Starting phenix.real_space_refine on Wed Mar 4 15:32:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihn_35450/03_2026/8ihn_35450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihn_35450/03_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_35450/03_2026/8ihn_35450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihn_35450/03_2026/8ihn_35450.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihn_35450/03_2026/8ihn_35450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihn_35450/03_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-5986/lib/python3.9/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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.43, per 1000 atoms: 0.23 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: 1.29 Conformation dependent library (CDL) restraints added in 554.8 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: 0.43 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: 2.26 Time building geometry restraints manager: 1.71 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 covalent geometry : bond 0.00527 (14909) covalent geometry : angle 0.88952 (20184) hydrogen bonds : bond 0.27729 ( 673) hydrogen bonds : angle 8.63384 ( 1953) metal coordination : bond 0.00389 ( 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 : 0.575 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: 0.1163 time to fit residues: 39.2940 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 : 0.563 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3863 r_free = 0.3863 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105818 restraints weight = 27631.501| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.34 r_work: 0.3359 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14910 Z= 0.146 Angle : 0.561 7.197 20184 Z= 0.306 Chirality : 0.040 0.160 2236 Planarity : 0.004 0.042 2620 Dihedral : 5.177 52.304 2039 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 0.95 % Allowed : 7.05 % Favored : 92.00 % 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: 0.68 (0.17), residues: 943 sheet: -0.21 (0.56), residues: 91 loop : -1.09 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 564 TYR 0.028 0.001 TYR O 556 PHE 0.013 0.001 PHE K1269 TRP 0.025 0.001 TRP K 966 HIS 0.015 0.001 HIS M 479 Details of bonding type rmsd covalent geometry : bond 0.00309 (14909) covalent geometry : angle 0.56082 (20184) hydrogen bonds : bond 0.05186 ( 673) hydrogen bonds : angle 4.82047 ( 1953) metal coordination : bond 0.00127 ( 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 221 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 961 ASN cc_start: 0.7797 (t0) cc_final: 0.7538 (t0) REVERT: M 323 GLU cc_start: 0.8340 (tt0) cc_final: 0.8043 (tt0) REVERT: M 343 ILE cc_start: 0.9032 (tp) cc_final: 0.8750 (tp) REVERT: M 373 SER cc_start: 0.9309 (p) cc_final: 0.8951 (t) REVERT: M 374 ASP cc_start: 0.8403 (t0) cc_final: 0.8104 (m-30) REVERT: M 560 MET cc_start: 0.8605 (tpt) cc_final: 0.8232 (tpt) REVERT: N 267 GLN cc_start: 0.8482 (pt0) cc_final: 0.8267 (pp30) REVERT: N 307 ASP cc_start: 0.8612 (t70) cc_final: 0.8389 (t0) REVERT: N 326 TYR cc_start: 0.8762 (m-80) cc_final: 0.8377 (m-80) REVERT: N 358 GLN cc_start: 0.7166 (tp-100) cc_final: 0.6867 (tm-30) REVERT: N 373 TYR cc_start: 0.8667 (m-10) cc_final: 0.8239 (m-10) REVERT: O 560 MET cc_start: 0.8418 (mpp) cc_final: 0.7976 (mpp) REVERT: P 270 GLU cc_start: 0.8960 (pm20) cc_final: 0.8456 (pm20) REVERT: P 394 TYR cc_start: 0.7449 (t80) cc_final: 0.7238 (t80) outliers start: 14 outliers final: 8 residues processed: 213 average time/residue: 0.1069 time to fit residues: 35.7124 Evaluate side-chains 196 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 186 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1221 HIS M 479 HIS N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.141574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110557 restraints weight = 30616.510| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.82 r_work: 0.3352 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14910 