Starting phenix.real_space_refine on Tue Sep 15 04:23:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.map" model { file = "/net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p7n_20267/09_2026/6p7n_20267.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17892 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 4 5.21 5 S 56 5.16 5 C 12876 2.51 5 N 3362 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20356 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8796 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1048} Chain breaks: 7 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 1, 'RNAv2': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: G, E, F Time building chain proxies: 12.06, per 1000 atoms: 0.59 Number of scatterers: 20356 At special positions: 0 Unit cell: (152.1, 165.6, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 50 15.00 Mg 4 11.99 O 4008 8.00 N 3362 7.00 C 12876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 967.7 milliseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 22 sheets defined 48.9% alpha, 13.3% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'C' and resid 128 through 148 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.552A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'G' and resid 129 through 148 Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.553A pdb=" N ARG G 155 " --> pdb=" O TYR G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 38 through 66 removed outlier: 4.581A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.670A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.221A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.597A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.968A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.762A pdb=" N GLU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.355A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.709A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.974A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.649A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.456A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 718 through 728 removed outlier: 4.083A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.115A pdb=" N GLU A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.609A pdb=" N GLU A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 969 through 973 removed outlier: 4.244A pdb=" N GLY A 973 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 3.506A pdb=" N PHE A1052 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.256A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A1125 " --> pdb=" O LYS A1121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.680A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 26 through 33 Processing helix chain 'E' and resid 38 through 66 removed outlier: 4.583A pdb=" N LYS E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.671A pdb=" N ARG E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 114 through 120 removed outlier: 4.221A pdb=" N PHE E 119 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 132 removed outlier: 3.597A pdb=" N LEU E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 144 removed outlier: 3.968A pdb=" N LEU E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 151 through 159 Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.763A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 201 through 211 removed outlier: 4.355A pdb=" N ILE E 205 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 312 through 327 Processing helix chain 'E' and resid 341 through 352 removed outlier: 3.709A pdb=" N SER E 345 " --> pdb=" O GLY E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 removed outlier: 3.974A pdb=" N ILE E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 392 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 409 through 431 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.650A pdb=" N PHE E 436 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 471 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.456A pdb=" N ASP E 489 " --> pdb=" O SER E 485 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 512 Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 718 through 728 removed outlier: 4.082A pdb=" N PHE E 728 " --> pdb=" O PHE E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 791 removed outlier: 4.115A pdb=" N GLU E 791 " --> pdb=" O ARG E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 811 through 822 Processing helix chain 'E' and resid 872 through 886 Processing helix chain 'E' and resid 890 through 919 removed outlier: 3.608A pdb=" N GLU E 894 " --> pdb=" O TRP E 890 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS E 909 " --> pdb=" O SER E 905 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS E 917 " --> pdb=" O GLU E 913 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 955 Processing helix chain 'E' and resid 969 through 973 removed outlier: 4.243A pdb=" N GLY E 973 " --> pdb=" O ALA E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 1020 through 1029 Processing helix chain 'E' and resid 1048 through 1052 removed outlier: 3.506A pdb=" N PHE E1052 " --> pdb=" O TYR E1049 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1102 Processing helix chain 'E' and resid 1111 through 1116 Processing helix chain 'E' and resid 1120 through 1135 removed outlier: 4.257A pdb=" N TYR E1124 " --> pdb=" O ASP E1120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER E1125 " --> pdb=" O LYS E1121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E1135 " --> pdb=" O MET E1131 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1178 through 1201 removed outlier: 3.679A pdb=" N VAL E1191 " --> pdb=" O ILE E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1205 through 1209 Processing helix chain 'E' and resid 1214 through 1225 Processing sheet with