Starting phenix.real_space_refine on Fri May 16 15:17:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihn_35450/05_2025/8ihn_35450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihn_35450/05_2025/8ihn_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_35450/05_2025/8ihn_35450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihn_35450/05_2025/8ihn_35450.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihn_35450/05_2025/8ihn_35450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihn_35450/05_2025/8ihn_35450.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 12, 'HIS: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: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} 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: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP: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: {'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2} 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: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 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: 8.50, per 1000 atoms: 0.58 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.41 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: 4.08 Time building geometry restraints manager: 4.20 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: 2.100 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP K 719 HIS 0.006 0.001 HIS P 369 PHE 0.038 0.001 PHE P 374 TYR 0.030 0.002 TYR N 373 ARG 0.012 0.001 ARG P 247 Details of bonding type rmsd hydrogen bonds : bond 0.27729 ( 673) hydrogen bonds : angle 8.63384 ( 1953) metal coordination : bond 0.00389 ( 1) covalent geometry : bond 0.00527 (14909) covalent geometry : angle 0.88952 (20184) *********************** 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 : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 306 MET cc_start: 0.9087 (ttp) cc_final: 0.8850 (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: 0.2526 time to fit residues: 84.6258 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 : 1.703 ------------------------------------------------------------------------------- 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 158 optimal weight: 0.0020 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.131757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105231 restraints weight = 27446.790| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.33 r_work: 0.3348 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14910 Z= 0.154 Angle : 0.567 7.132 20184 Z= 0.310 Chirality : 0.041 0.159 2236 Planarity : 0.004 0.042 2620 Dihedral : 5.212 52.250 2039 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 0.95 % Allowed : 6.98 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 1877 helix: 0.69 (0.17), residues: 938 sheet: -0.24 (0.56), residues: 91 loop : -1.09 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 966 HIS 0.017 0.001 HIS M 479 PHE 0.013 0.001 PHE K1269 TYR 0.028 0.002 TYR O 556 ARG 0.006 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 673) hydrogen bonds : angle 4.84075 ( 1953) metal coordination : bond 0.00226 ( 1) covalent geometry : bond 0.00341 (14909) covalent geometry : angle 0.56741 (20184) *********************** 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 219 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 961 ASN cc_start: 0.7981 (t0) cc_final: 0.7672 (t0) REVERT: M 343 ILE cc_start: 0.9074 (tp) cc_final: 0.8786 (tp) REVERT: M 373 SER cc_start: 0.9360 (p) cc_final: 0.8991 (t) REVERT: M 374 ASP cc_start: 0.8602 (t0) cc_final: 0.8266 (m-30) REVERT: M 560 MET cc_start: 0.8682 (tpt) cc_final: 0.8302 (tpt) REVERT: N 267 GLN cc_start: 0.8546 (pt0) cc_final: 0.8303 (pp30) REVERT: N 307 ASP cc_start: 0.8818 (t70) cc_final: 0.8600 (t0) REVERT: N 326 TYR cc_start: 0.8864 (m-80) cc_final: 0.8485 (m-80) REVERT: N 358 GLN cc_start: 0.7414 (tp-100) cc_final: 0.6948 (tm-30) REVERT: N 373 TYR cc_start: 0.8777 (m-10) cc_final: 0.8235 (m-10) REVERT: P 270 GLU cc_start: 0.9094 (pm20) cc_final: 0.8591 (pm20) REVERT: P 394 TYR cc_start: 0.7544 (t80) cc_final: 0.7304 (t80) outliers start: 14 outliers final: 9 residues processed: 211 average time/residue: 0.2413 time to fit residues: 79.3149 Evaluate side-chains 198 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain L residue 122 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 93 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 155 