weight = 43082.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123192 restraints weight = 30543.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123227 restraints weight = 30687.167| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17695 Z= 0.279 Angle : 0.662 6.422 25045 Z= 0.369 Chirality : 0.041 0.152 2829 Planarity : 0.005 0.046 2220 Dihedral : 28.838 177.746 4560 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.88 % Allowed : 16.32 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1362 helix: 1.21 (0.19), residues: 814 sheet: -1.08 (0.65), residues: 65 loop : -1.78 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I1005 TYR 0.017 0.002 TYR C 57 PHE 0.013 0.002 PHE A 84 TRP 0.013 0.002 TRP I 922 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.28 (17695) covalent geometry : angle 0.66224 / 0.37 (25045) hydrogen bonds : bond 0.06115 / 4.10 ( 820) hydrogen bonds : angle 3.85880 / 2.75 ( 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 228 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8593 (t) REVERT: B 25 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7859 (t0) REVERT: F 91 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8710 (ttmt) REVERT: G 99 ARG cc_start: 0.7834 (ptp-170) cc_final: 0.7592 (ptp-170) REVERT: I 749 MET cc_start: 0.4943 (ptt) cc_final: 0.4700 (ptt) REVERT: I 797 MET cc_start: 0.5099 (mmp) cc_final: 0.4856 (mmt) REVERT: I 864 ILE cc_start: 0.9300 (mm) cc_final: 0.9047 (mt) REVERT: I 870 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8549 (tp) REVERT: I 1051 MET cc_start: 0.8717 (ptp) cc_final: 0.8509 (ptm) REVERT: I 1235 ASP cc_start: 0.7846 (p0) cc_final: 0.6518 (t0) outliers start: 58 outliers final: 32 residues processed: 212 average time/residue: 0.1622 time to fit residues: 48.8644 Evaluate side-chains 193 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 50 ILE 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 59 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 109 HIS Chi-restraints excluded: chain H residue 116 LYS 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 870 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 897 LEU 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 1109 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS E 39 HIS H 82 HIS H 109 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1164 ASN I1253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126784 restraints weight = 22040.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124492 restraints weight = 41527.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125347 restraints weight = 41146.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125016 restraints weight = 29086.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125269 restraints weight = 29925.700| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17695 Z= 0.174 Angle : 0.578 7.887 25045 Z= 0.324 Chirality : 0.037 0.160 2829 Planarity : 0.004 0.051 2220 Dihedral : 28.480 176.714 4559 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.71 % Allowed : 17.91 % Favored : 77.38 % 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: 0.27 (0.23), residues: 1362 helix: 1.43 (0.19), residues: 814 sheet: -1.15 (0.66), residues: 65 loop : -1.86 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1325 TYR 0.017 0.001 TYR I 560 PHE 0.010 0.001 PHE I1234 TRP 0.008 0.001 TRP I 922 HIS 0.021 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (17695) covalent geometry : angle 0.57760 / 0.32 (25045) hydrogen bonds : bond 0.05051 / 3.34 ( 820) hydrogen bonds : angle 3.51131 / 2.49 ( 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 230 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 91 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8814 (ttmt) REVERT: I 756 GLN cc_start: 0.7875 (pm20) cc_final: 0.7617 (tm-30) REVERT: I 864 ILE cc_start: 0.9254 (mm) cc_final: 0.9018 (mt) REVERT: I 1017 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7659 (tp) REVERT: I 1084 LEU cc_start: 0.8026 (pp) cc_final: 0.7702 (pp) REVERT: I 1111 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8471 (mt) REVERT: I 1187 GLN cc_start: 0.7577 (pt0) cc_final: 0.7355 (pt0) REVERT: I 1235 ASP cc_start: 0.7822 (p0) cc_final: 0.6524 (t0) REVERT: I 1366 MET cc_start: 0.6878 (pmm) cc_final: 0.6633 (pmm) outliers start: 56 outliers final: 33 residues processed: 215 average time/residue: 0.1491 time to fit residues: 46.3410 Evaluate side-chains 200 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR 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 114 VAL Chi-restraints excluded: chain E residue 59 GLU 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 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 72 ASP 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 886 MET Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1017 LEU Chi-restraints excluded: chain I residue 1111 ILE 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: 2.9990 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS G 84 GLN 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 = 0.3894 r_free = 0.3894 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122663 restraints weight = 22105.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120813 restraints weight = 38079.