Z= 0.233 Angle : 0.582 6.434 20184 Z= 0.316 Chirality : 0.042 0.171 2236 Planarity : 0.004 0.072 2620 Dihedral : 5.104 45.423 2039 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 1.42 % Allowed : 10.31 % Favored : 88.27 % 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: -0.00 (0.19), residues: 1877 helix: 0.91 (0.17), residues: 945 sheet: -0.46 (0.57), residues: 92 loop : -0.97 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 303 TYR 0.019 0.002 TYR K 675 PHE 0.023 0.002 PHE M 262 TRP 0.030 0.002 TRP K 966 HIS 0.012 0.001 HIS M 479 Details of bonding type rmsd covalent geometry : bond 0.00541 (14909) covalent geometry : angle 0.58197 (20184) hydrogen bonds : bond 0.04944 ( 673) hydrogen bonds : angle 4.49225 ( 1953) metal coordination : bond 0.00810 ( 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 212 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: K 961 ASN cc_start: 0.8122 (t0) cc_final: 0.7795 (t0) REVERT: M 373 SER cc_start: 0.9238 (p) cc_final: 0.8871 (t) REVERT: M 374 ASP cc_start: 0.8502 (t0) cc_final: 0.8247 (m-30) REVERT: M 560 MET cc_start: 0.8597 (tpt) cc_final: 0.8176 (tpt) REVERT: N 267 GLN cc_start: 0.8711 (pt0) cc_final: 0.8301 (pp30) REVERT: N 307 ASP cc_start: 0.9022 (t70) cc_final: 0.8789 (t0) REVERT: N 358 GLN cc_start: 0.7949 (tp-100) cc_final: 0.6885 (tm-30) REVERT: O 305 GLU cc_start: 0.9004 (tt0) cc_final: 0.8717 (tm-30) REVERT: O 556 TYR cc_start: 0.9186 (t80) cc_final: 0.8790 (t80) REVERT: O 560 MET cc_start: 0.8595 (mpp) cc_final: 0.8034 (mpp) REVERT: P 270 GLU cc_start: 0.9154 (pm20) cc_final: 0.8537 (pm20) REVERT: P 323 ILE cc_start: 0.8785 (tt) cc_final: 0.8559 (tp) outliers start: 21 outliers final: 17 residues processed: 204 average time/residue: 0.1060 time to fit residues: 33.8870 Evaluate side-chains 202 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 437 ILE 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 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: 1.9990 chunk 167 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 10 optimal weight: 0.0050 chunk 88 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103987 restraints weight = 29534.448| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.80 r_work: 0.3408 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14910 Z= 0.125 Angle : 0.490 6.409 20184 Z= 0.265 Chirality : 0.039 0.192 2236 Planarity : 0.004 0.072 2620 Dihedral : 4.680 34.988 2039 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.36 % Allowed : 12.68 % Favored : 85.97 % 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: 0.35 (0.19), residues: 1877 helix: 1.27 (0.17), residues: 951 sheet: -0.29 (0.58), residues: 91 loop : -0.91 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 564 TYR 0.013 0.001 TYR P 238 PHE 0.019 0.001 PHE M 262 TRP 0.017 0.001 TRP K 966 HIS 0.004 0.001 HIS M 480 Details of bonding type rmsd covalent geometry : bond 0.00284 (14909) covalent geometry : angle 0.49037 (20184) hydrogen bonds : bond 0.03886 ( 673) hydrogen bonds : angle 4.08285 ( 1953) metal coordination : bond 0.00367 ( 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 212 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: K 961 ASN cc_start: 0.7813 (t0) cc_final: 0.7424 (t0) REVERT: M 373 SER cc_start: 0.9194 (p) cc_final: 0.8816 (t) REVERT: M 374 ASP cc_start: 0.8441 (t0) cc_final: 0.8180 (m-30) REVERT: M 560 MET cc_start: 0.8622 (tpt) cc_final: 0.8407 (tpt) REVERT: N 267 GLN cc_start: 0.8676 (pt0) cc_final: 0.8248 (pp30) REVERT: N 307 ASP cc_start: 0.8978 (t70) cc_final: 0.8763 (t0) REVERT: N 358 GLN cc_start: 0.7872 (tp-100) cc_final: 0.6806 (tm-30) REVERT: N 373 TYR cc_start: 0.8838 (m-10) cc_final: 0.7955 (m-10) REVERT: O 556 TYR cc_start: 0.9173 (t80) cc_final: 0.8669 (t80) REVERT: O 560 MET cc_start: 0.8434 (mpp) cc_final: 0.7922 (mpp) REVERT: P 264 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7930 (mm-30) REVERT: P 270 GLU cc_start: 0.9141 (pm20) cc_final: 0.8497 (pm20) REVERT: P 288 TYR cc_start: 0.9348 (t80) cc_final: 0.9122 (t80) REVERT: P 323 