id=AA1, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.894A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 222 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.894A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.893A pdb=" N CYS G 195 " --> pdb=" O CYS G 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 185 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR G 197 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN G 157 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 222 " --> pdb=" O ILE G 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.893A pdb=" N CYS G 195 " --> pdb=" O CYS G 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 185 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR G 197 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 6.464A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 925 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 863 removed outlier: 3.503A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.793A pdb=" N LEU A1065 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB4, first strand: chain 'A' and resid 1151 through 1155 removed outlier: 4.724A pdb=" N TYR A1162 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR E 553 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR E 794 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 737 " --> pdb=" O ALA E 801 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR E 553 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR E 794 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 337 through 339 Processing sheet with id=AB8, first strand: chain 'E' and resid 765 through 766 Processing sheet with id=AB9, first strand: chain 'E' and resid 850 through 855 removed outlier: 6.465A pdb=" N VAL E 843 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN E 853 " --> pdb=" O ILE E 841 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE E 841 " --> pdb=" O GLN E 853 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU E 925 " --> pdb=" O ILE E 831 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE E 922 " --> pdb=" O PHE E 994 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE E 996 " --> pdb=" O ILE E 922 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU E 924 " --> pdb=" O ILE E 996 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 858 through 863 removed outlier: 3.504A pdb=" N ILE E 868 " --> pdb=" O ASN E 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1033 through 1037 removed outlier: 3.793A pdb=" N LEU E1065 " --> pdb=" O PHE E1045 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1070 through 1073 Processing sheet with id=AC4, first strand: chain 'E' and resid 1151 through 1155 removed outlier: 4.724A pdb=" N TYR E1162 " --> pdb=" O SER E1152 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6240 1.34 - 1.46: 3449 1.46 - 1.57: 10977 1.57 - 1.69: 100 1.69 - 1.81: 94 Bond restraints: 20860 Sorted by residual: bond pdb=" CB GLU E 443 " pdb=" CG GLU E 443 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 bond pdb=" CB GLU A 443 " pdb=" CG GLU A 443 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 bond pdb=" CA ASP C 137 " pdb=" C ASP C 137 " ideal model delta sigma weight residual 1.522 1.509 0.013 1.40e-02 5.10e+03 7.97e-01 bond pdb=" CA ASP G 137 " pdb=" C ASP G 137 " ideal model delta sigma weight residual 1.522 1.509 0.012 1.40e-02 5.10e+03 7.52e-01 bond pdb=" CG LEU A1130 " pdb=" CD2 LEU A1130 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.10e-01 ... (remaining 20855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 27973 2.48 - 4.97: 307 4.97 - 7.45: 20 7.45 - 9.93: 2 9.93 - 12.41: 2 Bond angle restraints: 28304 Sorted by residual: angle pdb=" N LEU C 138 " pdb=" CA LEU C 138 " pdb=" C LEU C 138 " ideal model delta sigma weight residual 111.36 107.38 3.98 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N LEU G 138 " pdb=" CA LEU G 138 " pdb=" C LEU G 138 " ideal model delta sigma weight residual 111.36 107.39 3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" CA LEU C 138 " pdb=" CB LEU C 138 " pdb=" CG LEU C 138 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU G 138 " pdb=" CB LEU G 138 " pdb=" CG LEU G 138 " ideal model delta sigma weight residual 116.30 128.66 -12.36 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C LEU A 497 " pdb=" N LEU A 498 " pdb=" CA LEU A 498 " ideal model delta sigma weight residual 122.31 116.41 5.90 2.00e+00 2.50e-01 8.71e+00 ... (remaining 28299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 10690 15.47 - 30.94: 1349 30.94 - 46.41: 293 46.41 - 61.88: 144 61.88 - 77.34: 42 Dihedral angle restraints: 12518 sinusoidal: 5548 harmonic: 6970 Sorted by residual: dihedral pdb=" C4' U F 10 " pdb=" C3' U F 10 " pdb=" C2' U F 10 " pdb=" C1' U F 10 " ideal model delta sinusoidal sigma weight residual 36.34 -37.15 73.49 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' U B 10 " pdb=" C3' U B 10 " pdb=" C2' U B 10 " pdb=" C1' U B 10 " ideal model delta sinusoidal sigma weight residual 36.35 -37.08 73.42 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' A F 11 " pdb=" C3' A F 11 " pdb=" C2' A F 11 " pdb=" C1' A F 11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.78 73.13 1 3.10e+00 1.04e-01 7.09e+02 ... (remaining 12515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2565 0.057 - 0.113: 403 0.113 - 0.170: 40 0.170 - 0.226: 16 0.226 - 0.283: 72 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C2' A B 1 " pdb=" C3' A B 1 " pdb=" O2' A B 1 " pdb=" C1' A B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' A F 1 " pdb=" C3' A F 1 " pdb=" O2' A F 1 " pdb=" C1' A F 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' A B 2 " pdb=" C3' A B 2 " pdb=" O2' A B 2 " pdb=" C1' A B 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3093 not shown) Planarity restraints: 3434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 136 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE G 136 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE G 136 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP G 137 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE C 136 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE C 136 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 137 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 176 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ILE E 176 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 176 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN E 177 " -0.017 2.00e-02 2.50e+03 ... (remaining 3431 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 594 2.70 - 3.25: 20158 3.25 - 3.80: 31076 3.80 - 4.35: 43031 4.35 - 4.90: 70067 Nonbonded interactions: 164926 Sorted by model distance: nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.152 3.040 nonbonded pdb=" O SER E 68 " pdb=" OG SER E 68 " model vdw 2.152 3.040 nonbonded pdb=" OP2 A B 17 " pdb="MG MG A1301 " model vdw 2.195 2.170 nonbonded pdb=" OP2 A F 17 " pdb="MG MG E1301 " model vdw 2.202 2.170 nonbonded pdb=" OE1 GLU C 184 " pdb=" O5' A B 1 " model vdw 2.209 3.040 ... (remaining 164921 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 29.720 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 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 : 0.002 0.029 20860 Z= 0.105 Angle : 0.600 12.414 28304 Z= 0.315 Chirality : 0.057 0.283 3096 Planarity : 0.004 0.042 3434 Dihedral : 15.683 77.345 8018 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.33 % Allowed : 3.84 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.15), residues: 2316 helix: -1.44 (0.14), residues: 1052 sheet: -3.27 (0.29), residues: 212 loop : -2.70 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 187 TYR 0.011 0.001 TYR C 188 PHE 0.013 0.001 PHE E 946 TRP 0.010 0.001 TRP A1193 HIS 0.006 0.001 HIS E 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 (20860) covalent geometry : angle 0.60030 / 0.32 (28304) hydrogen bonds : bond 0.15089 / 10.12 ( 887) hydrogen bonds : angle 6.22256 / 4.26 ( 2547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8618 (pm20) REVERT: C 224 MET cc_start: 0.7124 (mtp) cc_final: 0.6570 (mtm) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0651 time to fit residues: 1.8903 Evaluate side-chains 16 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.035 Evaluate side-chains 79 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 701 MET cc_start: 0.9055 (ttm) cc_final: 0.8792 (tpp) REVERT: A 796 LEU cc_start: 0.9855 (tp) cc_final: 0.9629 (pp) outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 0.1127 time to fit residues: 11.9796 Evaluate side-chains 38 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.360 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0088 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 107 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.0546 > 50:) chunk 10 optimal weight: 60.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN A 67 HIS A 157 ASN A 268 GLN A 420 GLN A 793 GLN A 813 ASN A 861 ASN A 906 GLN A 909 HIS A 955 ASN A 978 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.040381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.030014 restraints weight = 12836.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.031303 restraints weight = 8807.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.032182 restraints weight = 6759.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.032840 restraints weight = 5632.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033333 restraints weight = 4864.681| |-----------------------------------------------------------------------------| r_work (final): 0.3007 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.036514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.025350 restraints weight = 149473.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.025760 restraints weight = 130670.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.026016 restraints weight = 119963.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.026279 restraints weight = 111171.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.026501 restraints weight = 102796.809| |-----------------------------------------------------------------------------| r_work (final): 0.3067 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.023044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.021139 restraints weight = 11790.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.021781 restraints weight = 5451.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.022185 restraints weight = 2994.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.022397 restraints weight = 1835.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.022562 restraints weight = 1288.696| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4339 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20860 Z= 0.132 Angle : 0.659 12.385 28304 Z= 0.315 Chirality : 0.057 0.767 3096 Planarity : 0.004 0.072 3434 Dihedral : 11.428 147.751 3150 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -1.46 (0.17), residues: 2316 helix: 0.19 (0.16), residues: 1056 sheet: -2.42 (0.30), residues: 236 loop : -1.82 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 217 TYR 0.017 0.001 TYR E1095 PHE 0.011 0.001 PHE E 863 TRP 0.008 0.001 TRP A1193 HIS 0.009 0.001 HIS E 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (20860) covalent geometry : angle 0.65883 / 0.31 (28304) hydrogen bonds : bond 0.03971 / 2.75 ( 887) hydrogen bonds : angle 4.58732 / 3.18 ( 2547) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8806 (pm20) REVERT: C 209 TYR cc_start: 0.9207 (m-80) cc_final: 0.8864 (m-80) REVERT: C 224 MET cc_start: 0.7795 (mtp) cc_final: 0.7482 (mtm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0616 time to fit residues: 1.2225 Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.027 Evaluate side-chains 41 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.9636 (tp) cc_final: 0.9353 (pp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1086 time to fit residues: 6.3614 Evaluate side-chains 32 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.252 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0053 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 184 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 205 optimal weight: 0.0570 chunk 28 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 0.0040 chunk 9 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 204 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A 759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031288 restraints weight = 12726.