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121365 restraints weight = 37627.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120844 restraints weight = 30326.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120978 restraints weight = 28938.941| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17695 Z= 0.218 Angle : 0.614 7.014 25045 Z= 0.342 Chirality : 0.038 0.152 2829 Planarity : 0.004 0.050 2220 Dihedral : 28.571 177.485 4559 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.54 % Allowed : 19.93 % Favored : 75.53 % 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: 0.24 (0.23), residues: 1362 helix: 1.39 (0.19), residues: 816 sheet: -1.37 (0.65), residues: 65 loop : -1.80 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 55 TYR 0.016 0.002 TYR C 57 PHE 0.012 0.001 PHE F 100 TRP 0.010 0.001 TRP I 922 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (17695) covalent geometry : angle 0.61427 / 0.34 (25045) hydrogen bonds : bond 0.05488 / 3.63 ( 820) hydrogen bonds : angle 3.60698 / 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 226 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 91 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8671 (ttmt) REVERT: I 756 GLN cc_start: 0.7856 (pm20) cc_final: 0.7651 (tm-30) REVERT: I 864 ILE cc_start: 0.9297 (mm) cc_final: 0.8979 (mt) REVERT: I 1084 LEU cc_start: 0.8117 (pp) cc_final: 0.7835 (pp) REVERT: I 1187 GLN cc_start: 0.7566 (pt0) cc_final: 0.7300 (pt0) REVERT: I 1208 ASN cc_start: 0.7354 (t0) cc_final: 0.7144 (t0) REVERT: I 1235 ASP cc_start: 0.7891 (p0) cc_final: 0.6741 (t0) outliers start: 54 outliers final: 41 residues processed: 208 average time/residue: 0.1560 time to fit residues: 46.7691 Evaluate side-chains 204 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR 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 114 VAL Chi-restraints excluded: chain E residue 59 GLU 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 46 ILE 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 886 MET 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 1112 MET 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 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: 0.5980 chunk 139 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS 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 = 0.3897 r_free = 0.3897 target = 0.166965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124964 restraints weight = 22174.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123891 restraints weight = 41487.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124033 restraints weight = 42147.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123496 restraints weight = 33452.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123833 restraints weight = 32465.414| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17695 Z= 0.216 Angle : 0.610 7.957 25045 Z= 0.340 Chirality : 0.038 0.153 2829 Planarity : 0.004 0.052 2220 Dihedral : 28.517 176.654 4559 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.63 % Allowed : 20.02 % Favored : 74.35 % 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: 0.26 (0.23), residues: 1362 helix: 1.44 (0.19), residues: 813 sheet: -1.46 (0.65), residues: 65 loop : -1.83 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 55 TYR 0.021 0.002 TYR H 83 PHE 0.009 0.001 PHE F 100 TRP 0.010 0.001 TRP I 922 HIS 0.011 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (17695) covalent geometry : angle 0.60999 / 0.34 (25045) hydrogen bonds : bond 0.05336 / 3.54 ( 820) hydrogen bonds : angle 3.54139 / 2.52 ( 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 237 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7946 (tm-30) REVERT: F 91 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8681 (ttmt) REVERT: I 864 ILE cc_start: 0.9354 (mm) cc_final: 0.9003 (mt) REVERT: I 1084 LEU cc_start: 0.8170 (pp) cc_final: 0.7862 (pp) REVERT: I 1187 GLN cc_start: 0.7362 (pt0) cc_final: 0.6935 (pt0) REVERT: I 1235 ASP cc_start: 0.7888 (p0) cc_final: 0.6751 (t0) outliers start: 67 outliers final: 45 residues processed: 222 average time/residue: 0.1608 time to fit residues: 51.1222 Evaluate side-chains 208 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 VAL 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 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 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 928 LEU Chi-restraints excluded: chain I residue 1016 VAL Chi-restraints excluded: chain I residue 1041 GLN Chi-restraints excluded: chain I residue 1111 ILE Chi-restraints excluded: chain I residue 1112 MET 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 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: 1.9990 chunk 81 optimal weight: 0.6980 chunk 124 optimal weight: 0.0020 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 82 HIS I 788 GLN ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.167977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127001 restraints weight = 22230.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124823 restraints weight = 47042.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125360 restraints weight = 43138.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125114 restraints weight = 33025.