Starting phenix.real_space_refine on Fri Jul 3 14:27:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihn_35450/07_2026/8ihn_35450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihn_35450/07_2026/8ihn_35450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihn_35450/07_2026/8ihn_35450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihn_35450/07_2026/8ihn_35450.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihn_35450/07_2026/8ihn_35450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihn_35450/07_2026/8ihn_35450.cif" } resolution = 3.37 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= 0.003 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 1 6.06 5 S 66 5.16 5 C 9281 2.51 5 N 2503 2.21 5 O 2759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14611 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 169 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 22} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 4716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4716 Classifications: {'peptide': 598} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 77} Link IDs: {'PTRANS': 14, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 3, 'ASN:plan1': 8, 'PHE:plan': 5, 'HIS:plan': 2, 'ASP:plan': 6, 'ARG:plan': 3, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 189 Chain: "L" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3082 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "M" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2707 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "N" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1410 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "O" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1133 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 3, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1392 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.48, per 1000 atoms: 0.17 Number of scatterers: 14611 At special positions: 0 Unit cell: (129.47, 143.38, 133.75, 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) Zn 1 29.99 Ca 1 19.99 S 66 16.00 O 2759 8.00 N 2503 7.00 C 9281 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: 1.14 Conformation dependent library (CDL) restraints added in 636.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 55.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'K' and resid 661 through 666 removed outlier: 3.775A pdb=" N GLU K 665 " --> pdb=" O SER K 661 " (cutoff:3.500A) Processing helix chain 'K' and resid 667 through 677 Processing helix chain 'K' and resid 678 through 694 removed outlier: 3.773A pdb=" N GLU K 684 " --> pdb=" O HIS K 680 " (cutoff:3.500A) Processing helix chain 'K' and resid 698 through 711 removed outlier: 3.868A pdb=" N PHE K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR K 709 " --> pdb=" O LYS K 705 " (cutoff:3.500A) Processing helix chain 'K' and resid 713 through 725 removed outlier: 3.605A pdb=" N TRP K 719 " --> pdb=" O GLU K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 765 removed outlier: 3.852A pdb=" N MET K 765 " --> pdb=" O ASP K 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 771 through 778 removed outlier: 3.538A pdb=" N TRP K 775 " --> pdb=" O ASP K 771 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 776 " --> pdb=" O ASP K 772 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 790 Processing helix chain 'K' and resid 805 through 841 removed outlier: 3.507A pdb=" N TYR K 820 " --> pdb=" O GLU K 816 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR K 827 " --> pdb=" O SER K 823 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 834 " --> pdb=" O CYS K 830 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) Processing helix chain 'K' and resid 842 through 848 removed outlier: 3.896A pdb=" N ASN K 848 " --> pdb=" O ASN K 844 " (cutoff:3.500A) Processing helix chain 'K' and resid 852 through 857 removed outlier: 4.021A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) Processing helix chain 'K' and resid 861 through 871 removed outlier: 3.702A pdb=" N ILE K 867 " --> pdb=" O TYR K 863 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 869 " --> pdb=" O LYS K 865 " (cutoff:3.500A) Processing helix chain 'K' and resid 874 through 886 removed outlier: 4.282A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 879 " --> pdb=" O ARG K 875 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 880 " --> pdb=" O GLY K 876 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 929 Proline residue: K 892 - end of helix removed outlier: 3.529A pdb=" N GLU K 911 " --> pdb=" O ARG K 907 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 914 " --> pdb=" O ARG K 910 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K 927 " --> pdb=" O VAL K 923 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 928 " --> pdb=" O PHE K 924 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP K 929 " --> pdb=" O PHE K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 929 through 934 removed outlier: 3.796A pdb=" N LEU K 933 " --> pdb=" O ASP K 929 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR K 934 " --> pdb=" O HIS K 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 929 through 934' Processing helix chain 'K' and resid 934 through 943 removed outlier: 3.962A pdb=" N LYS K 940 " --> pdb=" O LYS K 936 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS K 941 " --> pdb=" O GLN K 937 " (cutoff:3.500A) Processing helix chain 'K' and resid 946 through 965 removed outlier: 3.727A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE K 955 " --> pdb=" O GLU K 951 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS K 963 " --> pdb=" O GLN K 959 " (cutoff:3.500A) Processing helix chain 'K' and resid 982 through 999 removed outlier: 4.153A pdb=" N TYR K 986 " --> pdb=" O LYS K 982 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1022 removed outlier: 3.780A pdb=" N GLU K1008 " --> pdb=" O ASN K1004 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG K1009 " --> pdb=" O PRO K1005 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K1014 " --> pdb=" O LEU K1010 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K1015 " --> pdb=" O LYS K1011 " (cutoff:3.500A) Processing helix chain 'K' and resid 1025 through 1040 Processing helix chain 'K' and resid 1064 through 1069 Processing helix chain 'K' and resid 1070 through 1080 removed outlier: 4.345A pdb=" N LYS K1076 " --> pdb=" O SER K1072 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K1077 " --> pdb=" O ARG K1073 " (cutoff:3.500A) Processing helix chain 'K' and resid 1141 through 1175 removed outlier: 3.669A pdb=" N PHE K1147 " --> pdb=" O ASN K1143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE K1154 " --> pdb=" O HIS K1150 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET K1164 " --> pdb=" O GLU K1160 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU K1166 " --> pdb=" O LYS K1162 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG K1167 " --> pdb=" O GLN K1163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K1170 " --> pdb=" O GLU K1166 " (cutoff:3.500A) Processing helix chain 'K' and resid 1178 through 1183 Processing helix chain 'K' and resid 1189 through 1195 Processing helix chain 'K' and resid 1202 through 1216 removed outlier: 3.801A pdb=" N ARG K1213 " --> pdb=" O ARG K1209 " (cutoff:3.500A) Processing helix chain 'K' and resid 1220 through 1233 removed outlier: 3.547A pdb=" N LEU K1228 " --> pdb=" O PHE K1224 " (cutoff:3.500A) Processing helix chain 'K' and resid 1241 through 1258 removed outlier: 3.593A pdb=" N LEU K1256 " --> pdb=" O HIS K1252 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET K1257 " --> pdb=" O ALA K1253 " (cutoff:3.500A) Processing helix chain 'K' and resid 1259 through 1275 removed outlier: 3.786A pdb=" N LYS K1271 " --> pdb=" O ALA K1267 " (cutoff:3.500A) Processing helix chain 'K' and resid 1279 through 1294 removed outlier: 3.559A pdb=" N ILE K1284 " --> pdb=" O ALA K1280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS K1293 " --> pdb=" O GLN K1289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET K1294 " --> pdb=" O VAL K1290 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 removed outlier: 3.939A pdb=" N GLY L 30 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 55 removed outlier: 4.223A pdb=" N ARG L 46 " --> pdb=" O PRO L 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 72 through 77 removed outlier: 3.932A pdb=" N PHE L 77 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 89 removed outlier: 3.682A pdb=" N ARG L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.652A pdb=" N LEU L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 115 through 136 removed outlier: 3.802A pdb=" N GLY L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY L 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 174 removed outlier: 3.605A pdb=" N LEU L 168 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 195 Processing helix chain 'L' and resid 226 through 230 removed outlier: 3.587A pdb=" N LYS L 230 " --> pdb=" O GLY L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 262 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 287 through 300 removed outlier: 4.330A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 330 removed outlier: 3.642A pdb=" N ARG L 320 " --> pdb=" O ARG L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 381 removed outlier: 3.585A pdb=" N LYS L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 414 Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 318 through 330 removed outlier: 3.524A pdb=" N ILE M 322 " --> pdb=" O THR M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 335 No H-bonds generated for 'chain 'M' and resid 333 through 335' Processing helix chain 'M' and resid 336 through 343 Processing helix chain 'M' and resid 354 through 359 Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.732A pdb=" N THR M 405 " --> pdb=" O ASN M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 434 removed outlier: 3.685A pdb=" N ASN M 433 " --> pdb=" O HIS M 430 " (cutoff:3.500A) Processing helix chain 'M' and resid 544 through 577 removed outlier: 3.702A pdb=" N ILE M 574 " --> pdb=" O GLN M 570 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 241 removed outlier: 3.724A pdb=" N VAL N 233 " --> pdb=" O LYS N 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR N 240 " --> pdb=" O TRP N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 269 removed outlier: 3.965A pdb=" N GLN N 267 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU N 268 " --> pdb=" O GLU N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 297 removed outlier: 3.527A pdb=" N GLN N 275 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN N 277 " --> pdb=" O GLY N 273 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY N 294 " --> pdb=" O ASP N 290 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN N 295 " --> pdb=" O LYS N 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 297 " --> pdb=" O LEU N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 301 No H-bonds generated for 'chain 'N' and resid 299 through 301' Processing helix chain 'N' and resid 302 through 317 removed outlier: 3.653A pdb=" N LYS N 315 " --> pdb=" O LYS N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 326 removed outlier: 3.546A pdb=" N ILE N 325 " --> pdb=" O VAL