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.032367 restraints weight = 9293.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033228 restraints weight = 7465.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.033842 restraints weight = 6294.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.034334 restraints weight = 5518.707| |-----------------------------------------------------------------------------| r_work (final): 0.2996 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.036844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.025339 restraints weight = 149377.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.025805 restraints weight = 129969.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.026172 restraints weight = 114851.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.026397 restraints weight = 104979.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.026668 restraints weight = 98489.915| |-----------------------------------------------------------------------------| r_work (final): 0.3305 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.023035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.021295 restraints weight = 13987.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.021815 restraints weight = 7573.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.022119 restraints weight = 4678.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.022350 restraints weight = 3245.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.022510 restraints weight = 2282.376| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4250 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20860 Z= 0.096 Angle : 0.580 11.213 28304 Z= 0.278 Chirality : 0.049 0.363 3096 Planarity : 0.003 0.039 3434 Dihedral : 11.173 137.876 3150 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: -0.73 (0.18), residues: 2316 helix: 0.85 (0.17), residues: 1034 sheet: -2.43 (0.28), residues: 256 loop : -1.32 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 187 TYR 0.009 0.001 TYR E 794 PHE 0.011 0.001 PHE A 946 TRP 0.005 0.001 TRP A 362 HIS 0.003 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (20860) covalent geometry : angle 0.57993 / 0.28 (28304) hydrogen bonds : bond 0.03956 / 2.86 ( 887) hydrogen bonds : angle 4.25872 / 2.96 ( 2547) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8789 (pm20) REVERT: C 209 TYR cc_start: 0.9180 (m-80) cc_final: 0.8796 (m-80) REVERT: C 224 MET cc_start: 0.7786 (mtp) cc_final: 0.7448 (mtm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0557 time to fit residues: 1.0039 Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.036 Evaluate side-chains 40 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.360 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: A 555 LEU cc_start: 0.9617 (tp) cc_final: 0.9250 (pp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1154 time to fit residues: 6.4533 Evaluate side-chains 33 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.422 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0107 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 123 optimal weight: 0.0570 chunk 130 optimal weight: 0.0470 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 33 optimal weight: 0.0670 chunk 122 optimal weight: 5.9990 overall best weight: 1.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A 759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.042637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034244 restraints weight = 12315.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035098 restraints weight = 9677.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.035765 restraints weight = 8050.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.036257 restraints weight = 6924.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036613 restraints weight = 6151.313| |-----------------------------------------------------------------------------| r_work (final): 0.3039 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.036210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.025169 restraints weight = 151691.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.025552 restraints weight = 134981.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.025821 restraints weight = 122138.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.026089 restraints weight = 113224.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.026288 restraints weight = 106351.888| |-----------------------------------------------------------------------------| r_work (final): 0.3279 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.023268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.021530 restraints weight = 14517.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.022071 restraints weight = 7637.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.022401 restraints weight = 4600.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.022611 restraints weight = 2986.