Starting phenix.real_space_refine on Fri Jun 5 21:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21vv_68040/06_2026/21vv_68040.cif Found real_map, /net/cci-nas-00/data/ceres_data/21vv_68040/06_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_68040/06_2026/21vv_68040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21vv_68040/06_2026/21vv_68040.map" model { file = "/net/cci-nas-00/data/ceres_data/21vv_68040/06_2026/21vv_68040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21vv_68040/06_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-dev-6079/lib/python3.9/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: 5.88, per 1000 atoms: 0.25 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: 2.06 Conformation dependent library (CDL) restraints added in 933.6 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: 3.50 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: 6.36 Time building geometry restraints manager: 2.68 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=" CA ILE K 304 " pdb=" CB ILE K 304 " ideal model delta sigma weight residual 1.539 1.551 -0.012 5.40e-03 3.43e+04 5.24e+00 bond pdb=" CA MET I1317 " pdb=" C MET I1317 " ideal model delta sigma weight residual 1.522 1.498 0.025 1.38e-02 5.25e+03 3.18e+00 bond pdb=" C3' DT Y 15 " pdb=" O3' DT Y 15 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CG1 ILE A 51 " pdb=" CD1 ILE A 51 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 ... (remaining 24270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 32583 1.27 - 2.53: 1149 2.53 - 3.80: 159 3.80 - 5.06: 38 5.06 - 6.33: 17 Bond angle restraints: 33946 Sorted by residual: angle pdb=" N ILE I1111 " pdb=" CA ILE I1111 " pdb=" C ILE I1111 " ideal model delta sigma weight residual 112.98 107.99 4.99 1.25e+00 6.40e-01 1.60e+01 angle pdb=" C ALA G 14 " pdb=" N LYS G 15 " pdb=" CA LYS G 15 " ideal model delta sigma weight residual 121.54 127.05 -5.51 1.91e+00 2.74e-01 8.32e+00 angle pdb=" C3' DA X 52 " pdb=" C2' DA X 52 " pdb=" C1' DA X 52 " ideal model delta sigma weight residual 101.60 105.76 -4.16 1.50e+00 4.44e-01 7.67e+00 angle pdb=" C LYS I 800 " pdb=" N ARG I 801 " pdb=" CA ARG I 801 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.70e+00 angle pdb=" C LYS I 824 " pdb=" N TRP I 825 " pdb=" CA TRP I 825 " ideal model delta sigma weight residual 122.60 118.32 4.28 1.88e+00 2.83e-01 5.19e+00 ... (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 - 0.027: 2303 0.027 - 0.054: 1008 0.054 - 0.082: 294 0.082 - 0.109: 160 0.109 - 0.136: 46 Chirality restraints: 3811 Sorted by residual: chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" P DC Y 16 " pdb=" OP1 DC Y 16 " pdb=" OP2 DC Y 16 " pdb=" O5' DC Y 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL N 49 " pdb=" N VAL N 49 " pdb=" C VAL N 49 " pdb=" CB VAL N 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.850 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24275 Z= 0.171 Angle : 0.572 6.331 33946 Z= 0.328 Chirality : 0.037 0.136 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 0.00356 / 0.17 (24275) covalent geometry : angle 0.57218 / 0.33 (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 : 0.824 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: 0.8945 (mm-30) cc_final: 0.8286 (mm-30) REVERT: A 120 MET cc_start: 0.8750 (mtm) cc_final: 0.8410 (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: 0.9244 (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: 0.7547 (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: 0.8592 (mmmt) REVERT: I 748 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8047 (pt) REVERT: I 822 PHE cc_start: 0.8106 (m-10) cc_final: 0.7809 (m-80) REVERT: I 1012 GLN cc_start: 0.9118 (mt0) cc_final: 0.8800 (mt0) REVERT: I 1037 ASN cc_start: 0.7707 (t0) cc_final: 0.7499 (t0) REVERT: I 1046 CYS cc_start: 0.9457 (m) cc_final: 0.9187 (m) REVERT: I 1111 ILE cc_start: 0.9540 (tt) cc_final: 0.9221 (tt) REVERT: J 325 MET cc_start: 0.4802 (tpt) cc_final: 0.3986 (tpt) REVERT: K 82 MET cc_start: 0.3215 (tmm) cc_final: 0.2344 (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: 0.1685 time to fit residues: 119.8984 Evaluate side-chains 390 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 357 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 884 HIS ** I 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1012 GLN I1187 GLN ** I1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.128448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074431 restraints weight = 80823.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077334 restraints weight = 44443.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.079060 restraints weight = 30818.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080299 restraints weight = 24811.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081007 restraints weight = 21705.185| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24275 Z= 0.200 Angle : 0.615 7.200 33946 Z= 0.343 Chirality : 0.040 0.225 3811 Planarity : 0.004 0.058 3359 Dihedral : 25.999 165.633 5430 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: 0.42 (0.18), residues: 2158 helix: 0.74 (0.15), residues: 1162 sheet: 0.48 (0.41), residues: 177 loop : -0.28 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.036 0.002 TYR I 877 PHE 0.017 0.002 PHE C 25 TRP 0.014 0.002 TRP I 922 HIS 0.012 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (24275) covalent geometry : angle 0.61505 / 0.34 (33946) hydrogen bonds : bond 0.05249 / 3.67 ( 1135) hydrogen bonds : angle 4.77734 / 3.48 ( 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 453 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.948 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: A 94 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8635 (tp30) REVERT: A 97 GLU cc_start: 0.8558 (pp20) cc_final: 0.8263 (pp20) REVERT: A 120 MET cc_start: 0.8770 (mtm) cc_final: 0.8273 (mtm) REVERT: B 37 LEU cc_start: 0.9588 (mm) cc_final: 0.9284 (mm) REVERT: B 39 ARG cc_start: 0.9065 (mmp80) cc_final: 0.8606 (mmp80) REVERT: C 82 HIS cc_start: 0.9050 (m-70) cc_final: 0.8831 (m-70) REVERT: D 47 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8730 (tm-30) REVERT: D 59 MET cc_start: 0.9563 (mmm) cc_final: 0.9227 (mmm) REVERT: D 68 ASP cc_start: 0.9511 (t0) cc_final: 0.9277 (t0) REVERT: E 112 ILE cc_start: 0.9056 (mt) cc_final: 0.8837 (mt) REVERT: E 119 ILE cc_start: 0.8819 (pt) cc_final: 0.8515 (pt) REVERT: E 120 MET cc_start: 0.8028 (mpp) cc_final: 0.7560 (mpp) REVERT: F 55 ARG cc_start: 0.9171 (mtt-85) cc_final: 0.8368 (mtt-85) REVERT: G 92 GLU cc_start: 0.8804 (tt0) cc_final: 0.7906 (tt0) REVERT: H 46 LYS cc_start: 0.8953 (tppt) cc_final: 0.8609 (tppt) REVERT: H 52 THR cc_start: 0.8335 (p) cc_final: 0.8078 (p) REVERT: H 106 LEU cc_start: 0.9248 (mt) cc_final: 0.8686 (mt) REVERT: H 109 HIS cc_start: 0.8027 (m90) cc_final: 0.7790 (m170) REVERT: N 30 LYS cc_start: 0.9087 (mmpt) cc_final: 0.8817 (mmmt) REVERT: I 763 GLU cc_start: 0.8517 (tt0) cc_final: 0.8105 (mt-10) REVERT: I 822 PHE cc_start: 0.8065 (m-10) cc_final: 0.7664 (m-80) REVERT: I 859 THR cc_start: 0.9304 (p) cc_final: 0.9103 (p) REVERT: I 878 MET cc_start: 0.9055 (ttp) cc_final: 0.8671 (ttp) REVERT: I 884 HIS cc_start: 0.9032 (m90) cc_final: 0.8671 (m-70) REVERT: I 1009 ARG cc_start: 0.8691 (pmt-80) cc_final: 0.8111 (ttp80) REVERT: I 1012 GLN cc_start: 0.9069 (mt0) cc_final: 0.8778 (mt0) REVERT: I 1037 ASN cc_start: 0.7696 (t0) cc_final: 0.6935 (m-40) REVERT: I 1046 CYS cc_start: 0.9490 (m) cc_final: 0.9271 (m) REVERT: I 1085 LEU cc_start: 0.9618 (tp) cc_final: 0.9365 (tp) REVERT: J 190 MET cc_start: -0.3207 (mtm) cc_final: -0.3467 (mtm) REVERT: J 325 MET cc_start: 0.4879 (tpt) cc_final: 0.4129 (tpt) REVERT: K 82 MET cc_start: 0.3377 (tmm) cc_final: 0.2226 (tmm) REVERT: K 222 MET cc_start: 0.3202 (pmm) cc_final: 0.2326 (pmm) REVERT: K 295 CYS cc_start: 0.6814 (t) cc_final: 0.6255 (m) REVERT: K 297 PHE cc_start: 0.8818 (m-80) cc_final: 0.8416 (m-80) REVERT: K 376 MET cc_start: 0.3537 (ptt) cc_final: 0.3265 (ptm) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1792 time to fit residues: 124.4308 Evaluate side-chains 363 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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: 0.0370 chunk 116 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 149 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 770 ASN ** I 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1304 GLN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078627 restraints weight = 79399.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082310 restraints weight = 44589.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083052 restraints weight = 26580.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083401 restraints weight = 23810.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083756 restraints weight = 22636.368| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1699 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= 0.141 Angle : 0.578 7.942 33946 Z= 0.320 Chirality : 0.039 0.230 3811 Planarity : 0.004 0.054 3359 Dihedral : 25.995 168.175 5430 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % 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: 0.48 (0.18), residues: 2158 helix: 0.82 (0.15), residues: 1162 sheet: 0.48 (0.41), residues: 173 loop : -0.30 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 45 TYR 0.019 0.001 TYR I 877 PHE 0.014 0.001 PHE C 25 TRP 0.018 0.001 TRP I 922 HIS 0.009 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (24275) covalent geometry : angle 0.57803 / 0.32 (33946) hydrogen bonds : bond 0.04655 / 3.28 ( 1135) hydrogen bonds : angle 4.44684 / 3.25 ( 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 449 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 446 time to evaluate : 0.785 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: 0.8823 (mm-30) cc_final: 0.8501 (tp30) REVERT: A 97 GLU cc_start: 0.8568 (pp20) cc_final: 0.8197 (pp20) REVERT: A 120 MET cc_start: 0.8870 (mtm) cc_final: 0.8208 (mtm) REVERT: B 37 LEU cc_start: 0.9599 (mm) cc_final: 0.9229 (mm) REVERT: B 60 VAL cc_start: 0.9227 (t) cc_final: 0.8730 (t) REVERT: B 63 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 88 TYR cc_start: 0.9401 (t80) cc_final: 0.9178 (t80) REVERT: C 77 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.8123 (tpp80) REVERT: C 82 HIS cc_start: 0.9054 (m90) cc_final: 0.8668 (m-70) REVERT: C 104 GLN cc_start: 0.8935 (pm20) cc_final: 0.8658 (pm20) REVERT: C 112 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8404 (tp40) REVERT: D 47 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8804 (tm-30) REVERT: D 59 MET cc_start: 0.9512 (mmm) cc_final: 0.9060 (mmt) REVERT: D 68 ASP cc_start: 0.9517 (t70) cc_final: 0.9290 (t0) REVERT: E 68 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: E 119 ILE cc_start: 0.8675 (pt) cc_final: 0.8417 (pt) REVERT: E 120 MET cc_start: 0.7752 (mpp) cc_final: 0.7225 (mpp) REVERT: F 55 ARG cc_start: 0.9285 (mtt-85) cc_final: 0.8936 (mtt-85) REVERT: F 59 LYS cc_start: 0.9357 (ttmt) cc_final: 0.8837 (ttpt) REVERT: F 63 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8852 (mm-30) REVERT: G 23 LEU cc_start: 0.9173 (mt) cc_final: 0.8967 (mt) REVERT: G 64 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8795 (tm-30) REVERT: G 84 GLN cc_start: 0.9051 (tp40) cc_final: 0.8807 (tp-100) REVERT: G 92 GLU cc_start: 0.8813 (tt0) cc_final: 0.7878 (tt0) REVERT: G 95 LYS cc_start: 0.9501 (tppp) cc_final: 0.9047 (tppp) REVERT: H 78 SER cc_start: 0.9547 (t) cc_final: 0.9032 (p) REVERT: H 106 LEU cc_start: 0.9289 (mt) cc_final: 0.8871 (mt) REVERT: H 109 HIS cc_start: 0.8234 (m90) cc_final: 0.7433 (m170) REVERT: N 30 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8710 (mmmt) REVERT: I 763 GLU cc_start: 0.8543 (tt0) cc_final: 0.8169 (mt-10) REVERT: I 822 PHE cc_start: 0.7902 (m-10) cc_final: 0.7526 (m-80) REVERT: I 878 MET cc_start: 0.9161 (ttp) cc_final: 0.8724 (ttp) REVERT: I 884 HIS cc_start: 0.8967 (m90) cc_final: 0.8635 (m-70) REVERT: I 1036 MET cc_start: 0.8699 (pmm) cc_final: 0.8333 (pmm) REVERT: I 1037 ASN cc_start: 0.7974 (t0) cc_final: 0.7183 (m-40) REVERT: I 1046 CYS cc_start: 0.9507 (m) cc_final: 0.9246 (m) REVERT: I 1085 LEU cc_start: 0.9635 (tp) cc_final: 0.9385 (tp) REVERT: I 1112 MET cc_start: 0.9590 (tpt) cc_final: 0.9238 (tpt) REVERT: I 1116 PHE cc_start: 0.8940 (m-10) cc_final: 0.8690 (m-80) REVERT: I 1172 ILE cc_start: 0.9236 (mm) cc_final: 0.9027 (tp) REVERT: I 1177 ASP cc_start: 0.9285 (t0) cc_final: 0.9062 (t70) REVERT: J 88 HIS cc_start: 0.9154 (m90) cc_final: 0.8946 (m90) REVERT: J 190 MET cc_start: -0.3359 (mtm) cc_final: -0.3628 (mtm) REVERT: J 313 MET cc_start: 0.8096 (mmp) cc_final: 0.7460 (mmp) REVERT: J 325 MET cc_start: 0.5087 (tpt) cc_final: 0.4447 (tpt) REVERT: K 82 MET cc_start: 0.2764 (tmm) cc_final: 0.2028 (tmm) REVERT: K 295 CYS cc_start: 0.6701 (t) cc_final: 0.6057 (m) REVERT: K 297 PHE cc_start: 0.8748 (m-80) cc_final: 0.8364 (m-80) REVERT: K 376 MET cc_start: 0.3813 (ptt) cc_final: 0.3555 (ptm) outliers start: 3 outliers final: 0 residues processed: 448 average time/residue: 0.1767 time to fit residues: 121.2842 Evaluate side-chains 367 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 3.9990 chunk 213 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 555 GLN ** 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 = 0.4027 r_free = 0.4027 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077530 restraints weight = 79889.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080599 restraints weight = 43302.