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107786 restraints weight = 29965.132| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.85 r_work: 0.3440 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14910 Z= 0.164 Angle : 0.524 6.339 20184 Z= 0.285 Chirality : 0.040 0.158 2236 Planarity : 0.004 0.071 2620 Dihedral : 4.912 46.079 2039 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 1.36 % Allowed : 9.63 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1877 helix: 1.03 (0.17), residues: 951 sheet: -0.35 (0.57), residues: 92 loop : -0.93 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 966 HIS 0.011 0.001 HIS M 479 PHE 0.022 0.001 PHE M 262 TYR 0.017 0.001 TYR K 675 ARG 0.005 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 673) hydrogen bonds : angle 4.35599 ( 1953) metal coordination : bond 0.00442 ( 1) covalent geometry : bond 0.00378 (14909) covalent geometry : angle 0.52409 (20184) *********************** 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 219 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: K 961 ASN cc_start: 0.7975 (t0) cc_final: 0.7707 (t0) REVERT: M 343 ILE cc_start: 0.9103 (tp) cc_final: 0.8855 (tp) REVERT: M 373 SER cc_start: 0.9235 (p) cc_final: 0.8882 (t) REVERT: M 374 ASP cc_start: 0.8368 (t0) cc_final: 0.8161 (m-30) REVERT: M 560 MET cc_start: 0.8619 (tpt) cc_final: 0.8180 (tpt) REVERT: N 267 GLN cc_start: 0.8672 (pt0) cc_final: 0.8270 (pp30) REVERT: N 307 ASP cc_start: 0.9019 (t70) cc_final: 0.8802 (t0) REVERT: N 326 TYR cc_start: 0.8859 (m-80) cc_final: 0.8456 (m-80) REVERT: N 358 GLN cc_start: 0.7715 (tp-100) cc_final: 0.6890 (tm-30) REVERT: O 305 GLU cc_start: 0.8904 (tt0) cc_final: 0.8608 (tm-30) REVERT: O 556 TYR cc_start: 0.9181 (t80) cc_final: 0.8793 (t80) REVERT: O 560 MET cc_start: 0.8675 (mpp) cc_final: 0.7981 (mpp) REVERT: P 223 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7658 (tm-30) REVERT: P 270 GLU cc_start: 0.9143 (pm20) cc_final: 0.8499 (pm20) REVERT: P 323 ILE cc_start: 0.8803 (tt) cc_final: 0.8582 (tp) outliers start: 20 outliers final: 16 residues processed: 211 average time/residue: 0.2427 time to fit residues: 79.3583 Evaluate side-chains 204 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 840 ASN Chi-restraints excluded: chain K residue 944 THR Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 480 HIS 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 136 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 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 ** 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 = 0.3840 r_free = 0.3840 target = 0.131396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105048 restraints weight = 27424.937| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.31 r_work: 0.3327 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2432 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= 0.123 Angle : 0.483 6.484 20184 Z= 0.260 Chirality : 0.039 0.145 2236 Planarity : 0.004 0.071 2620 Dihedral : 4.561 35.078 2039 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 12.07 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 1877 helix: 1.37 (0.17), residues: 951 sheet: -0.16 (0.58), residues: 91 loop : -0.85 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 966 HIS 0.005 0.001 HIS M 479 PHE 0.024 0.001 PHE M 262 TYR 0.014 0.001 TYR P 238 ARG 0.005 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 673) hydrogen bonds : angle 4.02118 ( 1953) metal coordination : bond 0.00266 ( 1) covalent geometry : bond 0.00279 (14909) covalent geometry : angle 0.48269 (20184) *********************** 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 214 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: K 961 ASN cc_start: 0.7886 (t0) cc_final: 0.7638 (t0) REVERT: M 373 SER cc_start: 0.9299 (p) cc_final: 0.8885 (t) REVERT: N 267 GLN cc_start: 0.8602 (pt0) cc_final: 0.8298 (pp30) REVERT: N 307 ASP cc_start: 0.8815 (t70) cc_final: 0.8588 (t0) REVERT: N 326 TYR cc_start: 0.8773 (m-80) cc_final: 0.8447 (m-80) REVERT: N 358 GLN cc_start: 0.7705 (tp-100) cc_final: 0.6906 (tm-30) REVERT: N 373 TYR cc_start: 0.8711 (m-10) cc_final: 0.7888 (m-10) REVERT: O 556 TYR cc_start: 0.9136 (t80) cc_final: 0.8661 (t80) REVERT: O 560 MET cc_start: 0.8447 (mpp) cc_final: 0.8086 (mpp) REVERT: P 223 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7542 (tm-30) REVERT: P 264 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7874 (mm-30) REVERT: P 323 