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.022791 restraints weight = 2123.192| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4371 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20860 Z= 0.092 Angle : 0.551 10.050 28304 Z= 0.265 Chirality : 0.046 0.280 3096 Planarity : 0.003 0.039 3434 Dihedral : 11.029 137.828 3150 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -0.18 (0.18), residues: 2316 helix: 1.19 (0.17), residues: 1046 sheet: -1.99 (0.30), residues: 250 loop : -0.97 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 217 TYR 0.009 0.001 TYR A1102 PHE 0.015 0.001 PHE E 530 TRP 0.006 0.001 TRP A 355 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (20860) covalent geometry : angle 0.55095 / 0.27 (28304) hydrogen bonds : bond 0.04118 / 3.03 ( 887) hydrogen bonds : angle 4.04760 / 2.82 ( 2547) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.8910 (m-80) cc_final: 0.8481 (m-80) REVERT: C 224 MET cc_start: 0.6674 (mtp) cc_final: 0.6269 (mtp) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0656 time to fit residues: 0.9586 Evaluate side-chains 10 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.035 Evaluate side-chains 37 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.351 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: A 555 LEU cc_start: 0.9650 (tp) cc_final: 0.9324 (pp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1146 time to fit residues: 6.0241 Evaluate side-chains 32 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.293 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 148 optimal weight: 0.0270 chunk 122 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 223 optimal weight: 0.0670 chunk 115 optimal weight: 0.0980 chunk 155 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 21 optimal weight: 0.0040 chunk 198 optimal weight: 0.0010 chunk 32 optimal weight: 10.0000 overall best weight: 0.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.042457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033969 restraints weight = 11649.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034815 restraints weight = 9254.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.035425 restraints weight = 7778.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035896 restraints weight = 6778.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036247 restraints weight = 6078.267| |-----------------------------------------------------------------------------| r_work (final): 0.3018 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.036791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.025620 restraints weight = 151390.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026009 restraints weight = 133893.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.026380 restraints weight = 120732.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.026634 restraints weight = 110867.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.026770 restraints weight = 103800.104| |-----------------------------------------------------------------------------| r_work (final): 0.3274 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.023222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.021427 restraints weight = 11557.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.022035 restraints weight = 5419.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.022402 restraints weight = 3062.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.022613 restraints weight = 1769.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.022780 restraints weight = 1176.065| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4396 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20860 Z= 0.089 Angle : 0.544 11.064 28304 Z= 0.259 Chirality : 0.046 0.270 3096 Planarity : 0.002 0.036 3434 Dihedral : 11.013 138.861 3150 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 0.11 (0.18), residues: 2316 helix: 1.40 (0.17), residues: 1044 sheet: -1.64 (0.31), residues: 252 loop : -0.83 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 217 TYR 0.009 0.001 TYR E 794 PHE 0.016 0.001 PHE A 530 TRP 0.004 0.001 TRP E 890 HIS 0.005 0.001 HIS E 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.09 (20860) covalent geometry : angle 0.54432 / 0.26 (28304) hydrogen bonds : bond 0.03661 / 2.63 ( 887) hydrogen bonds : angle 3.96265 / 2.77 ( 2547) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.8844 (m-80) cc_final: 0.8347 (m-80) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0539 time to fit residues: 0.8451 Evaluate side-chains 9 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.035 Evaluate side-chains 39 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.297 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: A 555 LEU cc_start: 0.9657 (tp) cc_final: 0.9351 (pp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1111 time to fit residues: 6.2567 Evaluate side-chains 30 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.349 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0084 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 199 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 49 optimal weight: 0.1980 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN C 231 ASN A 813 ASN A1108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.039636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031423 restraints weight = 12770.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.032099 restraints weight = 10349.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.032582 restraints weight = 8844.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.032956 restraints weight = 7857.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.033204 restraints weight = 7169.707| |-----------------------------------------------------------------------------| r_work (final): 0.2904 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.034694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.023958 restraints weight = 154073.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.024363 restraints weight = 136539.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.024644 restraints weight = 122579.