Starting phenix.real_space_refine on Fri Aug 7 20:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21vv_68040/08_2026/21vv_68040.cif Found real_map, /net/cci-nas-00/data/ceres_data/21vv_68040/08_2026/21vv_68040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21vv_68040/08_2026/21vv_68040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21vv_68040/08_2026/21vv_68040.map" model { file = "/net/cci-nas-00/data/ceres_data/21vv_68040/08_2026/21vv_68040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21vv_68040/08_2026/21vv_68040.cif" } resolution = 4.7 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 82 5.16 5 Be 1 3.05 5 C 13837 2.51 5 N 4222 2.21 5 O 4855 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 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23277 Number of models: 1 Model: "" Number of chains: 15 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: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 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: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5409 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 19, 'TRANS': 638} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2585 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain breaks: 4 Chain: "K" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3152 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 22, 'TRANS': 381} Chain breaks: 1 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: 5.01, per 1000 atoms: 0.22 Number of scatterers: 23277 At special positions: 0 Unit cell: (150.7, 134.2, 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 82 16.00 P 276 15.00 Mg 1 11.99 F 3 9.00 O 4855 8.00 N 4222 7.00 C 13837 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: 1.97 Conformation dependent library (CDL) restraints added in 962.3 milliseconds 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 22 sheets defined 59.2% alpha, 8.4% beta 102 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.706A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.927A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.640A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.641A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.582A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.240A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.521A pdb=" N LYS B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.236A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.731A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.545A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.655A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.250A 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 77 removed outlier: 3.578A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.662A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.531A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.936A 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: 4.082A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.730A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.776A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.779A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.526A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU H 102 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.293A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 19 Processing helix chain 'I' and resid 465 through 515 removed outlier: 3.581A pdb=" N THR I 511 " --> pdb=" O TYR I 507 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN I 515 " --> pdb=" O THR I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 573 removed outlier: 3.650A pdb=" N GLN I 555 " --> pdb=" O ALA I 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN I 556 " --> pdb=" O TYR I 552 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 562 " --> pdb=" O ASP I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 736 removed outlier: 3.640A 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 784 through 800 removed outlier: 4.209A pdb=" N GLN I 788 " --> pdb=" O GLY I 784 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR I 789 " --> pdb=" O LYS I 785 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 826 Processing helix chain 'I' and resid 837 through 844 removed outlier: 3.835A pdb=" N PHE I 844 " --> pdb=" O ALA I 840 " (cutoff:3.500A) Processing helix chain 'I' and resid 844 through 851 Processing helix chain 'I' and resid 860 through 866 removed outlier: 3.709A pdb=" N ILE I 864 " --> pdb=" O TYR I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 871 Processing helix chain 'I' and resid 883 through 888 removed outlier: 4.125A pdb=" N ASN I 888 " --> pdb=" O ARG I 885 " (cutoff:3.500A) Processing helix chain 'I' and resid 891 through 899 Processing helix chain 'I' and resid 918 through 929 Processing helix chain 'I' and resid 929 through 934 removed outlier: 3.772A pdb=" N LYS I 934 " --> pdb=" O PRO I 930 " (cutoff:3.500A) Processing helix chain 'I' and resid 960 through 972 removed outlier: 4.274A pdb=" N LEU I 972 " --> pdb=" O LEU I 968 " (cutoff:3.500A) Processing helix chain 'I' and resid 973 through 976 removed outlier: 3.690A 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 Processing helix chain 'I' and resid 1001 through 1014 removed outlier: 3.782A pdb=" N ARG I1009 " --> pdb=" O ARG I1005 " (cutoff:3.500A) removed outlier: 4.018A 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: 3.724A pdb=" N PHE I1052 " --> pdb=" O PRO I1049 " (cutoff:3.500A) removed outlier: 3.591A 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 1064 removed outlier: 3.800A pdb=" N GLY I1064 " --> pdb=" O SER I1060 " (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 1119 removed outlier: 4.153A pdb=" N MET I1109 " --> pdb=" O MET I1105 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP I1114 " --> pdb=" O THR I1110 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR I1115 " --> pdb=" O ILE I1111 " (cutoff:3.500A) Processing helix chain 'I' and resid 1131 through 1144 removed outlier: 3.854A pdb=" N ARG I1135 " --> pdb=" O LYS I1131 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY I1136 " --> pdb=" O ALA I1132 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET I1137 " --> pdb=" O GLU I1133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I1144 " --> pdb=" O LYS I1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 1156 through 1160 Processing helix chain 'I' and resid 1179 through 1188 removed outlier: 4.226A 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 1210 through 1230 removed outlier: 4.048A pdb=" N VAL I1224 " --> pdb=" O TYR I1220 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I1228 " --> pdb=" O VAL I1224 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE I1229 " --> pdb=" O ASP I1225 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN I1230 " --> pdb=" O GLN I1226 " (cutoff:3.500A) Processing helix chain 'I' and resid 1241 through 1255 removed outlier: 4.648A pdb=" N ALA I1249 " --> pdb=" O ALA I1245 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE I1250 " --> pdb=" O PHE I1246 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU I1251 " --> pdb=" O LEU I1247 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU I1252 " --> pdb=" O GLN I1248 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU I1255 " --> pdb=" O LEU I1251 " (cutoff:3.500A) Processing helix chain 'I' and resid 1300 through 1307 removed outlier: 4.147A pdb=" N GLN I1304 " --> pdb=" O GLU I1300 " (cutoff:3.500A) Processing helix chain 'I' and resid 1309 through 1330 removed outlier: 3.682A pdb=" N LEU I1315 " --> pdb=" O GLU I1311 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE I1316 " --> pdb=" O GLU I1312 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET I1317 " --> pdb=" O PHE I1313 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG I1318 " --> pdb=" O ASP I1314 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET I1319 " --> pdb=" O LEU I1315 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU I1321 " --> pdb=" O MET I1317 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP I1322 " --> pdb=" O ARG I1318 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG I1329 " --> pdb=" O ARG I1325 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN I1330 " --> pdb=" O GLU I1326 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.578A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.517A pdb=" N GLU J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.822A pdb=" N MET J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.610A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 197 Processing helix chain 'J' and resid 202 through 216 removed outlier: 3.535A pdb=" N LYS J 215 " --> pdb=" O ASP J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 230 removed outlier: 3.999A pdb=" N ALA J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 257 removed outlier: 4.900A pdb=" N CYS J 257 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 removed outlier: 3.856A pdb=" N PHE J 262 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 268 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 289 through 295 removed outlier: 4.162A pdb=" N LEU J 293 " --> pdb=" O ILE J 289 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 337 through 347 Processing helix chain 'J' and resid 350 through 355 removed outlier: 3.596A pdb=" N GLN J 353 " --> pdb=" O SER J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'J' and resid 369 through 374 Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 95 through 110 Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.530A pdb=" N HIS K 118 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 144 removed outlier: 4.055A pdb=" N LYS K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR K 144 " --> pdb=" O MET K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 Processing helix chain 'K' and resid 198 through 211 removed outlier: 3.640A pdb=" N GLN K 211 " --> pdb=" O ARG K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 214 No H-bonds generated for 'chain 'K' and resid 212 through 214' Processing helix chain 'K' and resid 247 through 267 removed outlier: 3.519A pdb=" N MET K 254 " --> pdb=" O TRP K 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER K 265 " --> pdb=" O ASP K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 281 removed outlier: 3.707A pdb=" N ALA K 280 " --> pdb=" O GLN K 277 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN K 281 " --> pdb=" O VAL K 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 277 through 281' Processing helix chain 'K' and resid 299 through 307 removed outlier: 3.586A pdb=" N ILE K 304 " --> pdb=" O GLU K 300 " (cutoff:3.500A) Proline residue: K 305 - end of helix Processing helix chain 'K' and resid 308 through 309 No H-bonds generated for 'chain 'K' and resid 308 through 309' Processing helix chain 'K' and resid 310 through 314 Processing helix chain 'K' and resid 324 through 335 removed outlier: 3.567A pdb=" N MET K 335 " --> pdb=" O THR K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 removed outlier: 3.661A pdb=" N SER K 347 " --> pdb=" O GLY K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 357 removed outlier: 3.749A pdb=" N ILE K 357 " --> pdb=" O ASN K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 372 removed outlier: 4.138A pdb=" N ARG K 363 " --> pdb=" O SER K 359 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU K 364 " --> pdb=" O PHE K 360 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN K 370 " --> pdb=" O ARG K 366 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS K 371 " --> pdb=" O GLU K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 391 Processing helix chain 'K' and resid 391 through 402 Processing helix chain 'K' and resid 403 through 410 removed outlier: 4.297A pdb=" N GLN K 407 " --> pdb=" O GLY K 404 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET K 409 " --> pdb=" O PHE K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 420 Processing helix chain 'K' and resid 422 through 428 removed outlier: 4.123A pdb=" N ARG K 426 " --> pdb=" O GLN K 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.366A 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: 6.609A 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: 4.048A 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 97 removed outlier: 6.851A 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: 7.395A 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 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'N' and resid 31 through 37 Processing sheet with id=AA9, first strand: chain 'I' and resid 776 through 777 removed outlier: 6.291A pdb=" N MET I 878 " --> pdb=" O LEU I 907 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU I 909 " --> pdb=" O MET I 878 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL I 880 " --> pdb=" O LEU I 909 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU I 807 " --> pdb=" O TYR I 877 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE I 808 " --> pdb=" O THR I 858 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 992 through 996 removed outlier: 6.736A pdb=" N VAL I 992 " --> pdb=" O VAL I1201 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG I1203 " --> pdb=" O VAL I 992 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR I 994 " --> pdb=" O ARG I1203 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL I1171 " --> pdb=" O ARG I1200 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU I1124 " --> pdb=" O LEU I1153 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER I1155 " --> pdb=" O LEU I1124 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 1016 through 1018 Processing sheet with id=AB3, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.942A pdb=" N THR J 106 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 132 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'K' and resid 35 through 38 removed outlier: 6.485A pdb=" N LEU K 14 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N SER K 123 " --> pdb=" O LEU K 14 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE K 16 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL K 120 " --> pdb=" O PHE K 150 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N CYS K 152 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET K 122 " --> pdb=" O CYS K 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 67 through 69 removed outlier: 3.610A pdb=" N GLY K 42 " --> pdb=" O TYR K 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AC1, first strand: chain 'K' and resid 186 through 187 Processing sheet with id=AC2, first strand: chain 'K' and resid 186 through 187 removed outlier: 6.106A pdb=" N VAL K 348 " --> pdb=" O ILE K 381 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 223 through 227 removed outlier: 4.879A pdb=" N SER K 225 " --> pdb=" O LYS K 238 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS K 238 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN K 236 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 285 through 288 878 hydrogen bonds defined for protein. 