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125236 restraints weight = 34344.764| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17695 Z= 0.153 Angle : 0.568 7.858 25045 Z= 0.316 Chirality : 0.036 0.155 2829 Planarity : 0.004 0.049 2220 Dihedral : 28.269 176.744 4559 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.45 % Allowed : 22.12 % Favored : 74.43 % 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: 0.47 (0.23), residues: 1362 helix: 1.63 (0.19), residues: 816 sheet: -1.45 (0.65), residues: 65 loop : -1.82 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 842 TYR 0.021 0.001 TYR H 83 PHE 0.011 0.001 PHE I1234 TRP 0.008 0.001 TRP I 922 HIS 0.007 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (17695) covalent geometry : angle 0.56816 / 0.32 (25045) hydrogen bonds : bond 0.04770 / 3.11 ( 820) hydrogen bonds : angle 3.36965 / 2.39 ( 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 215 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7974 (tm-30) REVERT: D 59 MET cc_start: 0.9315 (mmm) cc_final: 0.9044 (tpp) REVERT: F 91 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8634 (ttmt) REVERT: H 59 MET cc_start: 0.9012 (tpp) cc_final: 0.8530 (tpp) REVERT: I 864 ILE cc_start: 0.9317 (mm) cc_final: 0.8980 (mt) REVERT: I 1084 LEU cc_start: 0.8122 (pp) cc_final: 0.7827 (pp) REVERT: I 1187 GLN cc_start: 0.7363 (pt0) cc_final: 0.7160 (pt0) REVERT: I 1235 ASP cc_start: 0.7802 (p0) cc_final: 0.6801 (t0) outliers start: 41 outliers final: 35 residues processed: 205 average time/residue: 0.1605 time to fit residues: 46.9837 Evaluate side-chains 201 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 THR 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 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 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 52 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 759 ILE 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 1041 GLN Chi-restraints excluded: chain I residue 1116 PHE Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1302 VAL Chi-restraints excluded: chain I residue 1366 MET 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: 1.9990 chunk 29 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132225 restraints weight = 22341.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130562 restraints weight = 37887.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130709 restraints weight = 37014.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130120 restraints weight = 28536.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130460 restraints weight = 28015.712| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17695 Z= 0.152 Angle : 0.570 8.091 25045 Z= 0.316 Chirality : 0.036 0.198 2829 Planarity : 0.004 0.053 2220 Dihedral : 28.216 176.982 4557 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.36 % Allowed : 22.96 % 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: 0.57 (0.23), residues: 1362 helix: 1.70 (0.19), residues: 816 sheet: -1.34 (0.66), residues: 65 loop : -1.77 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 967 TYR 0.019 0.001 TYR H 83 PHE 0.009 0.001 PHE F 100 TRP 0.009 0.001 TRP I 922 HIS 0.008 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (17695) covalent geometry : angle 0.57026 / 0.32 (25045) hydrogen bonds : bond 0.04735 / 3.09 ( 820) hydrogen bonds : angle 3.34063 / 2.38 ( 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 207 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 91 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8651 (ttmt) REVERT: H 59 MET cc_start: 0.9039 (tpp) cc_final: 0.8513 (tpp) REVERT: I 864 ILE cc_start: 0.9317 (mm) cc_final: 0.8982 (mt) REVERT: I 981 LYS cc_start: 0.6834 (mmtm) cc_final: 0.6592 (mmtm) REVERT: I 1084 LEU cc_start: 0.8218 (pp) cc_final: 0.7951 (pp) REVERT: I 1187 GLN cc_start: 0.7372 (pt0) cc_final: 0.7134 (pt0) REVERT: I 1235 ASP cc_start: 0.7810 (p0) cc_final: 0.6740 (t0) outliers start: 40 outliers final: 35 residues processed: 197 average time/residue: 0.1624 time to fit residues: 45.6060 Evaluate side-chains 198 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 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 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 45 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain I residue 759 ILE 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 1041 GLN 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 1161 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 155 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS H 82 HIS ** I 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137522 restraints weight = 22299.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136136 restraints weight = 33098.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135413 restraints weight = 33742.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134367 restraints weight = 30053.