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.024827 restraints weight = 113543.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025009 restraints weight = 107297.556| |-----------------------------------------------------------------------------| r_work (final): 0.3232 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.023744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.022089 restraints weight = 13982.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.022638 restraints weight = 7220.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.022969 restraints weight = 4263.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.023174 restraints weight = 2857.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.023312 restraints weight = 2101.126| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4398 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20860 Z= 0.119 Angle : 0.583 11.851 28304 Z= 0.285 Chirality : 0.045 0.252 3096 Planarity : 0.003 0.035 3434 Dihedral : 11.057 139.662 3150 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 0.18 (0.18), residues: 2316 helix: 1.37 (0.17), residues: 1064 sheet: -1.59 (0.32), residues: 250 loop : -0.72 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 217 TYR 0.017 0.001 TYR E 840 PHE 0.015 0.001 PHE A 197 TRP 0.011 0.001 TRP E 890 HIS 0.007 0.001 HIS E 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (20860) covalent geometry : angle 0.58252 / 0.29 (28304) hydrogen bonds : bond 0.04526 / 3.42 ( 887) hydrogen bonds : angle 4.01668 / 2.82 ( 2547) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 TYR cc_start: 0.9064 (m-80) cc_final: 0.8698 (m-80) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0647 time to fit residues: 0.9457 Evaluate side-chains 11 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.037 Evaluate side-chains 35 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.9677 (tp) cc_final: 0.9384 (pp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0886 time to fit residues: 4.6472 Evaluate side-chains 27 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.388 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A1108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.040440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.032049 restraints weight = 12636.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032751 restraints weight = 10194.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.033278 restraints weight = 8706.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033656 restraints weight = 7702.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.033938 restraints weight = 7009.075| |-----------------------------------------------------------------------------| r_work (final): 0.2938 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.034789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.024090 restraints weight = 151213.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.024479 restraints weight = 134490.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.024800 restraints weight = 120511.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.024967 restraints weight = 111731.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.025179 restraints weight = 105636.314| |-----------------------------------------------------------------------------| r_work (final): 0.3235 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.023791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.022173 restraints weight = 13410.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.022714 restraints weight = 6954.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.023031 restraints weight = 4117.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.023258 restraints weight = 2720.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.023378 restraints weight = 1933.056| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4372 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20860 Z= 0.093 Angle : 0.559 11.827 28304 Z= 0.268 Chirality : 0.045 0.256 3096 Planarity : 0.003 0.034 3434 Dihedral : 11.038 138.756 3150 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.42 (0.18), residues: 2316 helix: 1.54 (0.17), residues: 1064 sheet: -1.35 (0.32), residues: 246 loop : -0.60 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 217 TYR 0.015 0.001 TYR E 943 PHE 0.013 0.001 PHE A 530 TRP 0.007 0.001 TRP E 890 HIS 0.002 0.001 HIS E 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (20860) covalent geometry : angle 0.55885 / 0.27 (28304) hydrogen bonds : bond 0.03784 / 2.77 ( 887) hydrogen bonds : angle 3.95345 / 2.80 ( 2547) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0639 time to fit residues: 0.9332 Evaluate side-chains 10 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.034 Evaluate side-chains 37 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.9664 (tp) cc_final: 0.9363 (pp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1023 time to fit residues: 5.5959 Evaluate side-chains 28 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.340 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0084 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 80 optimal weight: 4.9990 chunk 196 optimal weight: 0.0470 chunk 14 optimal weight: 30.0000 chunk 233 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 122 optimal weight: 0.3980 chunk 134 optimal weight: 30.0000 chunk 183 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A 759 HIS A1108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.040307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.031943 restraints weight = 12169.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.032518 restraints weight = 10058.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033030 restraints weight = 8769.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.033408 restraints weight = 7829.