2511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 261 hydrogen bonds 506 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5653 1.33 - 1.45: 5833 1.45 - 1.57: 12099 1.57 - 1.69: 549 1.69 - 1.81: 141 Bond restraints: 24275 Sorted by residual: bond pdb=" CA VAL I 845 " pdb=" CB VAL I 845 " ideal model delta sigma weight residual 1.537 1.519 0.018 5.00e-03 4.00e+04 1.29e+01 bond pdb=" C3' DT Y 57 " pdb=" C2' DT Y 57 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT Y 107 " pdb=" C2' DT Y 107 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT Y 11 " pdb=" C2' DT Y 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.25e+00 bond pdb=" C3' DC X 51 " pdb=" C2' DC X 51 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 ... (remaining 24270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 31750 1.27 - 2.53: 1891 2.53 - 3.80: 243 3.80 - 5.06: 45 5.06 - 6.33: 17 Bond angle restraints: 33946 Sorted by residual: angle pdb=" O4' DC X 96 " pdb=" C4' DC X 96 " pdb=" C3' DC X 96 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT Y 105 " pdb=" C4 DT Y 105 " pdb=" O4 DT Y 105 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT X 117 " pdb=" C4 DT X 117 " pdb=" O4 DT X 117 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT X 46 " pdb=" C4 DT X 46 " pdb=" O4 DT X 46 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT X 88 " pdb=" C4 DT X 88 " pdb=" O4 DT X 88 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 33941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 12405 32.94 - 65.88: 1484 65.88 - 98.83: 59 98.83 - 131.77: 1 131.77 - 164.71: 3 Dihedral angle restraints: 13952 sinusoidal: 7544 harmonic: 6408 Sorted by residual: dihedral pdb=" O2A ADP I1803 " pdb=" O3A ADP I1803 " pdb=" PA ADP I1803 " pdb=" PB ADP I1803 " ideal model delta sinusoidal sigma weight residual -60.00 -173.93 113.94 1 2.00e+01 2.50e-03 3.37e+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 55.29 164.71 1 3.50e+01 8.16e-04 1.54e+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 57.85 162.15 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 13949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2689 0.039 - 0.078: 770 0.078 - 0.116: 316 0.116 - 0.155: 35 0.155 - 0.194: 1 Chirality restraints: 3811 Sorted by residual: chirality pdb=" C3' DG Y 94 " pdb=" C4' DG Y 94 " pdb=" O3' DG Y 94 " pdb=" C2' DG Y 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" C3' DA Y 100 " pdb=" C4' DA Y 100 " pdb=" O3' DA Y 100 " pdb=" C2' DA Y 100 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" C3' DC Y 98 " pdb=" C4' DC Y 98 " pdb=" O3' DC Y 98 " pdb=" C2' DC Y 98 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 3808 not shown) Planarity restraints: 3359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 49 " 0.021 2.00e-02 2.50e+03 9.09e-03 2.27e+00 pdb=" N9 DA X 49 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA X 49 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA X 49 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA X 49 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA X 49 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA X 49 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA X 49 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA X 49 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA X 49 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA X 49 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO G 80 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO H 103 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.021 5.00e-02 4.00e+02 ... (remaining 3356 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 243 2.56 - 3.15: 19313 3.15 - 3.73: 42543 3.73 - 4.32: 53930 4.32 - 4.90: 80422 Nonbonded interactions: 196451 Sorted by model distance: nonbonded pdb=" O2 DC X 143 " pdb=" N2 DG Y 5 " model vdw 1.976 2.496 nonbonded pdb=" O2 DC X 95 " pdb=" N2 DG Y 53 " model vdw 2.025 2.496 nonbonded pdb=" N2 DG X 148 " pdb=" O2 DC Y 0 " model vdw 2.040 2.496 nonbonded pdb=" OD2 ASP I 881 " pdb="MG MG I1802 " model vdw 2.074 2.170 nonbonded pdb="BE BEF I1801 " pdb=" O1B ADP I1803 " model vdw 2.160 2.420 ... (remaining 196446 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: 3.060 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: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.090 Process input model: 25.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 30.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24275 Z= 0.386 Angle : 0.663 6.331 33946 Z= 0.521 Chirality : 0.043 0.194 3811 Planarity : 0.004 0.037 3359 Dihedral : 22.341 164.712 9812 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.02 % Allowed : 11.90 % Favored : 84.08 % 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: 0.40 (0.19), residues: 2158 helix: 0.76 (0.15), residues: 1129 sheet: 0.48 (0.41), residues: 178 loop : -0.32 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 372 TYR 0.020 0.001 TYR I 560 PHE 0.011 0.001 PHE I 927 TRP 0.011 0.001 TRP I 922 HIS 0.006 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.39 (24275) covalent geometry : angle 0.66278 / 0.52 (33946) hydrogen bonds : bond 0.13671 / 9.42 ( 1135) hydrogen bonds : angle 5.77978 / 4.21 ( 3017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 416 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8286 (mm-30) REVERT: A 120 MET cc_start: 0.8750 (mtm) cc_final: 0.8411 (mtm) REVERT: C 104 GLN cc_start: 0.8809 (pm20) cc_final: 0.8480 (pm20) REVERT: C 112 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8352 (tp-100) REVERT: D 68 ASP cc_start: 0.9447 (t0) cc_final: 0.9243 (t0) REVERT: E 93 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7390 (tm-30) REVERT: E 120 MET cc_start: 0.8229 (mpp) cc_final: 0.7546 (mpp) REVERT: F 52 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8759 (mm-30) REVERT: F 55 ARG cc_start: 0.9363 (mtt-85) cc_final: 0.9105 (mtt-85) REVERT: G 92 GLU cc_start: 0.8828 (tt0) cc_final: 0.8268 (tt0) REVERT: H 46 LYS cc_start: 0.8876 (tppt) cc_final: 0.8643 (tppt) REVERT: H 109 HIS cc_start: 0.8258 (m170) cc_final: 0.7918 (m-70) REVERT: N 30 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8591 (mmmt) REVERT: I 748 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8048 (pt) REVERT: I 822 PHE cc_start: 0.8106 (m-10) cc_final: 0.7808 (m-80) REVERT: I 1012 GLN cc_start: 0.9118 (mt0) cc_final: 0.8799 (mt0) REVERT: I 1046 CYS cc_start: 0.9457 (m) cc_final: 0.9189 (m) REVERT: I 1111 ILE cc_start: 0.9540 (tt) cc_final: 0.9222 (tt) REVERT: J 325 MET cc_start: 0.4802 (tpt) cc_final: 0.3985 (tpt) REVERT: K 82 MET cc_start: 0.3215 (tmm) cc_final: 0.2343 (tmm) REVERT: K 150 PHE cc_start: 0.5441 (OUTLIER) cc_final: 0.4593 (m-10) REVERT: K 409 MET cc_start: 0.6504 (pmm) cc_final: 0.6265 (pmm) outliers start: 76 outliers final: 30 residues processed: 456 average time/residue: 0.1659 time to fit residues: 119.1006 Evaluate side-chains 391 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 358 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 49 HIS H 109 HIS I 508 HIS I 555 GLN ** I 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 884 HIS ** I 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1012 GLN ** I1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1187 GLN ** I1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.127534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074022 restraints weight = 80510.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076833 restraints weight = 44198.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078671 restraints weight = 30694.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079802 restraints weight = 24577.