N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 337 removed outlier: 3.586A pdb=" N LEU N 331 " --> pdb=" O GLY N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 345 removed outlier: 3.628A pdb=" N THR N 345 " --> pdb=" O LEU N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 369 Processing helix chain 'N' and resid 369 through 374 removed outlier: 3.601A pdb=" N TYR N 373 " --> pdb=" O HIS N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 400 removed outlier: 3.534A pdb=" N GLY N 396 " --> pdb=" O SER N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 315 through 330 Processing helix chain 'O' and resid 337 through 344 removed outlier: 4.118A pdb=" N ASP O 344 " --> pdb=" O LEU O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 354 through 361 removed outlier: 4.070A pdb=" N PHE O 361 " --> pdb=" O ILE O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 544 through 577 removed outlier: 3.918A pdb=" N LYS O 554 " --> pdb=" O ASP O 550 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET O 560 " --> pdb=" O TYR O 556 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL O 561 " --> pdb=" O LYS O 557 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU O 577 " --> pdb=" O LEU O 573 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 242 Processing helix chain 'P' and resid 253 through 265 Processing helix chain 'P' and resid 266 through 268 No H-bonds generated for 'chain 'P' and resid 266 through 268' Processing helix chain 'P' and resid 271 through 296 removed outlier: 3.861A pdb=" N ASP P 290 " --> pdb=" O LYS P 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS P 291 " --> pdb=" O LEU P 287 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY P 294 " --> pdb=" O ASP P 290 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 317 removed outlier: 3.595A pdb=" N LEU P 304 " --> pdb=" O ARG P 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN P 305 " --> pdb=" O LEU P 301 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU P 308 " --> pdb=" O LEU P 304 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU P 309 " --> pdb=" O GLN P 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P 310 " --> pdb=" O TYR P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 321 through 326 removed outlier: 3.730A pdb=" N ILE P 325 " --> pdb=" O VAL P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 345 removed outlier: 3.805A pdb=" N LEU P 331 " --> pdb=" O GLY P 327 " (cutoff:3.500A) Proline residue: P 339 - end of helix removed outlier: 3.639A pdb=" N SER P 343 " --> pdb=" O PRO P 339 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER P 344 " --> pdb=" O GLU P 340 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR P 345 " --> pdb=" O LEU P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 370 removed outlier: 3.509A pdb=" N THR P 359 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET P 368 " --> pdb=" O VAL P 364 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS P 369 " --> pdb=" O TRP P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 391 through 400 Processing sheet with id=AA1, first strand: chain 'K' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'K' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'L' and resid 63 through 64 removed outlier: 7.942A pdb=" N TYR L 64 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR L 23 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA L 142 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL L 267 " --> pdb=" O MET L 306 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL L 308 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU L 269 " --> pdb=" O VAL L 308 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU L 181 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN L 270 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE L 183 " --> pdb=" O GLN L 270 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL L 234 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR L 205 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL L 236 " --> pdb=" O THR L 205 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER L 207 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU L 238 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS L 209 " --> pdb=" O LEU L 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 272 through 274 Processing sheet with id=AA5, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'M' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'M' and resid 473 through 477 Processing sheet with id=AA8, first strand: chain 'M' and resid 504 through 506 removed outlier: 6.870A pdb=" N LEU M 504 " --> pdb=" O ILE M 539 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN M 541 " --> pdb=" O LEU M 504 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR M 506 " --> pdb=" O GLN M 541 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASP M 543 " --> pdb=" O TYR M 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'O' and resid 262 through 263 Processing sheet with id=AB2, first strand: chain 'O' and resid 272 through 274 Processing sheet with id=AB3, first strand: chain 'P' and resid 245 through 246 673 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2489 1.31 - 1.44: 3892 1.44 - 1.56: 8427 1.56 - 1.69: 2 1.69 - 1.81: 99 Bond restraints: 14909 Sorted by residual: bond pdb=" CA VAL M 452 " pdb=" C VAL M 452 " ideal model delta sigma weight residual 1.525 1.455 0.070 8.10e-03 1.52e+04 7.49e+01 bond pdb=" CA ASP L 403 " pdb=" C ASP L 403 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.32e-02 5.74e+03 2.39e+01 bond pdb=" CA CYS M 466 " pdb=" C CYS M 466 " ideal model delta sigma weight residual 1.528 1.471 0.057 1.18e-02 7.18e+03 