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134847 restraints weight = 26493.252| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17695 Z= 0.133 Angle : 0.554 8.573 25045 Z= 0.307 Chirality : 0.035 0.188 2829 Planarity : 0.004 0.048 2220 Dihedral : 28.012 177.058 4557 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.11 % Allowed : 23.80 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1362 helix: 1.81 (0.18), residues: 821 sheet: -1.18 (0.67), residues: 65 loop : -1.72 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 842 TYR 0.020 0.001 TYR H 83 PHE 0.011 0.001 PHE I1313 TRP 0.008 0.001 TRP I 818 HIS 0.008 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17695) covalent geometry : angle 0.55441 / 0.31 (25045) hydrogen bonds : bond 0.04433 / 2.87 ( 820) hydrogen bonds : angle 3.27867 / 2.34 ( 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 213 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7995 (tm-30) REVERT: F 91 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8714 (ttmt) REVERT: H 59 MET cc_start: 0.9006 (tpp) cc_final: 0.8469 (tpp) REVERT: I 864 ILE cc_start: 0.9265 (mm) cc_final: 0.8952 (mt) REVERT: I 1187 GLN cc_start: 0.7317 (pt0) cc_final: 0.6959 (pt0) REVERT: I 1235 ASP cc_start: 0.7762 (p0) cc_final: 0.6769 (t0) outliers start: 37 outliers final: 26 residues processed: 198 average time/residue: 0.1698 time to fit residues: 47.6951 Evaluate side-chains 193 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 58 LEU 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 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 63 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 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 1041 GLN Chi-restraints excluded: chain I residue 1062 HIS 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: 0.9980 chunk 128 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131265 restraints weight = 22181.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130142 restraints weight = 36063.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130281 restraints weight = 36270.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129468 restraints weight = 28152.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129875 restraints weight = 26675.059| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17695 Z= 0.169 Angle : 0.599 10.331 25045 Z= 0.327 Chirality : 0.037 0.211 2829 Planarity : 0.004 0.053 2220 Dihedral : 28.157 177.423 4557 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.20 % Allowed : 23.97 % Favored : 72.83 % 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: 0.66 (0.23), residues: 1362 helix: 1.78 (0.19), residues: 815 sheet: -1.17 (0.67), residues: 65 loop : -1.76 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 842 TYR 0.019 0.002 TYR I1379 PHE 0.020 0.001 PHE I 927 TRP 0.011 0.001 TRP I 922 HIS 0.008 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (17695) covalent geometry : angle 0.59926 / 0.33 (25045) hydrogen bonds : bond 0.04887 / 3.21 ( 820) hydrogen bonds : angle 3.40882 / 2.46 ( 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 203 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: F 91 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8685 (ttmt) REVERT: H 59 MET cc_start: 0.9027 (tpp) cc_final: 0.8484 (tpp) REVERT: I 1187 GLN cc_start: 0.7392 (pt0) cc_final: 0.6983 (pt0) REVERT: I 1235 ASP cc_start: 0.7902 (p0) cc_final: 0.6706 (t0) outliers start: 38 outliers final: 32 residues processed: 192 average time/residue: 0.1679 time to fit residues: 46.0158 Evaluate side-chains 190 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 60 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 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 51 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 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 1041 GLN Chi-restraints excluded: chain I residue 1112 MET Chi-restraints excluded: chain I residue 1116 PHE 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: 2.9990 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 75 optimal weight: 0.0000 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 143 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS H 82 HIS ** I 900 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 = 0.3998 r_free = 0.3998 target = 0.176197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135132 restraints weight = 22188.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132899 restraints weight = 34116.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132579 restraints weight = 33853.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131952 restraints weight = 27239.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131917 restraints weight = 27069.657| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17695 Z= 0.137 Angle : 0.578 9.420 25045 Z= 0.316 Chirality : 0.036 0.217 2829 Planarity : 0.004 0.047 2220 Dihedral : 27.992 177.281 4557 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.78 % Allowed : 24.73 % Favored : 72.50 % 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: 0.76 (0.23), residues: 1362 helix: 1.83 (0.18), residues: 823 sheet: -1.02 (0.68), residues: 64 loop : -1.74 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 842 TYR 0.022 0.001 TYR I1379 PHE 0.009 0.001 PHE I1234 TRP 0.009 0.001 TRP I 922 HIS 0.009 0.001 HIS I1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (17695) covalent geometry : angle 0.57817 / 0.32 (25045) hydrogen bonds : bond 0.04492 / 2.92 ( 820) hydrogen bonds : angle 3.26637 / 2.34 ( 2174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.03 seconds wall clock time: 42 minutes 30.08 seconds (2550.08 seconds total)