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.080525 restraints weight = 21546.622| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24275 Z= 0.221 Angle : 0.679 9.007 33946 Z= 0.385 Chirality : 0.045 0.330 3811 Planarity : 0.005 0.060 3359 Dihedral : 26.156 165.935 5430 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: 0.28 (0.18), residues: 2158 helix: 0.58 (0.15), residues: 1157 sheet: 0.40 (0.40), residues: 182 loop : -0.26 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.030 0.002 TYR I 877 PHE 0.023 0.002 PHE C 25 TRP 0.015 0.002 TRP K 410 HIS 0.013 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (24275) covalent geometry : angle 0.67927 / 0.39 (33946) hydrogen bonds : bond 0.05936 / 4.14 ( 1135) hydrogen bonds : angle 5.04217 / 3.68 ( 3017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8018 (tp30) REVERT: A 120 MET cc_start: 0.8794 (mtm) cc_final: 0.8293 (mtm) REVERT: B 37 LEU cc_start: 0.9611 (mm) cc_final: 0.9347 (mm) REVERT: C 82 HIS cc_start: 0.9081 (m-70) cc_final: 0.8859 (m-70) REVERT: D 47 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8683 (tm-30) REVERT: D 59 MET cc_start: 0.9547 (mmm) cc_final: 0.9155 (mmt) REVERT: D 68 ASP cc_start: 0.9517 (t0) cc_final: 0.9308 (t0) REVERT: E 96 SER cc_start: 0.9512 (m) cc_final: 0.9306 (m) REVERT: E 112 ILE cc_start: 0.9066 (mt) cc_final: 0.8832 (mt) REVERT: E 119 ILE cc_start: 0.8955 (pt) cc_final: 0.8606 (pt) REVERT: E 120 MET cc_start: 0.8145 (mpp) cc_final: 0.7601 (mpp) REVERT: F 18 HIS cc_start: 0.5952 (p-80) cc_final: 0.5742 (t70) REVERT: F 55 ARG cc_start: 0.9197 (mtt-85) cc_final: 0.8698 (mtt-85) REVERT: G 23 LEU cc_start: 0.9170 (mt) cc_final: 0.8967 (mt) REVERT: G 64 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8892 (tm-30) REVERT: G 92 GLU cc_start: 0.8821 (tt0) cc_final: 0.8196 (tt0) REVERT: H 46 LYS cc_start: 0.8884 (tppt) cc_final: 0.8634 (tppt) REVERT: N 30 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8766 (mmmt) REVERT: I 763 GLU cc_start: 0.8572 (tt0) cc_final: 0.8150 (mt-10) REVERT: I 822 PHE cc_start: 0.8123 (m-10) cc_final: 0.7778 (m-80) REVERT: I 878 MET cc_start: 0.9110 (ttp) cc_final: 0.8711 (ttp) REVERT: I 884 HIS cc_start: 0.9041 (m90) cc_final: 0.8677 (m-70) REVERT: I 1012 GLN cc_start: 0.9100 (mt0) cc_final: 0.8824 (mt0) REVERT: I 1046 CYS cc_start: 0.9483 (m) cc_final: 0.9257 (m) REVERT: I 1085 LEU cc_start: 0.9601 (tp) cc_final: 0.9352 (tp) REVERT: I 1102 PHE cc_start: 0.8168 (m-80) cc_final: 0.7968 (m-80) REVERT: J 190 MET cc_start: -0.3256 (mtm) cc_final: -0.3513 (mtm) REVERT: J 325 MET cc_start: 0.5079 (tpt) cc_final: 0.4353 (tpt) REVERT: K 82 MET cc_start: 0.3310 (tmm) cc_final: 0.2242 (tmm) REVERT: K 297 PHE cc_start: 0.8895 (m-80) cc_final: 0.8417 (m-80) REVERT: K 376 MET cc_start: 0.3535 (ptt) cc_final: 0.3208 (ptm) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.1677 time to fit residues: 115.7584 Evaluate side-chains 355 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 chunk 177 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 165 optimal weight: 0.1980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.129888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077842 restraints weight = 79869.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081259 restraints weight = 44554.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083146 restraints weight = 26126.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082981 restraints weight = 23127.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083101 restraints weight = 21885.021| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24275 Z= 0.143 Angle : 0.619 9.175 33946 Z= 0.349 Chirality : 0.044 0.365 3811 Planarity : 0.004 0.045 3359 Dihedral : 26.190 169.317 5430 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2158 helix: 0.69 (0.15), residues: 1165 sheet: 0.39 (0.41), residues: 177 loop : -0.37 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 335 TYR 0.020 0.002 TYR D 42 PHE 0.027 0.001 PHE I 933 TRP 0.017 0.002 TRP I 922 HIS 0.010 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (24275) covalent geometry : angle 0.61852 / 0.35 (33946) hydrogen bonds : bond 0.05310 / 3.73 ( 1135) hydrogen bonds : angle 4.63386 / 3.38 ( 3017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8473 (tp30) REVERT: A 97 GLU cc_start: 0.8524 (pp20) cc_final: 0.8185 (pp20) REVERT: A 120 MET cc_start: 0.8833 (mtm) cc_final: 0.8311 (mtm) REVERT: B 37 LEU cc_start: 0.9549 (mm) cc_final: 0.9203 (mm) REVERT: B 39 ARG cc_start: 0.8955 (mmp80) cc_final: 0.8586 (mmp80) REVERT: B 63 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8372 (mt-10) REVERT: C 77 ARG cc_start: 0.8848 (tpp-160) cc_final: 0.8136 (tpp80) REVERT: D 47 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 59 MET cc_start: 0.9511 (mmm) cc_final: 0.9232 (mmm) REVERT: D 68 ASP cc_start: 0.9466 (t0) cc_final: 0.9203 (t0) REVERT: E 119 ILE cc_start: 0.8695 (pt) cc_final: 0.8348 (pt) REVERT: E 120 MET cc_start: 0.7912 (mpp) cc_final: 0.7299 (mpp) REVERT: F 18 HIS cc_start: 0.5902 (p-80) cc_final: 0.5665 (t70) REVERT: F 55 ARG cc_start: 0.9236 (mtt-85) cc_final: 0.8954 (mtt-85) REVERT: F 59 LYS cc_start: 0.9370 (ttmt) cc_final: 0.8810 (ttpt) REVERT: F 63 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8779 (mm-30) REVERT: G 92 GLU cc_start: 0.8758 (tt0) cc_final: 0.8207 (tt0) REVERT: G 95 LYS cc_start: 0.9498 (tppp) cc_final: 0.9079 (tppp) REVERT: H 109 HIS cc_start: 0.8274 (m90) cc_final: 0.7499 (m90) REVERT: N 30 LYS cc_start: 0.8989 (mmpt) cc_final: 0.8683 (mmmt) REVERT: I 763 GLU cc_start: 0.8460 (tt0) cc_final: 0.8062 (mt-10) REVERT: I 822 PHE cc_start: 0.7842 (m-10) cc_final: 0.7537 (m-80) REVERT: I 878 MET cc_start: 0.9157 (ttp) cc_final: 0.8773 (ttp) REVERT: I 884 HIS cc_start: 0.9000 (m90) cc_final: 0.8666 (m-70) REVERT: I 1046 CYS cc_start: 0.9494 (m) cc_final: 0.9238 (m) REVERT: I 1085 LEU cc_start: 0.9633 (tp) cc_final: 0.9386 (tp) REVERT: I 1112 MET cc_start: 0.9574 (tpt) cc_final: 0.9211 (tpt) REVERT: I 1116 PHE cc_start: 0.8864 (m-10) cc_final: 0.8649 (m-80) REVERT: I 1171 VAL cc_start: 0.9606 (p) cc_final: 0.9364 (p) REVERT: I 1298 ASP cc_start: 0.7638 (m-30) cc_final: 0.7425 (m-30) REVERT: J 190 MET cc_start: -0.3132 (mtm) cc_final: -0.3444 (mtm) REVERT: J 313 MET cc_start: 0.8075 (mmp) cc_final: 0.7378 (mmp) REVERT: J 325 MET cc_start: 0.4947 (tpt) cc_final: 0.4239 (tpt) REVERT: K 82 MET cc_start: 0.2853 (tmm) cc_final: 0.2124 (tmm) REVERT: K 222 MET cc_start: 0.3424 (pmm) cc_final: 0.2159 (pmm) REVERT: K 297 PHE cc_start: 0.8832 (m-80) cc_final: 0.8367 (m-80) REVERT: K 376 MET cc_start: 0.3842 (ptt) cc_final: 0.3501 (ptm) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1659 time to fit residues: 113.5014 Evaluate side-chains 365 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS G 112 GLN I1182 GLN ** I1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 ASN ** 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 = 0.4021 r_free = 0.4021 target = 0.130009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076987 restraints weight = 79676.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.080050 restraints weight = 43333.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.082029 restraints weight = 29567.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083271 restraints weight = 23347.