2.33e+01 bond pdb=" CA LEU L 401 " pdb=" C LEU L 401 " ideal model delta sigma weight residual 1.522 1.476 0.047 1.20e-02 6.94e+03 1.52e+01 bond pdb=" CA ARG M 454 " pdb=" C ARG M 454 " ideal model delta sigma weight residual 1.520 1.477 0.044 1.20e-02 6.94e+03 1.32e+01 ... (remaining 14904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 20002 3.52 - 7.03: 146 7.03 - 10.55: 27 10.55 - 14.07: 8 14.07 - 17.59: 1 Bond angle restraints: 20184 Sorted by residual: angle pdb=" N VAL M 452 " pdb=" CA VAL M 452 " pdb=" C VAL M 452 " ideal model delta sigma weight residual 107.77 90.18 17.59 1.12e+00 7.97e-01 2.47e+02 angle pdb=" N PRO O 289 " pdb=" CA PRO O 289 " pdb=" C PRO O 289 " ideal model delta sigma weight residual 110.70 98.40 12.30 1.22e+00 6.72e-01 1.02e+02 angle pdb=" N ALA A 21 " pdb=" CA ALA A 21 " pdb=" C ALA A 21 " ideal model delta sigma weight residual 112.45 99.54 12.91 1.39e+00 5.18e-01 8.63e+01 angle pdb=" C VAL M 452 " pdb=" N PRO M 453 " pdb=" CA PRO M 453 " ideal model delta sigma weight residual 119.76 110.38 9.38 1.03e+00 9.43e-01 8.30e+01 angle pdb=" N LYS M 107 " pdb=" CA LYS M 107 " pdb=" C LYS M 107 " ideal model delta sigma weight residual 110.53 98.69 11.84 1.32e+00 5.74e-01 8.04e+01 ... (remaining 20179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 8176 18.15 - 36.29: 665 36.29 - 54.44: 128 54.44 - 72.58: 27 72.58 - 90.73: 12 Dihedral angle restraints: 9008 sinusoidal: 3396 harmonic: 5612 Sorted by residual: dihedral pdb=" C VAL M 452 " pdb=" N VAL M 452 " pdb=" CA VAL M 452 " pdb=" CB VAL M 452 " ideal model delta harmonic sigma weight residual -122.00 -104.42 -17.58 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" C ASN K1081 " pdb=" N ASN K1081 " pdb=" CA ASN K1081 " pdb=" CB ASN K1081 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.03e+01 dihedral pdb=" CA MET K 765 " pdb=" C MET K 765 " pdb=" N PRO K 766 " pdb=" CA PRO K 766 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2101 0.089 - 0.178: 124 0.178 - 0.267: 8 0.267 - 0.357: 1 0.357 - 0.446: 2 Chirality restraints: 2236 Sorted by residual: chirality pdb=" CA ASN K1081 " pdb=" N ASN K1081 " pdb=" C ASN K1081 " pdb=" CB ASN K1081 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA VAL M 452 " pdb=" N VAL M 452 " pdb=" C VAL M 452 " pdb=" CB VAL M 452 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASP L 407 " pdb=" N ASP L 407 " pdb=" C ASP L 407 " pdb=" CB ASP L 407 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2233 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS M 107 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C LYS M 107 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS M 107 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL M 108 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP O 288 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO O 289 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO O 289 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO O 289 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 105 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ASP M 105 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP M 105 " 0.017 2.00e-02 2.50e+03 pdb=" N SER M 106 " 0.016 2.00e-02 2.50e+03 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 110 2.54 - 3.13: 12170 3.13 - 3.72: 22120 3.72 - 4.31: 30594 4.31 - 4.90: 49649 Nonbonded interactions: 114643 Sorted by model distance: nonbonded pdb=" OD2 ASP L 186 " pdb="ZN ZN L 501 " model vdw 1.954 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 1.981 2.230 nonbonded pdb=" O PRO L 111 " pdb=" OH TYR L 162 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.232 2.230 nonbonded pdb=" O ASP K 981 " pdb=" OH TYR K1155 " model vdw 2.246 3.040 ... (remaining 114638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'N' and (resid 218 through 239 or (resid 240 and (name N or name CA or na \ me C or name O or name CB )) or resid 241 through 242 or (resid 243 and (name N \ or name CA or name C or name O or name CB )) or resid 244 or (resid 245 and (nam \ e N or name CA or name C or name O or name CB )) or resid 246 through 251 or (re \ sid 252 through 256 and (name N or name CA or name C or name O or name CB )) or \ resid 257 or (resid 258 and (name N or name CA or name C or name O or name CB )) \ or resid 259 through 279 or (resid 280 through 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 291 or (resid 292 through 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 29 \ 9 or (resid 300 and (name N or name CA or name C or name O or name CB )) or resi \ d 301 through 307 or (resid 308 through 309 and (name N or name CA or name C or \ name O or name CB )) or resid 310 through 312 or (resid 313 and (name N or name \ CA or name C or name O or name CB )) or resid 314 or (resid 315 and (name N or n \ ame CA or name C or name O or name CB )) or resid 316 through 334 or (resid 335 \ and (name N or name CA or name C or name O or name CB )) or resid 336 through 33 \ 9 or (resid 340 and (name N or name CA or name C or name O or name CB )) or resi \ d 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 through 348 or (resid 349 and (name N or name CA or name C or name O o \ r name CB )) or resid 350 through 352 or (resid 353 through 354 and (name N or n \ ame CA or name C or name O or name CB )) or resid 355 through 357 or (resid 358 \ and (name N or name CA or name C or name O or name CB )) or resid 359 through 36 \ 4 or (resid 365 through 367 and (name N or name CA or name C or name O or name C \ B )) or resid 368 through 370 or (resid 371 through 372 and (name N or name CA o \ r name C or name O or name CB )) or resid 373 through 374 or (resid 375 and (nam \ e