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082576 restraints weight = 29585.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083838 restraints weight = 23384.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084593 restraints weight = 20281.951| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1989 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= 0.142 Angle : 0.573 6.994 33946 Z= 0.316 Chirality : 0.039 0.223 3811 Planarity : 0.004 0.043 3359 Dihedral : 25.873 168.130 5430 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 0.50 (0.18), residues: 2158 helix: 0.85 (0.15), residues: 1161 sheet: 0.55 (0.41), residues: 171 loop : -0.32 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 45 TYR 0.029 0.001 TYR F 72 PHE 0.022 0.001 PHE C 25 TRP 0.024 0.001 TRP I 922 HIS 0.006 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (24275) covalent geometry : angle 0.57270 / 0.32 (33946) hydrogen bonds : bond 0.04481 / 3.16 ( 1135) hydrogen bonds : angle 4.32417 / 3.15 ( 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 448 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.833 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: 0.8827 (mm-30) cc_final: 0.7890 (tp30) REVERT: A 97 GLU cc_start: 0.8564 (pp20) cc_final: 0.8117 (pp20) REVERT: A 120 MET cc_start: 0.8918 (mtm) cc_final: 0.8314 (mtm) REVERT: B 37 LEU cc_start: 0.9538 (mm) cc_final: 0.9315 (mm) REVERT: B 39 ARG cc_start: 0.9117 (mmt-90) cc_final: 0.8913 (mmp80) REVERT: B 60 VAL cc_start: 0.9250 (t) cc_final: 0.8760 (t) REVERT: B 63 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8360 (mt-10) REVERT: C 77 ARG cc_start: 0.8902 (tpp-160) cc_final: 0.8084 (tpp80) REVERT: C 82 HIS cc_start: 0.9085 (m90) cc_final: 0.8802 (m-70) REVERT: C 102 ILE cc_start: 0.9609 (mm) cc_final: 0.9356 (tp) REVERT: C 104 GLN cc_start: 0.8891 (pm20) cc_final: 0.8592 (pm20) REVERT: D 47 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8790 (tm-30) REVERT: D 59 MET cc_start: 0.9521 (mmm) cc_final: 0.9268 (mmm) REVERT: D 68 ASP cc_start: 0.9571 (t70) cc_final: 0.9334 (t0) REVERT: E 85 GLN cc_start: 0.8219 (mt0) cc_final: 0.7984 (mt0) REVERT: E 93 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7184 (tm-30) REVERT: E 119 ILE cc_start: 0.8672 (pt) cc_final: 0.8276 (pt) REVERT: E 120 MET cc_start: 0.7790 (mpp) cc_final: 0.7244 (mpp) REVERT: E 123 ASP cc_start: 0.9421 (m-30) cc_final: 0.9154 (m-30) REVERT: F 59 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8736 (ttpt) REVERT: F 63 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8757 (mm-30) REVERT: G 23 LEU cc_start: 0.9111 (mt) cc_final: 0.8904 (mt) REVERT: G 64 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8767 (tm-30) REVERT: G 84 GLN cc_start: 0.9086 (tp40) cc_final: 0.8849 (tp-100) REVERT: G 92 GLU cc_start: 0.8812 (tt0) cc_final: 0.7913 (tt0) REVERT: G 95 LYS cc_start: 0.9475 (tppp) cc_final: 0.9035 (tppp) REVERT: H 52 THR cc_start: 0.8241 (p) cc_final: 0.8000 (p) REVERT: H 78 SER cc_start: 0.9625 (t) cc_final: 0.9153 (p) REVERT: H 106 LEU cc_start: 0.9308 (mt) cc_final: 0.8829 (mt) REVERT: H 109 HIS cc_start: 0.7998 (m90) cc_final: 0.7378 (m170) REVERT: N 30 LYS cc_start: 0.9076 (mmpt) cc_final: 0.8831 (mmmt) REVERT: I 763 GLU cc_start: 0.8721 (tt0) cc_final: 0.8333 (mt-10) REVERT: I 773 LEU cc_start: 0.9509 (tp) cc_final: 0.9041 (tp) REVERT: I 822 PHE cc_start: 0.7849 (m-10) cc_final: 0.7255 (m-10) REVERT: I 878 MET cc_start: 0.9070 (ttp) cc_final: 0.8334 (ttp) REVERT: I 884 HIS cc_start: 0.8993 (m90) cc_final: 0.8666 (m-70) REVERT: I 909 LEU cc_start: 0.9420 (mt) cc_final: 0.9172 (mt) REVERT: I 1036 MET cc_start: 0.8681 (pmm) cc_final: 0.8368 (pmm) REVERT: I 1037 ASN cc_start: 0.7988 (t0) cc_final: 0.7144 (m-40) REVERT: I 1046 CYS cc_start: 0.9518 (m) cc_final: 0.9268 (m) REVERT: I 1085 LEU cc_start: 0.9592 (tp) cc_final: 0.9332 (tp) REVERT: I 1112 MET cc_start: 0.9543 (tpt) cc_final: 0.9151 (tpt) REVERT: I 1116 PHE cc_start: 0.8909 (m-10) cc_final: 0.8690 (m-80) REVERT: I 1124 LEU cc_start: 0.9209 (mp) cc_final: 0.8994 (mp) REVERT: I 1125 ARG cc_start: 0.9135 (ttt-90) cc_final: 0.8636 (ttm170) REVERT: I 1152 PHE cc_start: 0.9130 (t80) cc_final: 0.8826 (t80) REVERT: I 1154 LEU cc_start: 0.8881 (mp) cc_final: 0.8375 (mp) REVERT: I 1177 ASP cc_start: 0.9472 (t0) cc_final: 0.9140 (t70) REVERT: I 1298 ASP cc_start: 0.7590 (m-30) cc_final: 0.7369 (m-30) REVERT: J 190 MET cc_start: -0.3061 (mtm) cc_final: -0.3347 (mtm) REVERT: J 313 MET cc_start: 0.7932 (mmp) cc_final: 0.7445 (mmp) REVERT: J 325 MET cc_start: 0.5028 (tpt) cc_final: 0.4366 (tpt) REVERT: K 82 MET cc_start: 0.3312 (tmm) cc_final: 0.2357 (tmm) REVERT: K 210 PHE cc_start: 0.9180 (m-10) cc_final: 0.8448 (m-10) REVERT: K 254 MET cc_start: 0.5223 (ptt) cc_final: 0.4922 (ptt) REVERT: K 297 PHE cc_start: 0.8724 (m-80) cc_final: 0.8215 (m-80) REVERT: K 409 MET cc_start: 0.6559 (pmm) cc_final: 0.6295 (pmm) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.1753 time to fit residues: 121.1912 Evaluate side-chains 368 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 0.6980 chunk 103 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 150 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1185 GLN ** J 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 HIS ** K 162 ASN ** 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 = 0.4014 r_free = 0.4014 target = 0.129600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076366 restraints weight = 79814.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079276 restraints weight = 43925.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081208 restraints weight = 30186.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082413 restraints weight = 23954.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083197 restraints weight = 20836.393| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2212 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= 0.155 Angle : 0.576 7.394 33946 Z= 0.318 Chirality : 0.039 0.186 3811 Planarity : 0.004 0.062 3359 Dihedral : 25.864 168.331 5430 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.48 (0.18), residues: 2158 helix: 0.84 (0.15), residues: 1173 sheet: 0.66 (0.43), residues: 158 loop : -0.39 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 24 TYR 0.019 0.001 TYR I 560 PHE 0.015 0.001 PHE C 25 TRP 0.024 0.002 TRP I 922 HIS 0.012 0.001 HIS J 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (24275) covalent geometry : angle 0.57582 / 0.32 (33946) hydrogen bonds : bond 0.04416 / 3.12 ( 1135) hydrogen bonds : angle 4.35595 / 3.18 ( 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 441 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.715 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 65 LEU cc_start: 0.9197 (tp) cc_final: 0.8996 (tp) REVERT: A 94 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 97 GLU cc_start: 0.8550 (pp20) cc_final: 0.8210 (pp20) REVERT: A 120 MET cc_start: 0.8953 (mtm) cc_final: 0.8324 (mtm) REVERT: B 37 LEU cc_start: 0.9559 (mm) cc_final: 0.9224 (mm) REVERT: B 39 ARG cc_start: 0.9149 (mmt-90) cc_final: 0.8933 (mmp80) REVERT: B 44 LYS cc_start: 0.8603 (tptt) cc_final: 0.8094 (tptp) REVERT: B 60 VAL cc_start: 0.9246 (t) cc_final: 0.8729 (t) REVERT: B 63 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8331 (mt-10) REVERT: C 77 ARG cc_start: 0.8927 (tpp-160) cc_final: 0.8039 (tpp80) REVERT: C 104 GLN cc_start: 0.8939 (pm20) cc_final: 0.8660 (pm20) REVERT: D 47 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8788 (tm-30) REVERT: D 59 MET cc_start: 0.9500 (mmm) cc_final: 0.9197 (mmm) REVERT: D 68 ASP cc_start: 0.9589 (t70) cc_final: 0.9354 (t0) REVERT: E 76 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8957 (tm-30) REVERT: E 77 ASP cc_start: 0.9333 (t70) cc_final: 0.9121 (t70) REVERT: E 85 GLN cc_start: 0.8212 (mt0) cc_final: 0.7984 (mt0) REVERT: E 90 MET cc_start: 0.8672 (ttt) cc_final: 0.8368 (ttt) REVERT: E 93 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7151 (tm-30) REVERT: E 112 ILE cc_start: 0.9131 (mt) cc_final: 0.8928 (mt) REVERT: E 119 ILE cc_start: 0.8742 (pt) cc_final: 0.8297 (pt) REVERT: E 120 MET cc_start: 0.8077 (mpp) cc_final: 0.7188 (mpp) REVERT: F 24 ASP cc_start: 0.7897 (t0) cc_final: 0.7677 (t0) REVERT: F 59 LYS cc_start: 0.9407 (ttmt) cc_final: 0.8837 (ttpt) REVERT: F 63 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8960 (mm-30) REVERT: G 64 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8773 (tm-30) REVERT: G 84 GLN cc_start: 0.9086 (tp40) cc_final: 0.8867 (tp-100) REVERT: G 92 GLU cc_start: 0.8893 (tt0) cc_final: 0.8290 (tt0) REVERT: G 95 LYS cc_start: 0.9496 (tppp) cc_final: 0.9055 (tppp) REVERT: H 35 GLU cc_start: 0.8204 (mp0) cc_final: 0.7885 (mp0) REVERT: H 52 THR cc_start: 0.8225 (p) cc_final: 0.8009 (p) REVERT: H 109 HIS cc_start: 0.7863 (m90) cc_final: 0.7218 (m170) REVERT: I 763 GLU cc_start: 0.8746 (tt0) cc_final: 0.8348 (mt-10) REVERT: I 822 PHE cc_start: 0.7934 (m-10) cc_final: 0.7568 (m-10) REVERT: I 878 MET cc_start: 0.9061 (ttp) cc_final: 0.8256 (ttp) REVERT: I 884 HIS cc_start: 0.8994 (m90) cc_final: 0.8678 (m-70) REVERT: I 907 LEU cc_start: 0.9422 (pp) cc_final: 0.8963 (tp) REVERT: I 1036 MET cc_start: 0.8720 (pmm) cc_final: 0.8433 (pmm) REVERT: I 1037 ASN cc_start: 0.8138 (t0) cc_final: 0.7326 (m110) REVERT: I 1046 CYS cc_start: 0.9534 (m) cc_final: 0.9142 (m) REVERT: I 1081 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8396 (mtpt) REVERT: I 1085 LEU cc_start: 0.9604 (tp) cc_final: 0.9329 (tp) REVERT: I 1112 MET cc_start: 0.9621 (tpt) cc_final: 0.9153 (tpt) REVERT: I 1116 PHE cc_start: 0.8959 (m-80) cc_final: 0.8724 (m-80) REVERT: I 1124 LEU cc_start: 0.9216 (mp) cc_final: 0.8977 (mp) REVERT: I 1152 PHE cc_start: 0.9170 (t80) cc_final: 0.8824 (t80) REVERT: I 1154 LEU cc_start: 0.8768 (mp) cc_final: 0.8159 (mp) REVERT: I 1177 ASP cc_start: 0.9506 (t0) cc_final: 0.9249 (t70) REVERT: I 1229 ILE cc_start: 0.9162 (pt) cc_final: 0.8871 (mt) REVERT: I 1298 ASP cc_start: 0.7494 (m-30) cc_final: 0.7282 (m-30) REVERT: J 190 MET cc_start: -0.3111 (mtm) cc_final: -0.3406 (mtm) REVERT: J 313 MET cc_start: 0.7967 (mmp) cc_final: 0.7343 (mmp) REVERT: J 325 MET cc_start: 0.5271 (tpt) cc_final: 0.4625 (tpt) REVERT: K 82 MET cc_start: 0.3233 (tmm) cc_final: 0.2281 (tmm) REVERT: K 142 GLU cc_start: 0.8630 (pp20) cc_final: 0.8066 (mm-30) REVERT: K 184 ASP cc_start: 0.9253 (m-30) cc_final: 0.8894 (t70) REVERT: K 254 MET cc_start: 0.5180 (ptt) cc_final: 0.4921 (ptt) REVERT: K 295 CYS cc_start: 0.6496 (t) cc_final: 0.5879 (m) REVERT: K 297 PHE cc_start: 0.8754 (m-80) cc_final: 0.8367 (m-80) REVERT: K 376 MET cc_start: 0.3440 (ptt) cc_final: 0.3226 (ptm) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.1737 time to fit residues: 118.5216 Evaluate side-chains 368 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 4.9990 chunk 181 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 140 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN K 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.124145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070363 restraints weight = 82235.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.073047 restraints weight = 45951.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074771 restraints weight = 32165.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075854 restraints weight = 25935.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076507 restraints weight = 22809.695| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24275 Z= 0.294 Angle : 0.682 7.859 33946 Z= 0.379 Chirality : 0.042 0.190 3811 Planarity : 0.005 0.059 3359 Dihedral : 26.005 164.737 5430 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2158 helix: 0.51 (0.15), residues: 1169 sheet: 0.71 (0.44), residues: 155 loop : -0.42 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 88 TYR 0.025 0.002 TYR F 72 PHE 0.022 0.002 PHE K 149 TRP 0.027 0.002 TRP I 922 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.29 (24275) covalent geometry : angle 0.68194 / 0.38 (33946) hydrogen bonds : bond 0.05638 / 3.91 ( 1135) hydrogen bonds : angle 4.88586 / 3.54 ( 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 426 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.771 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 93 GLN cc_start: 0.8762 (tp40) cc_final: 0.8284 (tp40) REVERT: A 120 MET cc_start: 0.8853 (mtm) cc_final: 0.8322 (mtm) REVERT: B 37 LEU cc_start: 0.9687 (mm) cc_final: 0.9326 (mm) REVERT: B 39 ARG cc_start: 0.9284 (mmt-90) cc_final: 0.8993 (mmp80) REVERT: B 44 LYS cc_start: 0.8546 (tptt) cc_final: 0.8085 (tptp) REVERT: C 77 ARG cc_start: 0.8833 (tpp-160) cc_final: 0.8164 (tpp80) REVERT: C 102 ILE cc_start: 0.9676 (mm) cc_final: 0.9379 (tp) REVERT: D 47 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8805 (tm-30) REVERT: D 59 MET cc_start: 0.9563 (mmm) cc_final: 0.9245 (mmm) REVERT: D 68 ASP cc_start: 0.9626 (t70) cc_final: 0.9398 (t0) REVERT: E 73 GLU cc_start: 0.8926 (tt0) cc_final: 0.8496 (mt-10) REVERT: E 74 ILE cc_start: 0.9613 (mm) cc_final: 0.9389 (tt) REVERT: E 76 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8924 (tm-30) REVERT: E 77 ASP cc_start: 0.9284 (t70) cc_final: 0.8986 (t70) REVERT: E 90 MET cc_start: 0.8776 (ttt) cc_final: 0.8526 (ttt) REVERT: E 93 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7299 (tm-30) REVERT: E 119 ILE cc_start: 0.9017 (pt) cc_final: 0.8591 (pt) REVERT: E 120 MET cc_start: 0.8443 (mpp) cc_final: 0.7669 (mpp) REVERT: F 18 HIS cc_start: 0.6299 (p-80) cc_final: 0.6049 (t70) REVERT: F 59 LYS cc_start: 0.9511 (ttmt) cc_final: 