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084035 restraints weight = 20233.468| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24275 Z= 0.145 Angle : 0.614 7.750 33946 Z= 0.346 Chirality : 0.044 0.373 3811 Planarity : 0.004 0.049 3359 Dihedral : 26.188 170.257 5430 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2158 helix: 0.71 (0.15), residues: 1161 sheet: 0.45 (0.42), residues: 171 loop : -0.37 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 45 TYR 0.028 0.001 TYR F 72 PHE 0.032 0.001 PHE I 486 TRP 0.017 0.001 TRP I 922 HIS 0.009 0.001 HIS I 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (24275) covalent geometry : angle 0.61397 / 0.35 (33946) hydrogen bonds : bond 0.05071 / 3.58 ( 1135) hydrogen bonds : angle 4.56041 / 3.32 ( 3017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8478 (tp30) REVERT: A 97 GLU cc_start: 0.8602 (pp20) cc_final: 0.8237 (pp20) REVERT: A 120 MET cc_start: 0.8885 (mtm) cc_final: 0.8294 (mtm) REVERT: B 37 LEU cc_start: 0.9558 (mm) cc_final: 0.9283 (mm) REVERT: B 39 ARG cc_start: 0.8999 (mmp80) cc_final: 0.8772 (mmp80) REVERT: B 60 VAL cc_start: 0.9244 (t) cc_final: 0.8721 (t) REVERT: B 63 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8382 (mt-10) REVERT: C 77 ARG cc_start: 0.8813 (tpp-160) cc_final: 0.8229 (tpp80) REVERT: D 47 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8720 (tm-30) REVERT: D 59 MET cc_start: 0.9520 (mmm) cc_final: 0.9261 (mmm) REVERT: D 68 ASP cc_start: 0.9532 (t70) cc_final: 0.9298 (t0) REVERT: E 119 ILE cc_start: 0.8848 (pt) cc_final: 0.8468 (pt) REVERT: E 120 MET cc_start: 0.7955 (mpp) cc_final: 0.7316 (mpp) REVERT: E 123 ASP cc_start: 0.9394 (m-30) cc_final: 0.9135 (m-30) REVERT: F 59 LYS cc_start: 0.9295 (ttmt) cc_final: 0.8770 (ttpt) REVERT: F 63 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8699 (mm-30) REVERT: G 23 LEU cc_start: 0.9129 (mt) cc_final: 0.8924 (mt) REVERT: G 64 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8799 (tm-30) REVERT: G 84 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8747 (tp40) REVERT: G 92 GLU cc_start: 0.8783 (tt0) cc_final: 0.7813 (tt0) REVERT: G 95 LYS cc_start: 0.9490 (tppp) cc_final: 0.9032 (tppp) REVERT: H 35 GLU cc_start: 0.8112 (mp0) cc_final: 0.7843 (mp0) REVERT: H 78 SER cc_start: 0.9589 (t) cc_final: 0.9118 (p) REVERT: H 106 LEU cc_start: 0.9276 (mt) cc_final: 0.8742 (mt) REVERT: H 109 HIS cc_start: 0.7945 (m90) cc_final: 0.7335 (m170) REVERT: N 30 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8735 (mmmt) REVERT: I 763 GLU cc_start: 0.8604 (tt0) cc_final: 0.8201 (mt-10) REVERT: I 822 PHE cc_start: 0.7695 (m-80) cc_final: 0.7287 (m-10) REVERT: I 878 MET cc_start: 0.9067 (ttp) cc_final: 0.8669 (ttp) REVERT: I 884 HIS cc_start: 0.9018 (m90) cc_final: 0.8693 (m-70) REVERT: I 1046 CYS cc_start: 0.9520 (m) cc_final: 0.9275 (m) REVERT: I 1085 LEU cc_start: 0.9595 (tp) cc_final: 0.9330 (tp) REVERT: I 1112 MET cc_start: 0.9534 (tpt) cc_final: 0.9208 (tpt) REVERT: I 1116 PHE cc_start: 0.8833 (m-80) cc_final: 0.8619 (m-80) REVERT: I 1124 LEU cc_start: 0.9227 (mp) cc_final: 0.8986 (mp) REVERT: I 1152 PHE cc_start: 0.9169 (t80) cc_final: 0.8831 (t80) REVERT: I 1154 LEU cc_start: 0.8943 (mp) cc_final: 0.8085 (mp) REVERT: I 1298 ASP cc_start: 0.7476 (m-30) cc_final: 0.7255 (m-30) REVERT: J 190 MET cc_start: -0.3094 (mtm) cc_final: -0.3413 (mtm) REVERT: J 313 MET cc_start: 0.8114 (mmp) cc_final: 0.7520 (mmp) REVERT: J 325 MET cc_start: 0.5075 (tpt) cc_final: 0.4390 (tpt) REVERT: K 82 MET cc_start: 0.3256 (tmm) cc_final: 0.2179 (tmm) REVERT: K 254 MET cc_start: 0.5601 (ptt) cc_final: 0.5353 (ptt) REVERT: K 297 PHE cc_start: 0.8777 (m-80) cc_final: 0.8311 (m-80) REVERT: K 376 MET cc_start: 0.3278 (ptt) cc_final: 0.2996 (ptm) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1673 time to fit residues: 117.8289 Evaluate side-chains 365 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 49 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 38 optimal weight: 0.0670 chunk 150 optimal weight: 0.0270 chunk 174 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS I 895 GLN ** I1304 GLN ** 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 = 0.4024 r_free = 0.4024 target = 0.130319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.077539 restraints weight = 78953.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080590 restraints weight = 43040.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082513 restraints weight = 29321.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083732 restraints weight = 23179.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084459 restraints weight = 20122.346| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24275 Z= 0.138 Angle : 0.609 7.745 33946 Z= 0.339 Chirality : 0.043 0.376 3811 Planarity : 0.005 0.112 3359 Dihedral : 26.154 171.153 5430 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.40 (0.18), residues: 2158 helix: 0.78 (0.15), residues: 1162 sheet: 0.49 (0.42), residues: 171 loop : -0.38 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 81 TYR 0.019 0.001 TYR I 877 PHE 0.019 0.001 PHE K 149 TRP 0.017 0.001 TRP I 922 HIS 0.006 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (24275) covalent geometry : angle 0.60946 / 0.34 (33946) hydrogen bonds : bond 0.04910 / 3.46 ( 1135) hydrogen bonds : angle 4.46145 / 3.25 ( 3017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8517 (pp20) cc_final: 0.8293 (pp20) REVERT: A 120 MET cc_start: 0.8927 (mtm) cc_final: 0.8337 (mtm) REVERT: B 37 LEU cc_start: 0.9540 (mm) cc_final: 0.9266 (mm) REVERT: B 39 ARG cc_start: 0.9003 (mmp80) cc_final: 0.8785 (mmp80) REVERT: B 60 VAL cc_start: 0.9231 (t) cc_final: 0.8702 (t) REVERT: B 63 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8383 (mt-10) REVERT: C 77 ARG cc_start: 0.8878 (tpp-160) cc_final: 0.8165 (tpp80) REVERT: D 47 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8710 (tm-30) REVERT: D 54 ILE cc_start: 0.8794 (mp) cc_final: 0.8575 (mp) REVERT: D 59 MET cc_start: 0.9557 (mmm) cc_final: 0.9080 (mmt) REVERT: D 68 ASP cc_start: 0.9566 (t70) cc_final: 0.9309 (t0) REVERT: E 119 ILE cc_start: 0.8816 (pt) cc_final: 0.8450 (pt) REVERT: E 120 MET cc_start: 0.7998 (mpp) cc_final: 0.7362 (mpp) REVERT: E 123 ASP cc_start: 0.9436 (m-30) cc_final: 0.9169 (m-30) REVERT: G 23 LEU cc_start: 0.9143 (mt) cc_final: 0.8936 (mt) REVERT: G 64 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8788 (tm-30) REVERT: G 92 GLU cc_start: 0.8774 (tt0) cc_final: 0.8220 (tt0) REVERT: G 95 LYS cc_start: 0.9459 (tppp) cc_final: 0.9020 (tppp) REVERT: H 52 THR cc_start: 0.8187 (p) cc_final: 0.7982 (p) REVERT: H 78 SER cc_start: 0.9609 (t) cc_final: 0.9132 (p) REVERT: H 109 HIS cc_start: 0.8036 (m90) cc_final: 0.7398 (m170) REVERT: N 30 LYS cc_start: 0.9069 (mmpt) cc_final: 0.8813 (mmmt) REVERT: I 763 GLU cc_start: 0.8699 (tt0) cc_final: 0.8292 (mt-10) REVERT: I 822 PHE cc_start: 0.7776 (m-80) cc_final: 0.7166 (m-80) REVERT: I 878 MET cc_start: 0.9084 (ttp) cc_final: 0.8665 (ttp) REVERT: I 884 HIS cc_start: 0.9004 (m90) cc_final: 0.8680 (m-70) REVERT: I 909 LEU cc_start: 0.9394 (mt) cc_final: 0.9152 (mt) REVERT: I 1046 CYS cc_start: 0.9507 (m) cc_final: 0.9255 (m) REVERT: I 1085 LEU cc_start: 0.9592 (tp) cc_final: 0.9329 (tp) REVERT: I 1087 ARG cc_start: 0.8666 (mtm180) cc_final: 0.8458 (mtm180) REVERT: I 1112 MET cc_start: 0.9547 (tpt) cc_final: 0.9193 (tpt) REVERT: I 1116 PHE cc_start: 0.8846 (m-80) cc_final: 0.8628 (m-80) REVERT: I 1124 LEU cc_start: 0.9206 (mp) cc_final: 0.8970 (mp) REVERT: I 1152 PHE cc_start: 0.9113 (t80) cc_final: 0.8807 (t80) REVERT: I 1154 LEU cc_start: 0.8907 (mp) cc_final: 0.8143 (mp) REVERT: I 1298 ASP cc_start: 0.7472 (m-30) cc_final: 0.7255 (m-30) REVERT: J 190 MET cc_start: -0.3101 (mtm) cc_final: -0.3404 (mtm) REVERT: J 313 MET cc_start: 0.8030 (mmp) cc_final: 0.7427 (mmp) REVERT: J 325 MET cc_start: 0.5075 (tpt) cc_final: 0.4387 (tpt) REVERT: K 82 MET cc_start: 0.3081 (tmm) cc_final: 0.2295 (tmm) REVERT: K 297 PHE cc_start: 0.8753 (m-80) cc_final: 0.8294 (m-80) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1650 time to fit residues: 115.6300 Evaluate side-chains 373 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.128744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075740 restraints weight = 80184.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078685 restraints weight = 43961.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080584 restraints weight = 30203.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081789 restraints weight = 23929.