N or name CA or name C or name O or name CB )) or resid 376 through 391 or (re \ sid 392 and (name N or name CA or name C or name O or name CB )) or resid 393 th \ rough 400)) selection = (chain 'P' and (resid 218 through 229 or (resid 230 and (name N or name CA or na \ me C or name O or name CB )) or resid 231 through 246 or (resid 247 through 248 \ and (name N or name CA or name C or name O or name CB )) or resid 249 through 25 \ 0 or (resid 251 through 256 and (name N or name CA or name C or name O or name C \ B )) or resid 257 through 280 or (resid 281 and (name N or name CA or name C or \ name O or name CB )) or resid 282 through 310 or (resid 311 and (name N or name \ CA or name C or name O or name CB )) or resid 312 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 323 or \ (resid 324 through 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 337 or (resid 338 and (name N or name CA or name C or name \ O or name CB )) or resid 339 through 355 or (resid 356 and (name N or name CA o \ r name C or name O or name CB )) or resid 357 through 362 or (resid 363 and (nam \ e N or name CA or name C or name O or name CB )) or resid 364 through 365 or (re \ sid 366 through 367 and (name N or name CA or name C or name O or name CB )) or \ resid 368 through 377 or (resid 378 and (name N or name CA or name C or name O o \ r name CB )) or resid 379 through 380 or (resid 381 and (name N or name CA or na \ me C or name O or name CB )) or resid 382 or (resid 383 through 385 and (name N \ or name CA or name C or name O or name CB )) or resid 386 through 400)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 14910 Z= 0.328 Angle : 0.890 17.587 20184 Z= 0.588 Chirality : 0.046 0.446 2236 Planarity : 0.005 0.080 2620 Dihedral : 14.377 90.730 5370 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 0.34 % Allowed : 1.02 % Favored : 98.64 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.41 % 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: -1.33 (0.18), residues: 1877 helix: -0.60 (0.17), residues: 901 sheet: -0.17 (0.56), residues: 98 loop : -1.18 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 247 TYR 0.030 0.002 TYR N 373 PHE 0.038 0.001 PHE P 374 TRP 0.012 0.001 TRP K 719 HIS 0.006 0.001 HIS P 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.33 (14909) covalent geometry : angle 0.88952 / 0.59 (20184) hydrogen bonds : bond 0.27729 / 18.04 ( 673) hydrogen bonds : angle 8.63384 / 6.12 ( 1953) metal coordination : bond 0.00389 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 306 MET cc_start: 0.9087 (ttp) cc_final: 0.8851 (ttm) REVERT: N 307 ASP cc_start: 0.8657 (t70) cc_final: 0.8448 (t0) REVERT: N 326 TYR cc_start: 0.8745 (m-80) cc_final: 0.8297 (m-80) REVERT: N 358 GLN cc_start: 0.7517 (tp-100) cc_final: 0.7037 (tm-30) REVERT: N 373 TYR cc_start: 0.8790 (m-10) cc_final: 0.8438 (m-10) REVERT: N 376 ASP cc_start: 0.8313 (p0) cc_final: 0.8091 (p0) REVERT: O 316 MET cc_start: 0.7776 (mmt) cc_final: 0.7414 (tpt) REVERT: P 220 ILE cc_start: 0.8231 (mm) cc_final: 0.8003 (mp) REVERT: P 270 GLU cc_start: 0.8945 (pm20) cc_final: 0.8349 (pm20) REVERT: P 401 MET cc_start: 0.4647 (mmm) cc_final: 0.4022 (mmm) outliers start: 5 outliers final: 1 residues processed: 224 average time/residue: 0.0962 time to fit residues: 32.7980 Evaluate side-chains 188 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 252 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 479 HIS N 223 GLN N 317 GLN P 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105286 restraints weight = 27661.529| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.33 r_work: 0.3370 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14910 Z= 0.148 Angle : 0.569 7.132 20184 Z= 0.312 Chirality : 0.040 0.157 2236 Planarity : 0.004 0.042 2620 Dihedral : 5.202 52.829 2039 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 0.95 % Allowed : 6.98 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 1877 helix: 0.70 (0.17), residues: 937 sheet: -0.32 (0.56), residues: 92 loop : -1.08 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 564 TYR 0.024 0.001 TYR O 556 PHE 0.013 0.001 PHE K1269 TRP 0.022 0.001 TRP K 966 HIS 0.014 0.001 HIS M 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (14909) covalent geometry : angle 0.56881 / 0.31 (20184) hydrogen bonds : bond 0.05594 / 3.64 ( 673) hydrogen bonds : angle 4.94708 / 3.55 ( 1953) metal coordination : bond 0.00176 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: K 961 ASN cc_start: 0.8054 (t0) cc_final: 0.7742 (t0) REVERT: M 343 ILE cc_start: 0.9065 (tp) cc_final: 0.8768 (tp) REVERT: M 373 SER cc_start: 0.9314 (p) cc_final: 0.8941 (t) REVERT: M 374 ASP cc_start: 0.8563 (t0) cc_final: 0.8216 (m-30) REVERT: M 549 TYR cc_start: 0.8739 (m-80) cc_final: 0.8487 (m-80) REVERT: M 560 MET cc_start: 0.8687 (tpt) cc_final: 0.8270 (tpt) REVERT: N 267 GLN cc_start: 0.8528 (pt0) cc_final: 0.8290 (pp30) REVERT: N 307 ASP cc_start: 0.8856 (t70) cc_final: 0.8642 (t0) REVERT: N 326 TYR cc_start: 0.8803 (m-80) cc_final: 0.8428 (m-80) REVERT: N 358 GLN cc_start: 0.7451 (tp-100) cc_final: 0.6946 (tm-30) REVERT: N 373 TYR cc_start: 0.8760 (m-10) cc_final: 0.8255 (m-10) REVERT: P 394 TYR cc_start: 0.7539 (t80) cc_final: 0.7291 (t80) outliers start: 14 outliers final: 8 residues processed: 207 average time/residue: 0.0829 time to fit residues: 26.8732 Evaluate side-chains 194 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 242 ASP Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 38 optimal weight: 0.0010 chunk 153 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1070 HIS M 479 HIS N 223 GLN ** O 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.110444 restraints