0.8835 (ttpt) REVERT: F 63 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8941 (mm-30) REVERT: G 23 LEU cc_start: 0.9093 (mt) cc_final: 0.8883 (mt) REVERT: G 64 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8798 (tm-30) REVERT: G 65 LEU cc_start: 0.9338 (mm) cc_final: 0.9115 (mm) REVERT: G 92 GLU cc_start: 0.8841 (tt0) cc_final: 0.7612 (tt0) REVERT: H 35 GLU cc_start: 0.8328 (mp0) cc_final: 0.7950 (mp0) REVERT: H 54 ILE cc_start: 0.9064 (tp) cc_final: 0.8849 (tp) REVERT: H 59 MET cc_start: 0.9277 (tpp) cc_final: 0.9056 (tpp) REVERT: H 105 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6121 (tm-30) REVERT: H 106 LEU cc_start: 0.9341 (mt) cc_final: 0.8485 (mt) REVERT: I 763 GLU cc_start: 0.8883 (tt0) cc_final: 0.8527 (mt-10) REVERT: I 822 PHE cc_start: 0.8082 (m-10) cc_final: 0.7649 (m-80) REVERT: I 878 MET cc_start: 0.9122 (ttp) cc_final: 0.8226 (ttp) REVERT: I 884 HIS cc_start: 0.8989 (m90) cc_final: 0.8685 (m-70) REVERT: I 907 LEU cc_start: 0.9466 (pp) cc_final: 0.9015 (tp) REVERT: I 1000 MET cc_start: 0.8821 (mpp) cc_final: 0.8296 (mpp) REVERT: I 1036 MET cc_start: 0.8879 (pmm) cc_final: 0.8598 (pmm) REVERT: I 1037 ASN cc_start: 0.8160 (t0) cc_final: 0.7413 (m110) REVERT: I 1046 CYS cc_start: 0.9601 (m) cc_final: 0.9263 (m) REVERT: I 1081 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8441 (mtpt) REVERT: I 1085 LEU cc_start: 0.9599 (tp) cc_final: 0.9392 (tp) REVERT: I 1112 MET cc_start: 0.9647 (tpt) cc_final: 0.9211 (tpp) REVERT: I 1116 PHE cc_start: 0.9059 (m-80) cc_final: 0.8821 (m-80) REVERT: I 1124 LEU cc_start: 0.9254 (mp) cc_final: 0.9005 (mp) REVERT: I 1152 PHE cc_start: 0.9115 (t80) cc_final: 0.8845 (t80) REVERT: I 1154 LEU cc_start: 0.8814 (mp) cc_final: 0.8319 (mp) REVERT: I 1177 ASP cc_start: 0.9562 (t0) cc_final: 0.9353 (t70) REVERT: I 1229 ILE cc_start: 0.9223 (pt) cc_final: 0.8978 (mt) REVERT: I 1233 MET cc_start: 0.3064 (tmm) cc_final: 0.2832 (tmm) REVERT: I 1298 ASP cc_start: 0.7763 (m-30) cc_final: 0.7554 (m-30) REVERT: I 1305 MET cc_start: 0.8638 (tpt) cc_final: 0.8389 (tpt) REVERT: J 190 MET cc_start: -0.3218 (mtm) cc_final: -0.3510 (mtm) REVERT: J 313 MET cc_start: 0.7967 (mmp) cc_final: 0.7345 (mmp) REVERT: J 325 MET cc_start: 0.5496 (tpt) cc_final: 0.4934 (tpt) REVERT: K 82 MET cc_start: 0.3385 (tmm) cc_final: 0.2462 (tmm) REVERT: K 184 ASP cc_start: 0.9232 (m-30) cc_final: 0.8812 (t70) REVERT: K 297 PHE cc_start: 0.8934 (m-80) cc_final: 0.8472 (m-80) REVERT: K 376 MET cc_start: 0.2875 (ptt) cc_final: 0.2590 (ptm) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.1719 time to fit residues: 113.4487 Evaluate side-chains 350 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 1.9990 chunk 224 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 229 optimal weight: 20.0000 chunk 51 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS H 109 HIS ** I 915 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 = 0.3969 r_free = 0.3969 target = 0.125935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.072521 restraints weight = 81953.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075340 restraints weight = 45483.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.077153 restraints weight = 31485.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078292 restraints weight = 25196.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079029 restraints weight = 22018.148| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24275 Z= 0.210 Angle : 0.627 7.919 33946 Z= 0.346 Chirality : 0.041 0.181 3811 Planarity : 0.004 0.041 3359 Dihedral : 26.101 167.088 5430 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2158 helix: 0.67 (0.15), residues: 1170 sheet: 0.79 (0.45), residues: 146 loop : -0.42 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 4 TYR 0.019 0.002 TYR I 560 PHE 0.021 0.002 PHE F 61 TRP 0.026 0.002 TRP I 922 HIS 0.014 0.001 HIS J 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (24275) covalent geometry : angle 0.62678 / 0.35 (33946) hydrogen bonds : bond 0.04860 / 3.41 ( 1135) hydrogen bonds : angle 4.62247 / 3.35 ( 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 441 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 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: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8643 (tp40) cc_final: 0.8102 (tp40) REVERT: A 120 MET cc_start: 0.8858 (mtm) cc_final: 0.8283 (mtm) REVERT: B 37 LEU cc_start: 0.9584 (mm) cc_final: 0.9328 (mm) REVERT: B 39 ARG cc_start: 0.9272 (mmt-90) cc_final: 0.8977 (mmp80) REVERT: B 53 GLU cc_start: 0.8785 (mp0) cc_final: 0.8518 (pm20) REVERT: B 60 VAL cc_start: 0.9198 (t) cc_final: 0.8543 (t) REVERT: B 63 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8305 (mt-10) REVERT: C 77 ARG cc_start: 0.8835 (tpp-160) cc_final: 0.8100 (tpp80) REVERT: C 102 ILE cc_start: 0.9664 (mm) cc_final: 0.9340 (tp) REVERT: D 47 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8828 (tm-30) REVERT: D 59 MET cc_start: 0.9561 (mmm) cc_final: 0.9175 (mmt) REVERT: D 68 ASP cc_start: 0.9587 (t70) cc_final: 0.9375 (t0) REVERT: E 73 GLU cc_start: 0.8927 (tt0) cc_final: 0.8520 (mt-10) REVERT: E 76 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8907 (tm-30) REVERT: E 77 ASP cc_start: 0.9233 (t70) cc_final: 0.9026 (t70) REVERT: E 90 MET cc_start: 0.8715 (ttt) cc_final: 0.8432 (ttt) REVERT: E 93 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 119 ILE cc_start: 0.8553 (pt) cc_final: 0.8203 (pt) REVERT: E 120 MET cc_start: 0.7460 (mpp) cc_final: 0.6809 (mpp) REVERT: E 123 ASP cc_start: 0.9154 (m-30) cc_final: 0.8776 (m-30) REVERT: F 18 HIS cc_start: 0.6641 (p-80) cc_final: 0.6390 (t70) REVERT: F 47 SER cc_start: 0.9459 (m) cc_final: 0.9141 (m) REVERT: F 55 ARG cc_start: 0.9339 (mtt-85) cc_final: 0.8823 (mtt-85) REVERT: F 67 ARG cc_start: 0.9335 (mtp-110) cc_final: 0.8270 (ttm-80) REVERT: G 36 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9156 (tmtt) REVERT: G 64 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8747 (tm-30) REVERT: G 65 LEU cc_start: 0.9280 (mm) cc_final: 0.9057 (mm) REVERT: G 92 GLU cc_start: 0.8872 (tt0) cc_final: 0.7711 (tt0) REVERT: H 33 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8642 (tpp80) REVERT: H 35 GLU cc_start: 0.8269 (mp0) cc_final: 0.7888 (mp0) REVERT: H 52 THR cc_start: 0.8298 (p) cc_final: 0.8066 (p) REVERT: H 54 ILE cc_start: 0.8977 (tp) cc_final: 0.8765 (tp) REVERT: H 59 MET cc_start: 0.9194 (tpp) cc_final: 0.8901 (tpp) REVERT: H 105 GLU cc_start: 0.7796 (tm-30) cc_final: 0.5876 (tm-30) REVERT: H 106 LEU cc_start: 0.9323 (mt) cc_final: 0.8479 (mt) REVERT: N 5 SER cc_start: 0.9528 (m) cc_final: 0.9211 (p) REVERT: I 763 GLU cc_start: 0.8799 (tt0) cc_final: 0.8431 (mt-10) REVERT: I 822 PHE cc_start: 0.8144 (m-10) cc_final: 0.7724 (m-80) REVERT: I 878 MET cc_start: 0.9184 (ttp) cc_final: 0.8281 (ttp) REVERT: I 907 LEU cc_start: 0.9466 (pp) cc_final: 0.9012 (tp) REVERT: I 1000 MET cc_start: 0.8888 (mpp) cc_final: 0.8363 (mpp) REVERT: I 1037 ASN cc_start: 0.8547 (t0) cc_final: 0.7671 (m110) REVERT: I 1046 CYS cc_start: 0.9580 (m) cc_final: 0.9254 (m) REVERT: I 1081 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8431 (mtpt) REVERT: I 1085 LEU cc_start: 0.9590 (tp) cc_final: 0.9372 (tp) REVERT: I 1124 LEU cc_start: 0.9212 (mp) cc_final: 0.8951 (mp) REVERT: I 1152 PHE cc_start: 0.9152 (t80) cc_final: 0.8826 (t80) REVERT: I 1154 LEU cc_start: 0.8847 (mp) cc_final: 0.8385 (mp) REVERT: I 1177 ASP cc_start: 0.9555 (t0) cc_final: 0.9314 (t70) REVERT: I 1233 MET cc_start: 0.3194 (tmm) cc_final: 0.2971 (tmm) REVERT: I 1298 ASP cc_start: 0.7815 (m-30) cc_final: 0.7605 (m-30) REVERT: J 190 MET cc_start: -0.3116 (mtm) cc_final: -0.3413 (mtm) REVERT: J 272 CYS cc_start: 0.5690 (m) cc_final: 0.4292 (p) REVERT: J 275 HIS cc_start: 0.6748 (p-80) cc_final: 0.6498 (p-80) REVERT: J 313 MET cc_start: 0.8007 (mmp) cc_final: 0.7399 (mmp) REVERT: J 325 MET cc_start: 0.5478 (tpt) cc_final: 0.4881 (tpt) REVERT: K 82 MET cc_start: 0.3572 (tmm) cc_final: 0.2678 (tmm) REVERT: K 184 ASP cc_start: 0.9239 (m-30) cc_final: 0.8829 (t0) REVERT: K 254 MET cc_start: 0.5790 (ptt) cc_final: 0.5576 (ptt) REVERT: K 297 PHE cc_start: 0.8910 (m-80) cc_final: 0.8438 (m-80) REVERT: K 376 MET cc_start: 0.2710 (ptt) cc_final: 0.2429 (ptm) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.1743 time to fit residues: 117.8702 Evaluate side-chains 366 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 0.1980 chunk 185 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 218 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 82 HIS F 75 HIS H 109 HIS ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.128957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075884 restraints weight = 80075.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078821 restraints weight = 43846.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080738 restraints weight = 30201.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081962 restraints weight = 23985.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082698 restraints weight = 20865.417| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24275 Z= 0.143 Angle : 0.601 9.218 33946 Z= 0.328 Chirality : 0.039 0.149 3811 Planarity : 0.004 0.041 3359 Dihedral : 26.053 167.209 5430 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2158 helix: 0.78 (0.15), residues: 1178 sheet: 0.83 (0.45), residues: 149 loop : -0.49 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 116 TYR 0.023 0.001 TYR I 560 PHE 0.028 0.002 PHE C 25 TRP 0.026 0.001 TRP I 922 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (24275) covalent geometry : angle 0.60117 / 0.33 (33946) hydrogen bonds : bond 0.04497 / 3.18 ( 1135) hydrogen bonds : angle 4.36263 / 3.17 ( 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 452 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.771 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 73 GLU cc_start: 0.8216 (pp20) cc_final: 0.7587 (pp20) REVERT: A 93 GLN cc_start: 0.8460 (tp40) cc_final: 0.8081 (tp40) REVERT: A 94 GLU cc_start: 0.8873 (mm-30) cc_final: 0.7674 (tp30) REVERT: A 97 GLU cc_start: 0.8643 (pp20) cc_final: 0.8236 (pp20) REVERT: A 120 MET cc_start: 0.8884 (mtm) cc_final: 0.8293 (mtm) REVERT: B 37 LEU cc_start: 0.9573 (mm) cc_final: 0.9278 (mm) REVERT: C 77 ARG cc_start: 0.8873 (tpp-160) cc_final: 0.8042 (tpp80) REVERT: D 47 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8821 (tm-30) REVERT: D 59 MET cc_start: 0.9524 (mmm) cc_final: 0.9154 (mmt) REVERT: D 68 ASP cc_start: 0.9573 (t70) cc_final: 0.9344 (t0) REVERT: E 73 GLU cc_start: 0.8920 (tt0) cc_final: 0.8585 (mt-10) REVERT: E 85 GLN cc_start: 0.8309 (mt0) cc_final: 0.8062 (mt0) REVERT: E 90 MET cc_start: 0.8653 (ttt) cc_final: 0.8353 (ttt) REVERT: E 93 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7158 (tm-30) REVERT: E 96 SER cc_start: 0.9528 (m) cc_final: 0.9293 (m) REVERT: E 119 ILE cc_start: 0.8488 (pt) cc_final: 0.8060 (pt) REVERT: E 120 MET cc_start: 0.7513 (mpp) cc_final: 0.6613 (mpp) REVERT: E 123 ASP cc_start: 0.9082 (m-30) cc_final: 0.8480 (m-30) REVERT: F 47 SER cc_start: 0.9577 (m) cc_final: 0.9291 (m) REVERT: F 59 LYS cc_start: 0.9457 (ttpt) cc_final: 0.8876 (ttpt) REVERT: F 63 GLU cc_start: 0.9449 (mm-30) cc_final: 0.8900 (mm-30) REVERT: F 67 ARG cc_start: 0.9275 (mtp-110) cc_final: 0.8340 (ttm-80) REVERT: G 23 LEU cc_start: 0.9009 (mt) cc_final: 0.8758 (mt) REVERT: G 36 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9137 (tmtt) REVERT: G 64 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8647 (tm-30) REVERT: G 92 GLU cc_start: 0.8881 (tt0) cc_final: 0.7677 (tt0) REVERT: G 95 LYS cc_start: 0.9455 (tppp) cc_final: 0.8953 (tppp) REVERT: H 33 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8599 (tpp80) REVERT: H 35 GLU cc_start: 0.8214 (mp0) cc_final: 0.7895 (mp0) REVERT: H 47 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8391 (tm-30) REVERT: H 76 GLU cc_start: 0.8661 (tp30) cc_final: 0.8077 (tp30) REVERT: H 79 ARG cc_start: 0.9121 (ttm170) cc_final: 0.8889 (ttm170) REVERT: H 105 GLU cc_start: 0.7635 (tm-30) cc_final: 0.5699 (tm-30) REVERT: H 106 LEU cc_start: 0.9303 (mt) cc_final: 0.8558 (mt) REVERT: N 5 SER cc_start: 0.9541 (m) cc_final: 0.9187 (p) REVERT: N 30 LYS cc_start: 0.9107 (mmpt) cc_final: 0.8887 (mmmt) REVERT: I 763 GLU cc_start: 0.8806 (tt0) cc_final: 0.8452 (mt-10) REVERT: I 793 ILE cc_start: 0.9730 (mm) cc_final: 0.9509 (mm) REVERT: I 796 LEU cc_start: 0.9535 (tp) cc_final: 0.9241 (tp) REVERT: I 797 MET cc_start: 0.8883 (mmm) cc_final: 0.8228 (mmm) REVERT: I 822 PHE cc_start: 0.7962 (m-10) cc_final: 0.7323 (m-80) REVERT: I 878 MET cc_start: 0.9114 (ttp) cc_final: 0.8294 (ttp) REVERT: I 907 LEU cc_start: 0.9425 (pp) cc_final: 0.8999 (tp) REVERT: I 1000 MET cc_start: 0.8854 (mpp) cc_final: 0.8339 (mpp) REVERT: I 1037 ASN cc_start: 0.8413 (t0) cc_final: 0.7549 (m110) REVERT: I 1046 CYS cc_start: 0.9561 (m) cc_final: 0.9274 (m) REVERT: I 1081 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8460 (mtpt) REVERT: I 1085 LEU cc_start: 0.9598 (tp) cc_final: 0.9341 (tp) REVERT: I 1109 MET cc_start: 0.9226 (ptt) cc_final: 0.9019 (ptt) REVERT: I 1112 MET cc_start: 0.9648 (tpt) cc_final: 0.9255 (tpp) REVERT: I 1116 PHE cc_start: 0.9123 (m-80) cc_final: 0.8853 (m-80) REVERT: I 1124 LEU cc_start: 0.9181 (mp) cc_final: 0.8907 (mp) REVERT: I 1152 PHE cc_start: 0.9163 (t80) cc_final: 0.8854 (t80) REVERT: I 1154 LEU cc_start: 0.8835 (mp) cc_final: 0.8170 (mp) REVERT: I 1177 ASP cc_start: 0.9545 (t0) cc_final: 0.9282 (t70) REVERT: I 1298 ASP cc_start: 0.7704 (m-30) cc_final: 0.7474 (m-30) REVERT: J 