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.033642 restraints weight = 7144.301| |-----------------------------------------------------------------------------| r_work (final): 0.2931 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.034320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.023773 restraints weight = 151974.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.024146 restraints weight = 134257.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.024430 restraints weight = 121507.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.024641 restraints weight = 112365.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.024765 restraints weight = 105701.210| |-----------------------------------------------------------------------------| r_work (final): 0.3225 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.022124 restraints weight = 13322.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.022640 restraints weight = 6777.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.022973 restraints weight = 4020.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.023168 restraints weight = 2658.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.023387 restraints weight = 1963.947| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4378 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20860 Z= 0.099 Angle : 0.580 12.120 28304 Z= 0.280 Chirality : 0.046 0.254 3096 Planarity : 0.004 0.109 3434 Dihedral : 11.057 138.562 3150 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2316 helix: 1.57 (0.17), residues: 1060 sheet: -1.39 (0.32), residues: 258 loop : -0.54 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1033 TYR 0.016 0.001 TYR G 209 PHE 0.012 0.001 PHE E 530 TRP 0.007 0.001 TRP A 355 HIS 0.002 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (20860) covalent geometry : angle 0.57963 / 0.28 (28304) hydrogen bonds : bond 0.03840 / 2.83 ( 887) hydrogen bonds : angle 4.06193 / 2.87 ( 2547) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8274 (tp30) cc_final: 0.7639 (pm20) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0624 time to fit residues: 0.9023 Evaluate side-chains 11 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.023 Evaluate side-chains 31 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.9662 (tp) cc_final: 0.9343 (pp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0895 time to fit residues: 4.4999 Evaluate side-chains 26 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.344 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 153 optimal weight: 0.0070 chunk 150 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A1108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.040599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031961 restraints weight = 12263.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.032620 restraints weight = 10135.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033105 restraints weight = 8779.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.033433 restraints weight = 7857.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.033793 restraints weight = 7161.629| |-----------------------------------------------------------------------------| r_work (final): 0.2934 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.034666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.023967 restraints weight = 147827.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.024305 restraints weight = 130837.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.024622 restraints weight = 118309.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.024893 restraints weight = 109696.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025041 restraints weight = 102250.723| |-----------------------------------------------------------------------------| r_work (final): 0.3251 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.024116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.022442 restraints weight = 12819.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.022965 restraints weight = 6578.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.023290 restraints weight = 3825.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.023484 restraints weight = 2418.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.023584 restraints weight = 1587.528| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4368 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20860 Z= 0.090 Angle : 0.573 12.581 28304 Z= 0.272 Chirality : 0.046 0.258 3096 Planarity : 0.003 0.044 3434 Dihedral : 11.007 137.359 3150 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2316 helix: 1.56 (0.17), residues: 1048 sheet: -1.27 (0.32), residues: 258 loop : -0.44 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1033 TYR 0.015 0.001 TYR G 209 PHE 0.012 0.001 PHE A1127 TRP 0.006 0.001 TRP E 890 HIS 0.002 0.001 HIS E 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (20860) covalent geometry : angle 0.57324 / 0.27 (28304) hydrogen bonds : bond 0.03564 / 2.58 ( 887) hydrogen bonds : angle 4.01858 / 2.84 ( 2547) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8321 (tp30) cc_final: 0.7816 (pm20) REVERT: C 209 TYR cc_start: 0.9206 (m-10) cc_final: 0.8986 (m-80) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0759 time to fit residues: 1.2478 Evaluate side-chains 12 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 Evaluate side-chains 33 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.9656 (tp) cc_final: 0.9341 (pp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0857 time to fit residues: 4.5610 Evaluate side-chains 28 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.417 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0106 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 159 optimal weight: 6.9990 chunk 210 optimal weight: 0.0870 chunk 198 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 0.0770 chunk 179 optimal weight: 0.0170 chunk 33 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 28 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A 718 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.044455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.035410 restraints weight = 10941.