weight = 29226.442| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.77 r_work: 0.3503 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14910 Z= 0.108 Angle : 0.489 7.883 20184 Z= 0.265 Chirality : 0.038 0.145 2236 Planarity : 0.004 0.072 2620 Dihedral : 4.670 46.326 2039 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.22 % Allowed : 9.02 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.37 (0.19), residues: 1877 helix: 1.24 (0.17), residues: 944 sheet: -0.17 (0.58), residues: 92 loop : -0.84 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 564 TYR 0.014 0.001 TYR P 238 PHE 0.020 0.001 PHE M 262 TRP 0.030 0.001 TRP K 966 HIS 0.012 0.001 HIS M 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14909) covalent geometry : angle 0.48901 / 0.27 (20184) hydrogen bonds : bond 0.04011 / 2.62 ( 673) hydrogen bonds : angle 4.20493 / 3.00 ( 1953) metal coordination : bond 0.00167 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.430 Fit side-chains REVERT: K 1257 MET cc_start: 0.8474 (mpp) cc_final: 0.8254 (mpp) REVERT: M 343 ILE cc_start: 0.9074 (tp) cc_final: 0.8868 (tp) REVERT: M 373 SER cc_start: 0.9188 (p) cc_final: 0.8840 (t) REVERT: M 560 MET cc_start: 0.8661 (tpt) cc_final: 0.8437 (tpt) REVERT: N 252 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8671 (p) REVERT: N 267 GLN cc_start: 0.8569 (pt0) cc_final: 0.8207 (pp30) REVERT: N 326 TYR cc_start: 0.8784 (m-80) cc_final: 0.8353 (m-80) REVERT: N 358 GLN cc_start: 0.7323 (tp-100) cc_final: 0.6752 (tm-30) REVERT: N 373 TYR cc_start: 0.8733 (m-10) cc_final: 0.8191 (m-10) REVERT: O 305 GLU cc_start: 0.8788 (tt0) cc_final: 0.8547 (tm-30) REVERT: O 556 TYR cc_start: 0.9124 (t80) cc_final: 0.8721 (t80) REVERT: O 560 MET cc_start: 0.8569 (mpp) cc_final: 0.8165 (mpp) REVERT: P 223 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7633 (tm-30) REVERT: P 288 TYR cc_start: 0.9255 (t80) cc_final: 0.8908 (t80) REVERT: P 401 MET cc_start: 0.4328 (mmm) cc_final: 0.4094 (mmm) outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 0.0877 time to fit residues: 28.9536 Evaluate side-chains 197 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 359 THR Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1221 HIS N 223 GLN O 583 GLN P 259 ASN P 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100981 restraints weight = 28177.904| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.31 r_work: 0.3265 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14910 Z= 0.251 Angle : 0.590 7.531 20184 Z= 0.316 Chirality : 0.043 0.165 2236 Planarity : 0.004 0.073 2620 Dihedral : 4.925 36.040 2039 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 1.22 % Allowed : 13.02 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1877 helix: 1.13 (0.17), residues: 944 sheet: -0.41 (0.57), residues: 92 loop : -0.92 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 564 TYR 0.019 0.002 TYR K 675 PHE 0.023 0.002 PHE M 262 TRP 0.016 0.002 TRP K 966 HIS 0.005 0.001 HIS L 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (14909) covalent geometry : angle 0.58994 / 0.32 (20184) hydrogen bonds : bond 0.04650 / 3.06 ( 673) hydrogen bonds : angle 4.33655 / 3.10 ( 1953) metal coordination : bond 0.00895 / 0.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.416 Fit side-chains REVERT: M 343 ILE cc_start: 0.9165 (tp) cc_final: 0.8905 (tp) REVERT: M 560 MET cc_start: 0.8710 (tpt) cc_final: 0.8465 (tpt) REVERT: N 242 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8864 (t0) REVERT: N 267 GLN cc_start: 0.8659 (pt0) cc_final: 0.8376 (pp30) REVERT: N 358 GLN cc_start: 0.7958 (tp-100) cc_final: 0.6982 (tm-30) REVERT: O 556 TYR cc_start: 0.9166 (t80) cc_final: 0.8680 (t80) REVERT: O 560 MET cc_start: 0.8511 (mpp) cc_final: 0.7987 (mpp) REVERT: P 223 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7652 (tm-30) outliers start: 18 outliers final: 13 residues processed: 196 average time/residue: 0.0937 time to fit residues: 28.1815 Evaluate side-chains 194 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 242 ASP Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 961 ASN N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105166 restraints weight = 27799.473| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.25 r_work: 0.3335 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14910 Z= 0.113 Angle : 0.484 7.566 20184 Z= 0.258 Chirality : 0.038 0.148 2236 Planarity : 0.004 0.073 2620 Dihedral : 4.462 25.218 2038 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 13.08 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.58 (0.19), residues: 1877 helix: 1.46 (0.17), residues: 946 sheet: -0.24 (0.58), residues: 91 loop : -0.78 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 247 TYR 0.016 0.001 TYR M 356 PHE 0.019 0.001 PHE M 262 TRP 0.013 0.001 TRP K 966 HIS 0.003 0.001 HIS L 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14909) covalent geometry : angle 0.48374 / 0.26 (20184) hydrogen bonds : bond 0.03601 / 2.38 ( 673) hydrogen bonds : angle 3.98209 / 2.83 ( 1953) metal coordination : bond 0.00269 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.522 Fit side-chains REVERT: M 343 ILE cc_start: 0.9040 (tp) cc_final: 0.8830 (tp) REVERT: M 560 MET cc_start: 0.8778 (tpt) cc_final: 0.8560 (tpt) REVERT: N 267 GLN cc_start: 0.8579 (pt0) cc_final: 0.8315 (pp30) REVERT: N 354 LEU cc_start: 0.9047 (tp) cc_final: 0.8784 (tt) REVERT: N 358 GLN cc_start: 0.7839 (tp-100) cc_final: 0.6913 (tm-30) REVERT: N 373 TYR cc_start: 0.8661 (m-10) cc_final: 0.7927 (m-10) REVERT: O 556 TYR cc_start: 0.9157 (t80) cc_final: 0.8670 (t80) REVERT: O 560 MET cc_start: 0.8316 (mpp) cc_final: 0.8055 (mpp) REVERT: P 223 