ILE cc_start: 0.8860 (tt) cc_final: 0.8637 (tp) REVERT: P 401 MET cc_start: 0.4085 (mmm) cc_final: 0.3779 (mmm) outliers start: 20 outliers final: 16 residues processed: 203 average time/residue: 0.1071 time to fit residues: 33.7633 Evaluate side-chains 198 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 LEU Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 452 VAL 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 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 373 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100852 restraints weight = 28159.336| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.41 r_work: 0.3219 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14910 Z= 0.241 Angle : 0.568 6.348 20184 Z= 0.303 Chirality : 0.042 0.178 2236 Planarity : 0.004 0.074 2620 Dihedral : 4.811 29.331 2039 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.17 % Allowed : 13.97 % Favored : 83.86 % 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: 0.26 (0.19), residues: 1877 helix: 1.18 (0.17), residues: 946 sheet: -0.50 (0.56), residues: 97 loop : -0.91 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 564 TYR 0.018 0.002 TYR K 675 PHE 0.018 0.002 PHE K 819 TRP 0.012 0.002 TRP K 966 HIS 0.004 0.001 HIS N 330 Details of bonding type rmsd covalent geometry : bond 0.00566 (14909) covalent geometry : angle 0.56751 (20184) hydrogen bonds : bond 0.04379 ( 673) hydrogen bonds : angle 4.24038 ( 1953) metal coordination : bond 0.00881 ( 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 215 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: M 373 SER cc_start: 0.9108 (p) cc_final: 0.8841 (t) REVERT: M 560 MET cc_start: 0.8648 (tpt) cc_final: 0.8395 (tpt) REVERT: N 267 GLN cc_start: 0.8527 (pt0) cc_final: 0.8233 (pp30) REVERT: N 307 ASP cc_start: 0.8670 (t70) cc_final: 0.8431 (t0) REVERT: N 358 GLN cc_start: 0.8052 (tp-100) cc_final: 0.6895 (tm-30) REVERT: N 373 TYR cc_start: 0.8703 (m-10) cc_final: 0.7941 (m-10) REVERT: O 556 TYR cc_start: 0.9103 (t80) cc_final: 0.8574 (t80) REVERT: O 560 MET cc_start: 0.8329 (mpp) cc_final: 0.7726 (mpp) REVERT: P 270 GLU cc_start: 0.9011 (pm20) cc_final: 0.8475 (pm20) REVERT: P 323 ILE cc_start: 0.8788 (tt) cc_final: 0.8530 (tp) REVERT: P 401 MET cc_start: 0.3991 (mmm) cc_final: 0.3722 (mmm) outliers start: 32 outliers final: 24 residues processed: 205 average time/residue: 0.1067 time to fit residues: 34.0856 Evaluate side-chains 202 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 698 ASP Chi-restraints excluded: chain K residue 825 LEU Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 957 VAL 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 122 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 324 SER 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 301 LEU 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 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: 0.0470 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 884 HIS ** K 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 ASN N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104725 restraints weight = 27610.082| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.41 r_work: 0.3288 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14910 Z= 0.107 Angle : 0.484 7.883 20184 Z= 0.257 Chirality : 0.038 0.166 2236 Planarity : 0.003 0.074 2620 Dihedral : 4.377 25.215 2038 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 14.78 % Favored : 83.39 % 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: 0.60 (0.20), residues: 1877 helix: 1.54 (0.17), residues: 949 sheet: -0.30 (0.59), residues: 91 loop : -0.86 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 564 TYR 0.015 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 M 480 Details of bonding type rmsd covalent geometry : bond 0.00233 (14909) covalent geometry : angle 0.48356 (20184) hydrogen bonds : bond 0.03491 ( 673) hydrogen bonds : angle 3.91071 ( 1953) metal coordination : bond 0.00257 ( 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 219 