190 MET cc_start: -0.3180 (mtm) cc_final: -0.3465 (mtm) REVERT: J 272 CYS cc_start: 0.5726 (m) cc_final: 0.4463 (p) REVERT: J 275 HIS cc_start: 0.6715 (p-80) cc_final: 0.6474 (p-80) REVERT: J 313 MET cc_start: 0.7964 (mmp) cc_final: 0.7421 (mmp) REVERT: J 325 MET cc_start: 0.5478 (tpt) cc_final: 0.4885 (tpt) REVERT: K 82 MET cc_start: 0.3673 (tmm) cc_final: 0.2259 (tmm) REVERT: K 142 GLU cc_start: 0.8735 (pp20) cc_final: 0.8164 (mm-30) REVERT: K 184 ASP cc_start: 0.9173 (m-30) cc_final: 0.8802 (t0) REVERT: K 297 PHE cc_start: 0.8859 (m-80) cc_final: 0.8375 (m-80) REVERT: K 376 MET cc_start: 0.2962 (ptt) cc_final: 0.2735 (ptm) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1776 time to fit residues: 122.8911 Evaluate side-chains 375 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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: 3.9990 chunk 124 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 167 optimal weight: 0.2980 chunk 168 optimal weight: 50.0000 chunk 232 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 177 optimal weight: 0.4980 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** H 109 HIS ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1191 HIS ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.126509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.073194 restraints weight = 80865.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.076021 restraints weight = 44681.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077826 restraints weight = 31004.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078978 restraints weight = 24772.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079678 restraints weight = 21646.031| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24275 Z= 0.211 Angle : 0.642 10.819 33946 Z= 0.351 Chirality : 0.040 0.165 3811 Planarity : 0.004 0.046 3359 Dihedral : 26.035 166.337 5430 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2158 helix: 0.72 (0.15), residues: 1169 sheet: 0.74 (0.45), residues: 149 loop : -0.47 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.019 0.002 TYR I 560 PHE 0.017 0.002 PHE C 25 TRP 0.025 0.001 TRP I 922 HIS 0.006 0.001 HIS I1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (24275) covalent geometry : angle 0.64201 / 0.35 (33946) hydrogen bonds : bond 0.04835 / 3.40 ( 1135) hydrogen bonds : angle 4.59378 / 3.32 ( 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 431 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.806 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: symmetry clash REVERT: A 93 GLN cc_start: 0.8519 (tp40) cc_final: 0.8280 (tp40) REVERT: A 94 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8781 (tp30) REVERT: A 97 GLU cc_start: 0.8706 (pp20) cc_final: 0.8460 (pp20) REVERT: A 120 MET cc_start: 0.8920 (mtm) cc_final: 0.8293 (mtm) REVERT: B 37 LEU cc_start: 0.9609 (mm) cc_final: 0.9319 (mm) REVERT: B 39 ARG cc_start: 0.9076 (mmp80) cc_final: 0.8781 (mmp80) REVERT: C 102 ILE cc_start: 0.9677 (mm) cc_final: 0.9412 (tp) REVERT: D 47 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 59 MET cc_start: 0.9586 (mmm) cc_final: 0.9192 (mmt) REVERT: D 68 ASP cc_start: 0.9622 (t70) cc_final: 0.9387 (t0) REVERT: E 90 MET cc_start: 0.8733 (ttt) cc_final: 0.8469 (ttt) REVERT: E 93 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7264 (tm-30) REVERT: E 119 ILE cc_start: 0.8560 (pt) cc_final: 0.8107 (pt) REVERT: E 120 MET cc_start: 0.7713 (mpp) cc_final: 0.6748 (mpp) REVERT: E 123 ASP cc_start: 0.9142 (m-30) cc_final: 0.8542 (m-30) REVERT: F 24 ASP cc_start: 0.7738 (t0) cc_final: 0.7313 (t0) REVERT: F 25 ASN cc_start: 0.8949 (m-40) cc_final: 0.8714 (m-40) REVERT: F 47 SER cc_start: 0.9545 (m) cc_final: 0.9286 (m) REVERT: G 64 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8702 (tm-30) REVERT: G 92 GLU cc_start: 0.8907 (tt0) cc_final: 0.7853 (tt0) REVERT: G 95 LYS cc_start: 0.9468 (tppp) cc_final: 0.8943 (tppp) REVERT: H 33 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8782 (tpp80) REVERT: H 35 GLU cc_start: 0.8308 (mp0) cc_final: 0.7932 (mp0) REVERT: H 59 MET cc_start: 0.9150 (tpp) cc_final: 0.8926 (tpp) REVERT: H 105 GLU cc_start: 0.7701 (tm-30) cc_final: 0.5572 (tm-30) REVERT: H 106 LEU cc_start: 0.9361 (mt) cc_final: 0.8618 (mt) REVERT: H 109 HIS cc_start: 0.8497 (m-70) cc_final: 0.8259 (m170) REVERT: N 5 SER cc_start: 0.9538 (m) cc_final: 0.9182 (p) REVERT: I 763 GLU cc_start: 0.8889 (tt0) cc_final: 0.8536 (mt-10) REVERT: I 793 ILE cc_start: 0.9737 (mm) cc_final: 0.9529 (mm) REVERT: I 796 LEU cc_start: 0.9525 (tp) cc_final: 0.9190 (tp) REVERT: I 797 MET cc_start: 0.8920 (mmm) cc_final: 0.8298 (mmm) REVERT: I 822 PHE cc_start: 0.8052 (m-10) cc_final: 0.7280 (m-80) REVERT: I 858 THR cc_start: 0.7668 (p) cc_final: 0.7412 (p) REVERT: I 878 MET cc_start: 0.9143 (ttp) cc_final: 0.8431 (ttp) REVERT: I 884 HIS cc_start: 0.9024 (m90) cc_final: 0.8703 (m90) REVERT: I 907 LEU cc_start: 0.9419 (pp) cc_final: 0.8999 (tp) REVERT: I 1000 MET cc_start: 0.8921 (mpp) cc_final: 0.8408 (mpp) REVERT: I 1037 ASN cc_start: 0.8473 (t0) cc_final: 0.7603 (m110) REVERT: I 1040 MET cc_start: 0.8989 (ttp) cc_final: 0.8768 (ttp) REVERT: I 1046 CYS cc_start: 0.9578 (m) cc_final: 0.9306 (m) REVERT: I 1081 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8570 (mtpt) REVERT: I 1085 LEU cc_start: 0.9589 (tp) cc_final: 0.9340 (tp) REVERT: I 1112 MET cc_start: 0.9652 (tpt) cc_final: 0.9129 (tpt) REVERT: I 1116 PHE cc_start: 0.9120 (m-80) cc_final: 0.8867 (m-80) REVERT: I 1124 LEU cc_start: 0.9151 (mp) cc_final: 0.8890 (mp) REVERT: I 1152 PHE cc_start: 0.9158 (t80) cc_final: 0.8845 (t80) REVERT: I 1154 LEU cc_start: 0.8809 (mp) cc_final: 0.8404 (mp) REVERT: I 1298 ASP cc_start: 0.7876 (m-30) cc_final: 0.7647 (m-30) REVERT: J 190 MET cc_start: -0.3349 (mtm) cc_final: -0.3605 (mtm) REVERT: J 272 CYS cc_start: 0.5559 (m) cc_final: 0.4361 (p) REVERT: J 275 HIS cc_start: 0.6620 (p-80) cc_final: 0.6363 (p-80) REVERT: J 313 MET cc_start: 0.8006 (mmp) cc_final: 0.7366 (mmp) REVERT: J 325 MET cc_start: 0.5452 (tpt) cc_final: 0.4886 (tpt) REVERT: K 82 MET cc_start: 0.3474 (tmm) cc_final: 0.2899 (tmm) REVERT: K 142 GLU cc_start: 0.8580 (pp20) cc_final: 0.7956 (mm-30) REVERT: K 184 ASP cc_start: 0.9137 (m-30) cc_final: 0.8757 (t70) REVERT: K 297 PHE cc_start: 0.8910 (m-80) cc_final: 0.8433 (m-80) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1728 time to fit residues: 115.2973 Evaluate side-chains 371 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 82 HIS ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1182 GLN I1191 HIS ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.126453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.073097 restraints weight = 80985.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075933 restraints weight = 44773.