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7496 (tm-30) REVERT: P 401 MET cc_start: 0.3889 (mmm) cc_final: 0.3638 (mmm) outliers start: 28 outliers final: 19 residues processed: 210 average time/residue: 0.0924 time to fit residues: 30.0903 Evaluate side-chains 200 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 334 LYS Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 373 TYR Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 ASN N 223 GLN O 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105899 restraints weight = 27938.465| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.35 r_work: 0.3318 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14910 Z= 0.135 Angle : 0.497 6.855 20184 Z= 0.264 Chirality : 0.039 0.150 2236 Planarity : 0.004 0.073 2620 Dihedral : 4.375 24.687 2038 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.03 % Allowed : 14.03 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.65 (0.19), residues: 1877 helix: 1.53 (0.17), residues: 948 sheet: -0.19 (0.58), residues: 91 loop : -0.77 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 564 TYR 0.016 0.001 TYR M 356 PHE 0.016 0.001 PHE M 262 TRP 0.011 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (14909) covalent geometry : angle 0.49679 / 0.26 (20184) hydrogen bonds : bond 0.03618 / 2.40 ( 673) hydrogen bonds : angle 3.94667 / 2.80 ( 1953) metal coordination : bond 0.00458 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.504 Fit side-chains REVERT: K 792 ASP cc_start: 0.8421 (t70) cc_final: 0.8168 (t70) REVERT: M 343 ILE cc_start: 0.9040 (tp) cc_final: 0.8826 (tp) REVERT: N 267 GLN cc_start: 0.8436 (pt0) cc_final: 0.8184 (pp30) REVERT: N 354 LEU cc_start: 0.9046 (tp) cc_final: 0.8808 (tt) REVERT: N 358 GLN cc_start: 0.7855 (tp-100) cc_final: 0.6859 (tm-30) REVERT: N 373 TYR cc_start: 0.8544 (m-10) cc_final: 0.7912 (m-10) REVERT: O 556 TYR cc_start: 0.9117 (t80) cc_final: 0.8570 (t80) REVERT: O 560 MET cc_start: 0.8133 (mpp) cc_final: 0.7823 (mpp) outliers start: 30 outliers final: 21 residues processed: 209 average time/residue: 0.0888 time to fit residues: 29.2440 Evaluate side-chains 206 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 334 LYS Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 373 TYR Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.0570 chunk 165 optimal weight: 20.0000 chunk 105 optimal weight: 0.4980 chunk 186 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 172 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 884 HIS N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107300 restraints weight = 27943.326| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.44 r_work: 0.3346 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14910 Z= 0.107 Angle : 0.474 7.242 20184 Z= 0.252 Chirality : 0.038 0.143 2236 Planarity : 0.003 0.072 2620 Dihedral : 4.191 24.412 2038 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.83 % Allowed : 14.92 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.83 (0.20), residues: 1877 helix: 1.72 (0.17), residues: 942 sheet: -0.10 (0.59), residues: 91 loop : -0.72 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 564 TYR 0.016 0.001 TYR M 356 PHE 0.014 0.001 PHE M 262 TRP 0.011 0.001 TRP K 966 HIS 0.003 0.001 HIS K 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14909) covalent geometry : angle 0.47417 / 0.25 (20184) hydrogen bonds : bond 0.03281 / 2.17 ( 673) hydrogen bonds : angle 3.83040 / 2.71 ( 1953) metal coordination : bond 0.00239 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.549 Fit side-chains REVERT: K 792 ASP cc_start: 0.8439 (t70) cc_final: 0.8068 (t0) REVERT: N 267 GLN cc_start: 0.8405 (pt0) cc_final: 0.8119 (pp30) REVERT: N 358 GLN cc_start: 0.7882 (tp-100) cc_final: 0.6823 (tm-30) REVERT: N 373 TYR cc_start: 0.8567 (m-10) cc_final: 0.7923 (m-10) REVERT: P 264 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7879 (mm-30) REVERT: P 288 TYR cc_start: 0.9227 (t80) cc_final: 0.8856 (t80) outliers start: 27 outliers final: 18 residues processed: 203 average time/residue: 0.0939 time to fit residues: 30.3373 Evaluate side-chains 196 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 373 TYR Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 76 optimal weight: 0.3980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN N 223 GLN O 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107305 restraints weight = 27789.518| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.44 r_work: 0.3329 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14910 Z= 0.110 Angle : 0.499 10.328 20184 Z= 0.260 Chirality : 0.038 0.167 2236 Planarity : 0.003 0.063 2620 Dihedral : 4.124 24.307 2038 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.63 % Allowed : 15.73 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.82 (0.20), residues: 1877 helix: 1.73 (0.17), residues: 942 sheet: -0.08 (0.58), residues: 91 loop : -0.75 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 564 TYR 0.037 0.001 TYR O 556 PHE 0.013 0.001 PHE M 262 TRP 0.011 0.001 TRP K 966 HIS 0.004 0.001 HIS M 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14909) covalent geometry : angle 0.49880 / 0.26 (20184) hydrogen bonds : bond 0.03278 / 2.17 ( 673) hydrogen bonds : angle 3.81399 / 2.70 ( 1953) metal coordination : bond 0.00318 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.495 Fit side-chains REVERT: K 792 ASP cc_start: 0.8399 (t70) cc_final: 0.8007 (t0) REVERT: N 353 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6796 (mp10) REVERT: N 358 GLN cc_start: 0.7981 (tp-100) cc_final: 0.6728 (tm-30) REVERT: N 373 TYR cc_start: 0.8590 (m-10) cc_final: 0.7873 (m-10) REVERT: P 264 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7952 (mm-30) REVERT: P 288 TYR cc_start: 0.9271 (t80) cc_final: 0.8865 (t80) REVERT: P 373 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7215 (p90) outliers start: 24 outliers final: 20 residues processed: 198 average time/residue: 0.0934 time to fit residues: 29.0281 Evaluate side-chains 200 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 334 LYS Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 373 TYR Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 479 HIS N 223 GLN O 329 GLN O 583 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.131660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105067 restraints weight = 27908.845| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.38 r_work: 0.3332 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14910 Z= 0.129 Angle : 0.509 9.253 20184 Z= 0.266 Chirality : 0.039 0.166 2236 Planarity : 0.004 0.060 2620 Dihedral : 4.153 23.874 2038 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.90 % Allowed : 15.66 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.79 (0.20), residues: 1877 helix: 1.69 (0.17), residues: 949 sheet: -0.19 (0.57), residues: 91 loop : -0.76 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 564 TYR 0.018 0.001 TYR L 176 PHE 0.012 0.001 PHE M 262 TRP 0.012 0.001 TRP K 966 HIS 0.010 0.001 HIS M 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14909) covalent geometry : angle 0.50860 / 0.27 (20184) hydrogen bonds : bond 0.03361 / 2.23 ( 673) hydrogen bonds : angle 3.86078 / 2.73 ( 1953) metal coordination : bond 0.00405 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.571 Fit side-chains REVERT: K 792 ASP cc_start: 0.8402 (t70) cc_final: 0.7998 (t0) REVERT: N 335 ILE cc_start: 0.9157 (mm) cc_final: 0.8884 (mt) REVERT: N 353 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: N 358 GLN cc_start: 0.8015 (tp-100) cc_final: 0.6724 (tm-30) REVERT: N 373 TYR cc_start: 0.8608 (m-10) cc_final: 0.7896 (m-10) REVERT: P 236 TRP cc_start: 0.8820 (t60) cc_final: 0.8375 (t60) REVERT: P 288 TYR cc_start: 0.9325 (t80) cc_final: 0.8946 (t80) outliers start: 28 outliers final: 24 residues processed: 201 average time/residue: 0.0992 time to fit residues: 30.7684 Evaluate side-chains 208 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 334 LYS Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 364 VAL Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 0.0270 chunk 149 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 GLN O 329 GLN O 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.129690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102711 restraints weight = 27864.182| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.36 r_work: 0.3282 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14910 Z= 0.156 Angle : 0.536 9.344 20184 Z= 0.281 Chirality : 0.040 0.162 2236 Planarity : 0.004 0.054 2620 Dihedral : 4.244 24.083 2038 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.83 % Allowed : 16.00 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.75 (0.19), residues: 1877 helix: 1.67 (0.17), residues: 938 sheet: -0.37 (0.57), residues: 92 loop : -0.74 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 564 TYR 0.029 0.001 TYR O 556 PHE 0.014 0.001 PHE K 819 TRP 0.011 0.001 TRP K 966 HIS 0.004 0.001 HIS M 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14909) covalent geometry : angle 0.53567 / 0.28 (20184) hydrogen bonds : bond 0.03555 / 2.36 ( 673) hydrogen bonds : angle 3.94699 / 2.79 ( 1953) metal coordination : bond 0.00544 / 0.29 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: K 792 ASP cc_start: 0.8665 (t70) cc_final: 0.8114 (t0) REVERT: M 564 ARG cc_start: 0.8664 (mmt180) cc_final: 0.8387 (mmp-170) REVERT: N 335 ILE cc_start: 0.9194 (mm) cc_final: 0.8912 (mt) REVERT: N 353 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: N 373 TYR cc_start: 0.8725 (m-10) cc_final: 0.8050 (m-10) REVERT: P 236 TRP cc_start: 0.8860 (t60) cc_final: 0.8410 (t60) REVERT: P 288 TYR cc_start: 0.9335 (t80) cc_final: 0.9009 (t80) outliers start: 27 outliers final: 24 residues processed: 194 average time/residue: 0.0931 time to fit residues: 28.1032 Evaluate side-chains 200 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 861 THR Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 334 LYS Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 235 ASP Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 91 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 480 HIS N 223 GLN O 329 GLN O 583 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.130848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104120 restraints weight = 27816.242| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.32 r_work: 0.3305 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14910 Z= 0.124 Angle : 0.515 9.215 20184 Z= 0.270 Chirality : 0.039 0.159 2236 Planarity : 0.004 0.052 2620 Dihedral : 4.145 23.646 2038 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.63 % Allowed : 16.27 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.79 (0.20), residues: 1877 helix: 1.72 (0.17), residues: 941 sheet: -0.36 (0.58), residues: 90 loop : -0.74 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 564 TYR 0.017 0.001 TYR L 176 PHE 0.011 0.001 PHE M 262 TRP 0.012 0.001 TRP K 966 HIS 0.003 0.001 HIS M 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14909) covalent geometry : angle 0.51504 / 0.27 (20184) hydrogen bonds : bond 0.03313 / 2.20 ( 673) hydrogen bonds : angle 3.87111 / 2.73 ( 1953) metal coordination : bond 0.00327 / 0.17 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.89 seconds wall clock time: 50 minutes 4.36 seconds (3004.36 seconds total)