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.672 Fit side-chains REVERT: K 792 ASP cc_start: 0.8474 (t70) cc_final: 0.8179 (t70) REVERT: K 961 ASN cc_start: 0.7478 (t0) cc_final: 0.7240 (t0) REVERT: M 373 SER cc_start: 0.9107 (p) cc_final: 0.8780 (t) REVERT: N 267 GLN cc_start: 0.8464 (pt0) cc_final: 0.8171 (pp30) REVERT: N 307 ASP cc_start: 0.8621 (t70) cc_final: 0.8387 (t0) REVERT: N 354 LEU cc_start: 0.9012 (tp) cc_final: 0.8761 (tt) REVERT: N 358 GLN cc_start: 0.7958 (tp-100) cc_final: 0.6844 (tm-30) REVERT: N 373 TYR cc_start: 0.8586 (m-10) cc_final: 0.7902 (m-10) REVERT: O 556 TYR cc_start: 0.9115 (t80) cc_final: 0.8536 (t80) REVERT: O 560 MET cc_start: 0.8181 (mpp) cc_final: 0.7791 (mpp) REVERT: P 264 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7828 (mm-30) REVERT: P 288 TYR cc_start: 0.9262 (t80) cc_final: 0.9037 (t80) REVERT: P 323 ILE cc_start: 0.8719 (tt) cc_final: 0.8509 (tp) outliers start: 27 outliers final: 19 residues processed: 210 average time/residue: 0.1070 time to fit residues: 35.0115 Evaluate side-chains 204 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU 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 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 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 310 LEU 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: 5.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 186 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 172 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 690 ASN ** K 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103037 restraints weight = 27841.029| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.35 r_work: 0.3289 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14910 Z= 0.121 Angle : 0.488 7.110 20184 Z= 0.259 Chirality : 0.039 0.163 2236 Planarity : 0.004 0.063 2620 Dihedral : 4.263 24.456 2038 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 15.25 % Favored : 83.05 % 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: 0.70 (0.20), residues: 1877 helix: 1.66 (0.17), residues: 944 sheet: -0.29 (0.58), residues: 91 loop : -0.83 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 564 TYR 0.014 0.001 TYR M 356 PHE 0.013 0.001 PHE M 262 TRP 0.010 0.001 TRP K 966 HIS 0.003 0.001 HIS K 930 Details of bonding type rmsd covalent geometry : bond 0.00278 (14909) covalent geometry : angle 0.48775 (20184) hydrogen bonds : bond 0.03476 ( 673) hydrogen bonds : angle 3.87116 ( 1953) metal coordination : bond 0.00382 ( 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 211 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.492 Fit side-chains REVERT: K 792 ASP cc_start: 0.8428 (t70) cc_final: 0.8066 (t0) REVERT: K 961 ASN cc_start: 0.7566 (t0) cc_final: 0.7255 (t0) REVERT: N 267 GLN cc_start: 0.8409 (pt0) cc_final: 0.8142 (pp30) REVERT: N 307 ASP cc_start: 0.8592 (t70) cc_final: 0.8343 (t0) REVERT: N 354 LEU cc_start: 0.9022 (tp) cc_final: 0.8810 (tt) REVERT: N 358 GLN cc_start: 0.7992 (tp-100) cc_final: 0.6722 (tm-30) REVERT: N 373 TYR cc_start: 0.8596 (m-10) cc_final: 0.7879 (m-10) REVERT: P 323 ILE cc_start: 0.8631 (tt) cc_final: 0.8399 (tp) REVERT: P 350 GLN cc_start: 0.8341 (mt0) cc_final: 0.8097 (mt0) REVERT: P 401 MET cc_start: 0.3037 (mmm) cc_final: 0.2614 (mpp) outliers start: 25 outliers final: 20 residues processed: 202 average time/residue: 0.0968 time to fit residues: 31.2505 Evaluate side-chains 199 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU 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 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 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 310 LEU 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: 4.9990 chunk 134 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 961 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 = 0.3812 r_free = 0.3812 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104070 restraints weight = 27850.646| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.39 r_work: 0.3280 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14910 