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077753 restraints weight = 31060.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078933 restraints weight = 24845.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079670 restraints weight = 21708.794| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24275 Z= 0.195 Angle : 0.636 10.037 33946 Z= 0.348 Chirality : 0.040 0.154 3811 Planarity : 0.004 0.045 3359 Dihedral : 26.083 167.349 5430 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.05 % Allowed : 0.16 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2158 helix: 0.69 (0.15), residues: 1173 sheet: 0.77 (0.45), residues: 149 loop : -0.51 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 99 TYR 0.013 0.001 TYR C 50 PHE 0.021 0.002 PHE A 104 TRP 0.026 0.002 TRP I 922 HIS 0.014 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (24275) covalent geometry : angle 0.63573 / 0.35 (33946) hydrogen bonds : bond 0.04760 / 3.35 ( 1135) hydrogen bonds : angle 4.58294 / 3.32 ( 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 426 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 0.786 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 65 LEU cc_start: 0.9275 (tp) cc_final: 0.9061 (tp) REVERT: A 93 GLN cc_start: 0.8501 (tp40) cc_final: 0.8300 (tp40) REVERT: A 97 GLU cc_start: 0.8723 (pp20) cc_final: 0.8456 (pp20) REVERT: A 120 MET cc_start: 0.8892 (mtm) cc_final: 0.8254 (mtm) REVERT: B 37 LEU cc_start: 0.9596 (mm) cc_final: 0.9292 (mm) REVERT: B 39 ARG cc_start: 0.9070 (mmp80) cc_final: 0.8714 (mmp80) REVERT: B 53 GLU cc_start: 0.8827 (mp0) cc_final: 0.8620 (mp0) REVERT: B 60 VAL cc_start: 0.9181 (t) cc_final: 0.8532 (t) REVERT: B 63 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8289 (mt-10) REVERT: C 102 ILE cc_start: 0.9691 (mm) cc_final: 0.9342 (tp) REVERT: C 112 GLN cc_start: 0.8925 (mm110) cc_final: 0.8579 (tp-100) REVERT: D 59 MET cc_start: 0.9566 (mmm) cc_final: 0.9211 (mmt) REVERT: D 68 ASP cc_start: 0.9611 (t70) cc_final: 0.9385 (t0) REVERT: E 56 LYS cc_start: 0.9577 (tttm) cc_final: 0.9199 (tptm) REVERT: E 90 MET cc_start: 0.8733 (ttt) cc_final: 0.8450 (ttt) REVERT: E 93 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 119 ILE cc_start: 0.8515 (pt) cc_final: 0.8095 (pt) REVERT: E 120 MET cc_start: 0.7672 (mpp) cc_final: 0.6737 (mpp) REVERT: E 123 ASP cc_start: 0.9140 (m-30) cc_final: 0.8542 (m-30) REVERT: F 24 ASP cc_start: 0.7757 (t0) cc_final: 0.7397 (t0) REVERT: F 25 ASN cc_start: 0.8944 (m-40) cc_final: 0.8736 (m-40) REVERT: F 61 PHE cc_start: 0.9692 (t80) cc_final: 0.9472 (t80) REVERT: G 23 LEU cc_start: 0.9058 (mt) cc_final: 0.8814 (mt) REVERT: G 64 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8655 (tm-30) REVERT: G 92 GLU cc_start: 0.8914 (tt0) cc_final: 0.8123 (tt0) REVERT: G 95 LYS cc_start: 0.9468 (tppp) cc_final: 0.8925 (tppp) REVERT: H 33 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8806 (tpp80) REVERT: H 35 GLU cc_start: 0.8194 (mp0) cc_final: 0.7923 (mp0) REVERT: H 105 GLU cc_start: 0.7571 (tm-30) cc_final: 0.5568 (tm-30) REVERT: H 106 LEU cc_start: 0.9374 (mt) cc_final: 0.8934 (mt) REVERT: H 109 HIS cc_start: 0.8405 (m-70) cc_final: 0.7487 (m170) REVERT: I 763 GLU cc_start: 0.8867 (tt0) cc_final: 0.8508 (mt-10) REVERT: I 796 LEU cc_start: 0.9522 (tp) cc_final: 0.9209 (tp) REVERT: I 797 MET cc_start: 0.8934 (mmm) cc_final: 0.8286 (mmm) REVERT: I 822 PHE cc_start: 0.8069 (m-10) cc_final: 0.7279 (m-80) REVERT: I 867 LYS cc_start: 0.9202 (pptt) cc_final: 0.8934 (pptt) REVERT: I 878 MET cc_start: 0.9157 (ttp) cc_final: 0.8448 (ttp) REVERT: I 884 HIS cc_start: 0.9054 (m90) cc_final: 0.8763 (m90) REVERT: I 907 LEU cc_start: 0.9451 (pp) cc_final: 0.9000 (tp) REVERT: I 1000 MET cc_start: 0.8923 (mpp) cc_final: 0.8419 (mpp) REVERT: I 1037 ASN cc_start: 0.8562 (t0) cc_final: 0.7790 (m110) REVERT: I 1040 MET cc_start: 0.8956 (ttp) cc_final: 0.8693 (ttp) REVERT: I 1046 CYS cc_start: 0.9550 (m) cc_final: 0.9249 (m) REVERT: I 1081 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8554 (mtpt) REVERT: I 1085 LEU cc_start: 0.9587 (tp) cc_final: 0.9336 (tp) REVERT: I 1112 MET cc_start: 0.9669 (tpt) cc_final: 0.9256 (tpp) REVERT: I 1116 PHE cc_start: 0.9091 (m-80) cc_final: 0.8876 (m-80) REVERT: I 1124 LEU cc_start: 0.9165 (mp) cc_final: 0.8900 (mp) REVERT: I 1152 PHE cc_start: 0.9186 (t80) cc_final: 0.8883 (t80) REVERT: I 1154 LEU cc_start: 0.8905 (mp) cc_final: 0.8486 (mp) REVERT: I 1298 ASP cc_start: 0.7926 (m-30) cc_final: 0.7633 (m-30) REVERT: I 1305 MET cc_start: 0.8639 (tpt) cc_final: 0.8359 (tpt) REVERT: J 190 MET cc_start: -0.3289 (mtm) cc_final: -0.3542 (mtm) REVERT: J 272 CYS cc_start: 0.5665 (m) cc_final: 0.4510 (p) REVERT: J 275 HIS cc_start: 0.6667 (p-80) cc_final: 0.6410 (p-80) REVERT: J 313 MET cc_start: 0.8000 (mmp) cc_final: 0.7367 (mmp) REVERT: J 325 MET cc_start: 0.5593 (tpt) cc_final: 0.5047 (tpt) REVERT: K 82 MET cc_start: 0.4106 (tmm) cc_final: 0.2634 (tmm) REVERT: K 184 ASP cc_start: 0.9140 (m-30) cc_final: 0.8751 (t70) REVERT: K 297 PHE cc_start: 0.8925 (m-80) cc_final: 0.8437 (m-80) outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.1722 time to fit residues: 113.7150 Evaluate side-chains 367 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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: 4.9990 chunk 234 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1182 GLN I1187 GLN I1191 HIS ** J 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS K 251 HIS K 313 ASN K 370 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.123407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.069724 restraints weight = 82897.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.072409 restraints weight = 46789.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074112 restraints weight = 32860.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075165 restraints weight = 26559.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075848 restraints weight = 23414.386| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 24275 Z= 0.288 Angle : 0.711 11.466 33946 Z= 0.391 Chirality : 0.044 0.198 3811 Planarity : 0.005 0.068 3359 Dihedral : 26.235 167.984 5430 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2158 helix: 0.38 (0.15), residues: 1178 sheet: 0.59 (0.45), residues: 150 loop : -0.53 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 99 TYR 0.021 0.002 TYR H 40 PHE 0.035 0.002 PHE A 104 TRP 0.027 0.002 TRP I 922 HIS 0.014 0.002 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.29 (24275) covalent geometry : angle 0.71133 / 0.39 (33946) hydrogen bonds : bond 0.05774 / 4.00 ( 1135) hydrogen bonds : angle 4.95027 / 3.57 ( 3017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5671.80 seconds wall clock time: 98 minutes 14.43 seconds (5894.43 seconds total)