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082537 restraints weight = 20764.089| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24275 Z= 0.167 Angle : 0.617 7.731 33946 Z= 0.346 Chirality : 0.043 0.381 3811 Planarity : 0.004 0.046 3359 Dihedral : 26.179 170.591 5430 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.41 (0.18), residues: 2158 helix: 0.80 (0.15), residues: 1157 sheet: 0.56 (0.44), residues: 158 loop : -0.39 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 99 TYR 0.027 0.001 TYR F 72 PHE 0.018 0.001 PHE F 61 TRP 0.018 0.002 TRP I 922 HIS 0.005 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (24275) covalent geometry : angle 0.61730 / 0.35 (33946) hydrogen bonds : bond 0.04962 / 3.50 ( 1135) hydrogen bonds : angle 4.54146 / 3.31 ( 3017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8573 (mm-30) REVERT: A 120 MET cc_start: 0.8941 (mtm) cc_final: 0.8321 (mtm) REVERT: B 37 LEU cc_start: 0.9580 (mm) cc_final: 0.9246 (mm) REVERT: B 44 LYS cc_start: 0.8478 (tptt) cc_final: 0.8199 (tmtt) REVERT: C 77 ARG cc_start: 0.8886 (tpp-160) cc_final: 0.8184 (tpp80) REVERT: D 47 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8753 (tm-30) REVERT: D 59 MET cc_start: 0.9572 (mmm) cc_final: 0.9279 (mmm) REVERT: D 68 ASP cc_start: 0.9606 (t70) cc_final: 0.9345 (t0) REVERT: E 119 ILE cc_start: 0.8877 (pt) cc_final: 0.8465 (pt) REVERT: E 120 MET cc_start: 0.8206 (mpp) cc_final: 0.7294 (mpp) REVERT: F 58 LEU cc_start: 0.9369 (tp) cc_final: 0.9021 (tt) REVERT: G 23 LEU cc_start: 0.9116 (mt) cc_final: 0.8906 (mt) REVERT: G 64 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8796 (tm-30) REVERT: G 92 GLU cc_start: 0.8843 (tt0) cc_final: 0.8224 (tt0) REVERT: G 95 LYS cc_start: 0.9484 (tppp) cc_final: 0.9019 (tppp) REVERT: H 78 SER cc_start: 0.9616 (t) cc_final: 0.9162 (p) REVERT: H 109 HIS cc_start: 0.7935 (m90) cc_final: 0.7583 (m170) REVERT: I 763 GLU cc_start: 0.8709 (tt0) cc_final: 0.8316 (mt-10) REVERT: I 822 PHE cc_start: 0.7893 (m-80) cc_final: 0.7510 (m-10) REVERT: I 878 MET cc_start: 0.9117 (ttp) cc_final: 0.8624 (ttp) REVERT: I 884 HIS cc_start: 0.8963 (m90) cc_final: 0.8672 (m-70) REVERT: I 907 LEU cc_start: 0.9425 (pp) cc_final: 0.9161 (tp) REVERT: I 1046 CYS cc_start: 0.9530 (m) cc_final: 0.9321 (m) REVERT: I 1085 LEU cc_start: 0.9590 (tp) cc_final: 0.9340 (tp) REVERT: I 1112 MET cc_start: 0.9581 (tpt) cc_final: 0.9176 (tpt) REVERT: I 1124 LEU cc_start: 0.9226 (mp) cc_final: 0.8982 (mp) REVERT: I 1152 PHE cc_start: 0.9149 (t80) cc_final: 0.8844 (t80) REVERT: I 1154 LEU cc_start: 0.8887 (mp) cc_final: 0.8143 (mp) REVERT: I 1171 VAL cc_start: 0.9614 (p) cc_final: 0.9413 (p) REVERT: I 1172 ILE cc_start: 0.9201 (mm) cc_final: 0.8919 (tp) REVERT: I 1182 GLN cc_start: 0.9092 (pp30) cc_final: 0.8870 (pp30) REVERT: I 1298 ASP cc_start: 0.7501 (m-30) cc_final: 0.7281 (m-30) REVERT: J 190 MET cc_start: -0.3039 (mtm) cc_final: -0.3338 (mtm) REVERT: J 313 MET cc_start: 0.8083 (mmp) cc_final: 0.7511 (mmp) REVERT: J 325 MET cc_start: 0.5184 (tpt) cc_final: 0.4564 (tpt) REVERT: K 82 MET cc_start: 0.3456 (tmm) cc_final: 0.2479 (tmm) REVERT: K 254 MET cc_start: 0.5108 (ptt) cc_final: 0.4769 (ptt) REVERT: K 297 PHE cc_start: 0.8780 (m-80) cc_final: 0.8321 (m-80) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1660 time to fit residues: 115.8728 Evaluate side-chains 369 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 157 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 229 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.126311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073517 restraints weight = 82118.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076278 restraints weight = 45638.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078084 restraints weight = 31664.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079216 restraints weight = 25294.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079921 restraints weight = 22123.408| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24275 Z= 0.230 Angle : 0.670 7.632 33946 Z= 0.375 Chirality : 0.045 0.393 3811 Planarity : 0.005 0.048 3359 Dihedral : 26.268 169.500 5430 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 (0.18), residues: 2158 helix: 0.60 (0.15), residues: 1158 sheet: 0.78 (0.45), residues: 151 loop : -0.40 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 29 TYR 0.021 0.002 TYR D 40 PHE 0.035 0.002 PHE I1116 TRP 0.029 0.002 TRP N 31 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.23 (24275) covalent geometry : angle 0.66963 / 0.37 (33946) hydrogen bonds : bond 0.05435 / 3.82 ( 1135) hydrogen bonds : angle 4.78951 / 3.47 ( 3017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8650 (tp40) cc_final: 0.8297 (tp40) REVERT: A 120 MET cc_start: 0.8938 (mtm) cc_final: 0.8307 (mtm) REVERT: B 50 ILE cc_start: 0.9183 (mm) cc_final: 0.8956 (mm) REVERT: C 77 ARG cc_start: 0.8929 (tpp-160) cc_final: 0.8359 (tpp80) REVERT: C 102 ILE cc_start: 0.9680 (mm) cc_final: 0.9394 (tp) REVERT: D 47 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8786 (tm-30) REVERT: D 59 MET cc_start: 0.9586 (mmm) cc_final: 0.9320 (mmm) REVERT: D 68 ASP cc_start: 0.9608 (t70) cc_final: 0.9354 (t0) REVERT: E 105 GLU cc_start: 0.8980 (tp30) cc_final: 0.8770 (tp30) REVERT: E 119 ILE cc_start: 0.8999 (pt) cc_final: 0.8628 (pt) REVERT: E 120 MET cc_start: 0.8036 (mpp) cc_final: 0.7342 (mpp) REVERT: F 24 ASP cc_start: 0.7987 (t0) cc_final: 0.7786 (t0) REVERT: F 66 ILE cc_start: 0.9631 (mm) cc_final: 0.9314 (tp) REVERT: G 23 LEU cc_start: 0.9081 (mt) cc_final: 0.8874 (mt) REVERT: G 64 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8805 (tm-30) REVERT: G 92 GLU cc_start: 0.8924 (tt0) cc_final: 0.8169 (tt0) REVERT: H 35 GLU cc_start: 0.8338 (mp0) cc_final: 0.7943 (mp0) REVERT: H 105 GLU cc_start: 0.7668 (tm-30) cc_final: 0.6452 (tm-30) REVERT: N 30 LYS cc_start: 0.9070 (mmpt) cc_final: 0.8849 (mmmt) REVERT: I 763 GLU cc_start: 0.8809 (tt0) cc_final: 0.8428 (mt-10) REVERT: I 773 LEU cc_start: 0.9522 (tp) cc_final: 0.8979 (tp) REVERT: I 822 PHE cc_start: 0.7941 (m-80) cc_final: 0.7553 (m-80) REVERT: I 878 MET cc_start: 0.9193 (ttp) cc_final: 0.8415 (ttp) REVERT: I 884 HIS cc_start: 0.8960 (m90) cc_final: 0.8677 (m-70) REVERT: I 907 LEU cc_start: 0.9469 (pp) cc_final: 0.9086 (tp) REVERT: I 1046 CYS cc_start: 0.9555 (m) cc_final: 0.9275 (m) REVERT: I 1081 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8438 (mtpt) REVERT: I 1085 LEU cc_start: 0.9593 (tp) cc_final: 0.9381 (tp) REVERT: I 1124 LEU cc_start: 0.9209 (mp) cc_final: 0.8947 (mp) REVERT: I 1152 PHE cc_start: 0.9141 (t80) cc_final: 0.8858 (t80) REVERT: I 1154 LEU cc_start: 0.8907 (mp) cc_final: 0.8229 (mp) REVERT: I 1182 GLN cc_start: 0.9047 (pp30) cc_final: 0.8800 (pp30) REVERT: I 1229 ILE cc_start: 0.9225 (pt) cc_final: 0.8952 (mt) REVERT: I 1233 MET cc_start: 0.2351 (tmm) cc_final: 0.2111 (tmm) REVERT: I 1298 ASP cc_start: 0.7704 (m-30) cc_final: 0.7459 (m-30) REVERT: J 190 MET cc_start: -0.3069 (mtm) cc_final: -0.3376 (mtm) REVERT: J 313 MET cc_start: 0.8060 (mmp) cc_final: 0.7463 (mmp) REVERT: J 325 MET cc_start: 0.5311 (tpt) cc_final: 0.4699 (tpt) REVERT: K 82 MET cc_start: 0.3461 (tmm) cc_final: 0.2436 (tmm) REVERT: K 184 ASP cc_start: 0.9243 (m-30) cc_final: 0.8867 (t70) REVERT: K 297 PHE cc_start: 0.8841 (m-80) cc_final: 0.8383 (m-80) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1570 time to fit residues: 105.3195 Evaluate side-chains 361 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 138 optimal weight: 0.0770 chunk 185 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 212 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1185 GLN I1304 GLN ** J 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.128537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.075194 restraints weight = 80641.