Z= 0.141 Angle : 0.511 10.148 20184 Z= 0.268 Chirality : 0.039 0.172 2236 Planarity : 0.003 0.058 2620 Dihedral : 4.260 24.629 2038 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: 0.73 (0.20), residues: 1877 helix: 1.69 (0.17), residues: 950 sheet: -0.36 (0.56), residues: 96 loop : -0.83 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 564 TYR 0.014 0.001 TYR M 356 PHE 0.011 0.001 PHE K 819 TRP 0.010 0.001 TRP K 966 HIS 0.004 0.001 HIS M 480 Details of bonding type rmsd covalent geometry : bond 0.00330 (14909) covalent geometry : angle 0.51074 (20184) hydrogen bonds : bond 0.03522 ( 673) hydrogen bonds : angle 3.87606 ( 1953) metal coordination : bond 0.00474 ( 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 209 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.638 Fit side-chains REVERT: K 792 ASP cc_start: 0.8471 (t70) cc_final: 0.8101 (t0) REVERT: K 961 ASN cc_start: 0.7607 (t0) cc_final: 0.7342 (t0) REVERT: N 267 GLN cc_start: 0.8440 (pt0) cc_final: 0.8165 (pp30) REVERT: N 307 ASP cc_start: 0.8607 (t70) cc_final: 0.8350 (t0) REVERT: N 353 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: N 354 LEU cc_start: 0.9010 (tp) cc_final: 0.8781 (tt) REVERT: N 373 TYR cc_start: 0.8597 (m-10) cc_final: 0.7950 (m-10) REVERT: P 323 ILE cc_start: 0.8660 (tt) cc_final: 0.8407 (tp) REVERT: P 350 GLN cc_start: 0.8336 (mt0) cc_final: 0.8108 (mt0) REVERT: P 373 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7198 (p90) outliers start: 27 outliers final: 23 residues processed: 198 average time/residue: 0.1015 time to fit residues: 31.8024 Evaluate side-chains 202 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU 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 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 357 ILE Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 310 LEU 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: 0.0970 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 163 optimal weight: 0.0070 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 GLN O 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.133345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105801 restraints weight = 27840.894| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.47 r_work: 0.3304 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14910 Z= 0.105 Angle : 0.489 9.457 20184 Z= 0.256 Chirality : 0.038 0.160 2236 Planarity : 0.003 0.056 2620 Dihedral : 4.088 24.128 2038 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 16.27 % Favored : 81.97 % 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: 0.88 (0.20), residues: 1877 helix: 1.84 (0.17), residues: 943 sheet: -0.33 (0.57), residues: 91 loop : -0.78 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 564 TYR 0.016 0.001 TYR O 556 PHE 0.010 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 covalent geometry : bond 0.00239 (14909) covalent geometry : angle 0.48918 (20184) hydrogen bonds : bond 0.03193 ( 673) hydrogen bonds : angle 3.79722 ( 1953) metal coordination : bond 0.00225 ( 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 216 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.549 Fit side-chains REVERT: K 792 ASP cc_start: 0.8438 (t70) cc_final: 0.8029 (t0) REVERT: K 961 ASN cc_start: 0.7615 (t0) cc_final: 0.7367 (t0) REVERT: M 262 PHE cc_start: 0.8768 (p90) cc_final: 0.8565 (p90) REVERT: N 307 ASP cc_start: 0.8623 (t70) cc_final: 0.8385 (t0) REVERT: N 353 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.6802 (mp10) REVERT: N 358 GLN cc_start: 0.8005 (tp-100) cc_final: 0.6719 (tm-30) REVERT: N 373 TYR cc_start: 0.8582 (m-10) cc_final: 0.7901 (m-10) REVERT: P 236 TRP cc_start: 0.8845 (t60) cc_final: 0.8372 (t60) outliers start: 26 outliers final: 22 residues processed: 205 average time/residue: 0.1020 time to fit residues: 32.5372 Evaluate side-chains 205 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 825 LEU 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 61 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 