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036071 restraints weight = 9103.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036640 restraints weight = 7767.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036951 restraints weight = 7026.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037241 restraints weight = 6481.112| |-----------------------------------------------------------------------------| r_work (final): 0.2998 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.035407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.024471 restraints weight = 146758.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.024899 restraints weight = 128833.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.025174 restraints weight = 115780.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.025470 restraints weight = 105648.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.025618 restraints weight = 99031.619| |-----------------------------------------------------------------------------| r_work (final): 0.3283 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.023649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.022054 restraints weight = 14000.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.022539 restraints weight = 7261.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.022892 restraints weight = 4441.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.023110 restraints weight = 2936.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.023264 restraints weight = 1945.081| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4298 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20860 Z= 0.091 Angle : 0.573 12.994 28304 Z= 0.272 Chirality : 0.046 0.265 3096 Planarity : 0.002 0.029 3434 Dihedral : 10.905 136.752 3150 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.64 (0.18), residues: 2316 helix: 1.68 (0.17), residues: 1044 sheet: -1.12 (0.33), residues: 248 loop : -0.43 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 203 TYR 0.011 0.001 TYR G 209 PHE 0.014 0.001 PHE A 304 TRP 0.004 0.001 TRP A1218 HIS 0.002 0.000 HIS E 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (20860) covalent geometry : angle 0.57294 / 0.27 (28304) hydrogen bonds : bond 0.03345 / 2.40 ( 887) hydrogen bonds : angle 3.98382 / 2.82 ( 2547) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8315 (tp30) cc_final: 0.7794 (pm20) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0601 time to fit residues: 1.0757 Evaluate side-chains 13 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.037 Evaluate side-chains 37 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.9616 (tp) cc_final: 0.9296 (pp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0823 time to fit residues: 4.7944 Evaluate side-chains 25 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.369 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0098 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 231 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 10 optimal weight: 70.0000 chunk 129 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 142 GLN A 177 ASN A 759 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.042880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034196 restraints weight = 11320.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.034911 restraints weight = 9335.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035453 restraints weight = 8053.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.035760 restraints weight = 7172.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036121 restraints weight = 6585.249| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.034961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.024183 restraints weight = 149764.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.024586 restraints weight = 130644.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.024852 restraints weight = 117476.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.025120 restraints weight = 108396.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.025260 restraints weight = 101665.416| |-----------------------------------------------------------------------------| r_work (final): 0.3271 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.023844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.022169 restraints weight = 13674.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.022655 restraints weight = 7334.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.023040 restraints weight = 4557.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.023248 restraints weight = 2914.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.023375 restraints weight = 2079.666| |-----------------------------------------------------------------------------| r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4298 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20860 Z= 0.086 Angle : 0.565 13.481 28304 Z= 0.267 Chirality : 0.045 0.248 3096 Planarity : 0.003 0.029 3434 Dihedral : 10.885 136.731 3150 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.77 (0.18), residues: 2316 helix: 1.71 (0.17), residues: 1046 sheet: -0.96 (0.33), residues: 248 loop : -0.30 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 217 TYR 0.010 0.001 TYR A 840 PHE 0.011 0.001 PHE E 946 TRP 0.006 0.001 TRP A 890 HIS 0.002 0.000 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (20860) covalent geometry : angle 0.56477 / 0.27 (28304) hydrogen bonds : bond 0.03373 / 2.44 ( 887) hydrogen bonds : angle 3.90021 / 2.77 ( 2547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.60 seconds wall clock time: 43 minutes 6.73 seconds (2586.73 seconds total)