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078092 restraints weight = 44553.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080001 restraints weight = 30792.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081195 restraints weight = 24485.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081924 restraints weight = 21306.525| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24275 Z= 0.148 Angle : 0.623 8.123 33946 Z= 0.348 Chirality : 0.043 0.387 3811 Planarity : 0.004 0.039 3359 Dihedral : 26.272 171.455 5430 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.05 % Allowed : 1.22 % Favored : 98.73 % 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: 0.36 (0.18), residues: 2158 helix: 0.72 (0.15), residues: 1168 sheet: 0.83 (0.46), residues: 149 loop : -0.44 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.031 0.002 TYR F 72 PHE 0.034 0.002 PHE I1116 TRP 0.032 0.002 TRP I 922 HIS 0.005 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (24275) covalent geometry : angle 0.62325 / 0.35 (33946) hydrogen bonds : bond 0.04956 / 3.51 ( 1135) hydrogen bonds : angle 4.53186 / 3.29 ( 3017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8261 (tp30) REVERT: A 97 GLU cc_start: 0.8674 (pp20) cc_final: 0.8416 (pp20) REVERT: A 120 MET cc_start: 0.8818 (mtm) cc_final: 0.8227 (mtm) REVERT: B 37 LEU cc_start: 0.9531 (mm) cc_final: 0.9306 (mm) REVERT: B 52 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8102 (mm-30) REVERT: C 33 LEU cc_start: 0.9640 (tp) cc_final: 0.9417 (tt) REVERT: C 77 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.8267 (tpp80) REVERT: D 47 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 59 MET cc_start: 0.9526 (mmm) cc_final: 0.9311 (mmm) REVERT: D 68 ASP cc_start: 0.9598 (t70) cc_final: 0.9349 (t0) REVERT: E 119 ILE cc_start: 0.8658 (pt) cc_final: 0.8264 (pt) REVERT: E 120 MET cc_start: 0.7570 (mpp) cc_final: 0.6698 (mpp) REVERT: E 123 ASP cc_start: 0.9134 (m-30) cc_final: 0.8628 (m-30) REVERT: F 24 ASP cc_start: 0.7904 (t0) cc_final: 0.7679 (t0) REVERT: F 55 ARG cc_start: 0.9386 (mtt-85) cc_final: 0.8670 (mtt-85) REVERT: F 58 LEU cc_start: 0.9352 (tp) cc_final: 0.9027 (tt) REVERT: G 64 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8794 (tm-30) REVERT: G 92 GLU cc_start: 0.8817 (tt0) cc_final: 0.8204 (tt0) REVERT: H 35 GLU cc_start: 0.8244 (mp0) cc_final: 0.7933 (mp0) REVERT: H 105 GLU cc_start: 0.7861 (tm-30) cc_final: 0.6000 (tm-30) REVERT: N 30 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8702 (mmmt) REVERT: I 763 GLU cc_start: 0.8762 (tt0) cc_final: 0.8378 (mt-10) REVERT: I 822 PHE cc_start: 0.7884 (m-80) cc_final: 0.7357 (m-80) REVERT: I 878 MET cc_start: 0.9096 (ttp) cc_final: 0.8343 (ttp) REVERT: I 884 HIS cc_start: 0.8971 (m90) cc_final: 0.8663 (m-70) REVERT: I 907 LEU cc_start: 0.9464 (pp) cc_final: 0.9053 (tp) REVERT: I 1046 CYS cc_start: 0.9545 (m) cc_final: 0.9311 (m) REVERT: I 1085 LEU cc_start: 0.9579 (tp) cc_final: 0.9338 (tp) REVERT: I 1124 LEU cc_start: 0.9179 (mp) cc_final: 0.8927 (mp) REVERT: I 1152 PHE cc_start: 0.9145 (t80) cc_final: 0.8867 (t80) REVERT: I 1154 LEU cc_start: 0.8892 (mp) cc_final: 0.8202 (mp) REVERT: I 1171 VAL cc_start: 0.9583 (p) cc_final: 0.9291 (p) REVERT: I 1172 ILE cc_start: 0.9229 (mm) cc_final: 0.8975 (tp) REVERT: I 1182 GLN cc_start: 0.9001 (pp30) cc_final: 0.8784 (pp30) REVERT: I 1229 ILE cc_start: 0.9235 (pt) cc_final: 0.8947 (mt) REVERT: I 1233 MET cc_start: 0.2606 (tmm) cc_final: 0.2332 (tmm) REVERT: I 1298 ASP cc_start: 0.7719 (m-30) cc_final: 0.7516 (m-30) REVERT: J 190 MET cc_start: -0.3073 (mtm) cc_final: -0.3366 (mtm) REVERT: J 313 MET cc_start: 0.8031 (mmp) cc_final: 0.7438 (mmp) REVERT: J 325 MET cc_start: 0.5232 (tpt) cc_final: 0.4592 (tpt) REVERT: K 82 MET cc_start: 0.3569 (tmm) cc_final: 0.2577 (tmm) REVERT: K 184 ASP cc_start: 0.9209 (m-30) cc_final: 0.8819 (t0) REVERT: K 254 MET cc_start: 0.5632 (ptt) cc_final: 0.5361 (ptt) REVERT: K 297 PHE cc_start: 0.8837 (m-80) cc_final: 0.8386 (m-80) REVERT: K 376 MET cc_start: 0.3289 (ptt) cc_final: 0.3047 (ptm) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.1585 time to fit residues: 112.2350 Evaluate side-chains 381 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 168 optimal weight: 50.0000 chunk 232 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 237 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 chunk 177 optimal weight: 4.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS I 895 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076724 restraints weight = 79957.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.079653 restraints weight = 43730.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081587 restraints weight = 30014.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.082825 restraints weight = 23749.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083600 restraints weight = 20623.325| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24275 Z= 0.135 Angle : 0.626 10.903 33946 Z= 0.346 Chirality : 0.044 0.371 3811 Planarity : 0.004 0.039 3359 Dihedral : 26.244 172.577 5430 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 0.35 (0.18), residues: 2158 helix: 0.72 (0.15), residues: 1170 sheet: 0.88 (0.46), residues: 149 loop : -0.45 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.019 0.001 TYR I 560 PHE 0.035 0.002 PHE I1116 TRP 0.030 0.002 TRP I 922 HIS 0.005 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (24275) covalent geometry : angle 0.62593 / 0.35 (33946) hydrogen bonds : bond 0.04793 / 3.40 ( 1135) hydrogen bonds : angle 4.47324 / 3.24 ( 3017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8180 (pp20) cc_final: 0.7522 (pp20) REVERT: A 94 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8564 (mm-30) REVERT: A 120 MET cc_start: 0.8861 (mtm) cc_final: 0.8268 (mtm) REVERT: B 36 ARG cc_start: 0.9111 (mtm-85) cc_final: 0.8728 (mtm-85) REVERT: B 44 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8058 (tmtt) REVERT: B 52 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8282 (mm-30) REVERT: C 33 LEU cc_start: 0.9632 (tp) cc_final: 0.9418 (tt) REVERT: C 77 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8142 (tpp80) REVERT: D 47 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8744 (tm-30) REVERT: D 59 MET cc_start: 0.9531 (mmm) cc_final: 0.9268 (mmm) REVERT: D 68 ASP cc_start: 0.9592 (t70) cc_final: 0.9341 (t0) REVERT: E 93 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7514 (tm-30) REVERT: E 119 ILE cc_start: 0.8477 (pt) cc_final: 0.8028 (pt) REVERT: E 120 MET cc_start: 0.7551 (mpp) cc_final: 0.6611 (mpp) REVERT: E 123 ASP cc_start: 0.9098 (m-30) cc_final: 0.8518 (m-30) REVERT: F 24 ASP cc_start: 0.7893 (t0) cc_final: 0.7531 (t0) REVERT: F 55 ARG cc_start: 0.9383 (mtt-85) cc_final: 0.8680 (mtt-85) REVERT: G 23 LEU cc_start: 0.9036 (mt) cc_final: 0.8794 (mt) REVERT: G 36 LYS cc_start: 0.9304 (tmtt) cc_final: 0.9094 (tmtt) REVERT: G 64 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8754 (tm-30) REVERT: G 92 GLU cc_start: 0.8784 (tt0) cc_final: 0.7683 (tt0) REVERT: G 95 LYS cc_start: 0.9443 (tppp) cc_final: 0.8940 (tppp) REVERT: H 35 GLU cc_start: 0.8268 (mp0) cc_final: 0.7910 (mp0) REVERT: H 105 GLU cc_start: 0.7876 (tm-30) cc_final: 0.5739 (tm-30) REVERT: H 106 LEU cc_start: 0.9263 (mt) cc_final: 0.8630 (mt) REVERT: N 30 LYS cc_start: 0.8972 (mmpt) cc_final: 0.8710 (mmmt) REVERT: I 763 GLU cc_start: 0.8744 (tt0) cc_final: 0.8373 (mt-10) REVERT: I 822 PHE cc_start: 0.7817 (m-80) cc_final: 0.7261 (m-80) REVERT: I 878 MET cc_start: 0.9085 (ttp) cc_final: 0.8258 (ttp) REVERT: I 884 HIS cc_start: 0.8974 (m90) cc_final: 0.8669 (m-70) REVERT: I 907 LEU cc_start: 0.9445 (pp) cc_final: 0.9020 (tp) REVERT: I 1046 CYS cc_start: 0.9523 (m) cc_final: 0.9142 (m) REVERT: I 1081 