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 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 319 LEU Chi-restraints excluded: chain O residue 357 ILE Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 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: 0.0980 chunk 149 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 178 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 GLN O 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106136 restraints weight = 27773.378| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.42 r_work: 0.3308 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3238 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= 0.109 Angle : 0.503 9.680 20184 Z= 0.261 Chirality : 0.038 0.155 2236 Planarity : 0.003 0.054 2620 Dihedral : 4.029 23.658 2038 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.90 % Allowed : 16.54 % Favored : 81.56 % 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: 0.92 (0.20), residues: 1877 helix: 1.86 (0.17), residues: 941 sheet: -0.32 (0.55), residues: 96 loop : -0.74 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 564 TYR 0.015 0.001 TYR L 176 PHE 0.010 0.001 PHE M 262 TRP 0.012 0.001 TRP K 966 HIS 0.004 0.001 HIS M 480 Details of bonding type rmsd covalent geometry : bond 0.00251 (14909) covalent geometry : angle 0.50339 (20184) hydrogen bonds : bond 0.03186 ( 673) hydrogen bonds : angle 3.77985 ( 1953) metal coordination : bond 0.00280 ( 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 217 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.538 Fit side-chains REVERT: K 792 ASP cc_start: 0.8428 (t70) cc_final: 0.7990 (t0) REVERT: K 961 ASN cc_start: 0.7611 (t0) cc_final: 0.7385 (t0) REVERT: M 262 PHE cc_start: 0.8703 (p90) cc_final: 0.8460 (p90) REVERT: M 564 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8357 (mmp-170) REVERT: N 307 ASP cc_start: 0.8629 (t70) cc_final: 0.8377 (t0) REVERT: N 353 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6800 (mp10) REVERT: N 358 GLN cc_start: 0.7978 (tp-100) cc_final: 0.6622 (tm-30) REVERT: N 373 TYR cc_start: 0.8562 (m-10) cc_final: 0.7871 (m-10) REVERT: P 236 TRP cc_start: 0.8823 (t60) cc_final: 0.8369 (t60) REVERT: P 350 GLN cc_start: 0.8323 (mt0) cc_final: 0.8006 (mt0) outliers start: 28 outliers final: 24 residues processed: 208 average time/residue: 0.1052 time to fit residues: 33.9579 Evaluate side-chains 205 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 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 319 LEU Chi-restraints excluded: chain O residue 357 ILE Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 348 ASP 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: 1.9990 chunk 156 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** K 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 GLN O 329 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 = 0.3729 r_free = 0.3729 target = 0.126526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098886 restraints weight = 28182.120| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.44 r_work: 0.3189 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14910 Z= 0.136 Angle : 0.520 9.534 20184 Z= 0.270 Chirality : 0.039 0.160 2236 Planarity : 0.004 0.050 2620 Dihedral : 4.092 23.314 2038 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.90 % Allowed : 16.75 % Favored : 81.36 % 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: 0.88 (0.20), residues: 1877 helix: 1.86 (0.17), residues: 937 sheet: -0.40 (0.54), residues: 96 loop : -0.78 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 564 TYR 0.020 0.001 TYR O 556 PHE 0.010 0.001 PHE K 819 TRP 0.012 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 Details of bonding type rmsd covalent geometry : bond 0.00319 (14909) covalent geometry : angle 0.52009 (20184) hydrogen bonds : bond 0.03361 ( 673) hydrogen bonds : angle 3.82015 ( 1953) metal coordination : bond 0.00424 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.73 seconds wall clock time: 51 minutes 46.42 seconds (3106.42 seconds total)