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8277 (mtpt) REVERT: I 1085 LEU cc_start: 0.9577 (tp) cc_final: 0.9322 (tp) REVERT: I 1124 LEU cc_start: 0.9160 (mp) cc_final: 0.8917 (mp) REVERT: I 1152 PHE cc_start: 0.9150 (t80) cc_final: 0.8867 (t80) REVERT: I 1154 LEU cc_start: 0.8912 (mp) cc_final: 0.8467 (mp) REVERT: I 1171 VAL cc_start: 0.9580 (p) cc_final: 0.9107 (p) REVERT: I 1182 GLN cc_start: 0.9018 (pp30) cc_final: 0.8809 (pp30) REVERT: I 1229 ILE cc_start: 0.9218 (pt) cc_final: 0.8947 (mt) REVERT: I 1233 MET cc_start: 0.2143 (tmm) cc_final: 0.1872 (tmm) REVERT: I 1298 ASP cc_start: 0.7711 (m-30) cc_final: 0.7485 (m-30) REVERT: J 190 MET cc_start: -0.3128 (mtm) cc_final: -0.3412 (mtm) REVERT: J 272 CYS cc_start: 0.5724 (m) cc_final: 0.5462 (m) REVERT: J 313 MET cc_start: 0.7948 (mmp) cc_final: 0.7337 (mmp) REVERT: J 325 MET cc_start: 0.5329 (tpt) cc_final: 0.4746 (tpt) REVERT: K 82 MET cc_start: 0.3227 (tmm) cc_final: 0.1852 (tmm) REVERT: K 184 ASP cc_start: 0.9210 (m-30) cc_final: 0.8817 (t0) REVERT: K 297 PHE cc_start: 0.8813 (m-80) cc_final: 0.8358 (m-80) REVERT: K 376 MET cc_start: 0.2946 (ptt) cc_final: 0.2729 (ptm) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1634 time to fit residues: 115.6261 Evaluate side-chains 383 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 202 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS G 84 GLN H 109 HIS I 473 GLN I 770 ASN I 895 GLN I 915 GLN ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1181 HIS ** J 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076547 restraints weight = 80208.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079529 restraints weight = 43955.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.081494 restraints weight = 30092.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082666 restraints weight = 23808.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083430 restraints weight = 20658.812| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24275 Z= 0.138 Angle : 0.636 12.340 33946 Z= 0.348 Chirality : 0.043 0.367 3811 Planarity : 0.004 0.038 3359 Dihedral : 26.234 171.922 5430 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2158 helix: 0.74 (0.15), residues: 1171 sheet: 0.55 (0.45), residues: 145 loop : -0.44 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.032 0.001 TYR F 72 PHE 0.034 0.002 PHE I1116 TRP 0.029 0.002 TRP I 922 HIS 0.005 0.001 HIS J 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (24275) covalent geometry : angle 0.63553 / 0.35 (33946) hydrogen bonds : bond 0.04797 / 3.41 ( 1135) hydrogen bonds : angle 4.44824 / 3.21 ( 3017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4316 Ramachandran restraints generated. 2158 Oldfield, 0 Emsley, 2158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8180 (pp20) cc_final: 0.7442 (pp20) REVERT: A 97 GLU cc_start: 0.8678 (pp20) cc_final: 0.8449 (pp20) REVERT: A 120 MET cc_start: 0.8863 (mtm) cc_final: 0.8263 (mtm) REVERT: B 36 ARG cc_start: 0.9121 (mtm-85) cc_final: 0.8704 (mtm-85) REVERT: B 44 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8085 (tmtt) REVERT: B 52 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 77 ARG cc_start: 0.8896 (tpp-160) cc_final: 0.8125 (tpp80) REVERT: D 47 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8760 (tm-30) REVERT: D 68 ASP cc_start: 0.9600 (t70) cc_final: 0.9357 (t0) REVERT: E 85 GLN cc_start: 0.8159 (mt0) cc_final: 0.7932 (mt0) REVERT: E 93 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7690 (tm-30) REVERT: E 119 ILE cc_start: 0.8468 (pt) cc_final: 0.7976 (pt) REVERT: E 120 MET cc_start: 0.7539 (mpp) cc_final: 0.6493 (mpp) REVERT: E 123 ASP cc_start: 0.9111 (m-30) cc_final: 0.8467 (m-30) REVERT: F 24 ASP cc_start: 0.7934 (t0) cc_final: 0.7574 (t0) REVERT: F 47 SER cc_start: 0.9626 (m) cc_final: 0.9409 (m) REVERT: G 23 LEU cc_start: 0.9032 (mt) cc_final: 0.8797 (mt) REVERT: G 36 LYS cc_start: 0.9336 (tmtt) cc_final: 0.9099 (tmtt) REVERT: G 64 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8746 (tm-30) REVERT: G 92 GLU cc_start: 0.8802 (tt0) cc_final: 0.7749 (tt0) REVERT: G 95 LYS cc_start: 0.9445 (tppp) cc_final: 0.8938 (tppp) REVERT: H 33 ARG cc_start: 0.8982 (tpp80) cc_final: 0.8766 (tpp80) REVERT: H 35 GLU cc_start: 0.8289 (mp0) cc_final: 0.7821 (mp0) REVERT: H 105 GLU cc_start: 0.7828 (tm-30) cc_final: 0.5692 (tm-30) REVERT: H 106 LEU cc_start: 0.9273 (mt) cc_final: 0.8722 (mt) REVERT: N 30 LYS cc_start: 0.8980 (mmpt) cc_final: 0.8722 (mmmt) REVERT: I 763 GLU cc_start: 0.8747 (tt0) cc_final: 0.8370 (mt-10) REVERT: I 822 PHE cc_start: 0.8031 (m-80) cc_final: 0.7370 (m-80) REVERT: I 857 LEU cc_start: 0.9033 (mm) cc_final: 0.8825 (mm) REVERT: I 878 MET cc_start: 0.9075 (ttp) cc_final: 0.8289 (ttp) REVERT: I 884 HIS cc_start: 0.8947 (m90) cc_final: 0.8624 (m-70) REVERT: I 907 LEU cc_start: 0.9401 (pp) cc_final: 0.8940 (tp) REVERT: I 1037 ASN cc_start: 0.7512 (t0) cc_final: 0.7026 (m110) REVERT: I 1046 CYS cc_start: 0.9529 (m) cc_final: 0.9210 (m) REVERT: I 1081 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8373 (mtpt) REVERT: I 1085 LEU cc_start: 0.9580 (tp) cc_final: 0.9326 (tp) REVERT: I 1102 PHE cc_start: 0.7626 (m-80) cc_final: 0.7161 (m-80) REVERT: I 1116 PHE cc_start: 0.8931 (m-80) cc_final: 0.8728 (m-80) REVERT: I 1124 LEU cc_start: 0.9161 (mp) cc_final: 0.8944 (mp) REVERT: I 1152 PHE cc_start: 0.9169 (t80) cc_final: 0.8873 (t80) REVERT: I 1154 LEU cc_start: 0.8824 (mp) cc_final: 0.8078 (mp) REVERT: I 1182 GLN cc_start: 0.9007 (pp30) cc_final: 0.8794 (pp30) REVERT: I 1229 ILE cc_start: 0.9148 (pt) cc_final: 0.8941 (mt) REVERT: I 1298 ASP cc_start: 0.7766 (m-30) cc_final: 0.7525 (m-30) REVERT: J 190 MET cc_start: -0.3130 (mtm) cc_final: -0.3411 (mtm) REVERT: J 272 CYS cc_start: 0.5828 (m) cc_final: 0.5567 (m) REVERT: J 313 MET cc_start: 0.7934 (mmp) cc_final: 0.7324 (mmp) REVERT: J 325 MET cc_start: 0.5230 (tpt) cc_final: 0.4641 (tpt) REVERT: K 82 MET cc_start: 0.3114 (tmm) cc_final: 0.2134 (tmm) REVERT: K 184 ASP cc_start: 0.9223 (m-30) cc_final: 0.8830 (t0) REVERT: K 297 PHE cc_start: 0.8816 (m-80) cc_final: 0.8352 (m-80) REVERT: K 376 MET cc_start: 0.3016 (ptt) cc_final: 0.2764 (ptm) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.1537 time to fit residues: 110.9302 Evaluate side-chains 392 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 207 optimal weight: 9.9990 chunk 234 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS H 109 HIS ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.127643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.074204 restraints weight = 81527.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077054 restraints weight = 45455.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078918 restraints weight = 31446.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.080098 restraints weight = 25019.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080831 restraints weight = 21781.841| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24275 Z= 0.175 Angle : 0.647 10.783 33946 Z= 0.357 Chirality : 0.044 0.372 3811 Planarity : 0.004 0.035 3359 Dihedral : 26.267 170.806 5430 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 (0.18), residues: 2158 helix: 0.70 (0.15), residues: 1170 sheet: 0.61 (0.45), residues: 150 loop : -0.43 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.019 0.001 TYR I 560 PHE 0.041 0.002 PHE E 67 TRP 0.029 0.002 TRP I 922 HIS 0.007 0.001 HIS I 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (24275) covalent geometry : angle 0.64737 / 0.36 (33946) hydrogen bonds : bond 0.04975 / 3.52 ( 1135) hydrogen bonds : angle 4.55921 / 3.30 ( 3017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.76 seconds wall clock time: 90 minutes 3.03 seconds (5403.03 seconds total)