ILE cc_start: 0.8693 (tt) cc_final: 0.8486 (tp) REVERT: P 401 MET cc_start: 0.3906 (mmm) cc_final: 0.3609 (mmm) outliers start: 19 outliers final: 15 residues processed: 205 average time/residue: 0.2294 time to fit residues: 73.6313 Evaluate side-chains 201 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 M residue 324 SER Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 452 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 87 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** L 331 ASN N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106818 restraints weight = 27918.369| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.32 r_work: 0.3326 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2611 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= 0.130 Angle : 0.488 6.577 20184 Z= 0.259 Chirality : 0.039 0.149 2236 Planarity : 0.004 0.072 2620 Dihedral : 4.429 28.647 2039 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.69 % Allowed : 13.08 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1877 helix: 1.49 (0.17), residues: 950 sheet: -0.12 (0.59), residues: 91 loop : -0.77 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 966 HIS 0.003 0.001 HIS K 930 PHE 0.020 0.001 PHE M 262 TYR 0.016 0.001 TYR M 356 ARG 0.006 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 673) hydrogen bonds : angle 3.94462 ( 1953) metal coordination : bond 0.00439 ( 1) covalent geometry : bond 0.00298 (14909) covalent geometry : angle 0.48750 (20184) *********************** 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: 25 poor density : 190 time to evaluate : 1.571 Fit side-chains REVERT: K 961 ASN cc_start: 0.7776 (t0) cc_final: 0.7455 (t0) REVERT: N 252 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8754 (p) REVERT: N 267 GLN cc_start: 0.8575 (pt0) cc_final: 0.8288 (pp30) REVERT: N 307 ASP cc_start: 0.8743 (t70) cc_final: 0.8510 (t0) REVERT: N 354 LEU cc_start: 0.9076 (tp) cc_final: 0.8827 (tt) REVERT: N 358 GLN cc_start: 0.7820 (tp-100) cc_final: 0.6907 (tm-30) REVERT: N 373 TYR cc_start: 0.8609 (m-10) cc_final: 0.7911 (m-10) REVERT: O 556 TYR cc_start: 0.9199 (t80) cc_final: 0.8702 (t80) REVERT: O 560 MET cc_start: 0.8387 (mpp) cc_final: 0.8109 (mpp) REVERT: P 223 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7460 (tm-30) REVERT: P 264 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7998 (mm-30) REVERT: P 288 TYR cc_start: 0.9216 (t80) cc_final: 0.8814 (t80) REVERT: P 323 ILE cc_start: 0.8664 (tt) cc_final: 0.8413 (tp) outliers start: 25 outliers final: 17 residues processed: 206 average time/residue: 0.2269 time to fit residues: 72.3132 Evaluate side-chains 203 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 1215 ILE 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 437 ILE Chi-restraints excluded: chain M residue 452 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 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 60 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105011 restraints weight = 27861.173| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.32 r_work: 0.3343 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2758 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= 0.124 Angle : 0.489 7.664 20184 Z= 0.258 Chirality : 0.038 0.146 2236 Planarity : 0.003 0.073 2620 Dihedral : 4.335 27.077 2039 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.97 % Allowed : 13.83 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1877 helix: 1.63 (0.17), residues: 943 sheet: -0.09 (0.59), residues: 91 loop : -0.77 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 PHE 0.016 0.001 PHE M 262 TYR 0.016 0.001 TYR M 356 ARG 0.007 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 673) hydrogen bonds : angle 3.87246 ( 1953) metal coordination : bond 0.00383 ( 1) covalent geometry : bond 0.00285 (14909) covalent geometry : angle 0.48892 (20184) *********************** 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 218 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.751 Fit side-chains REVERT: K 792 ASP cc_start: 0.8347 (t70) cc_final: 0.8025 (t0) REVERT: N 252 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8734 (p) REVERT: N 267 GLN cc_start: 0.8378 (pt0) cc_final: 0.8145 (pp30) REVERT: N 307 ASP cc_start: 0.8519 (t70) cc_final: 0.8279 (t0) REVERT: N 354 LEU cc_start: 0.9025 (tp) cc_final: 0.8805 (tt) REVERT: N 358 GLN cc_start: 0.7731 (tp-100) cc_final: 0.6865 (tm-30) REVERT: N 373 TYR cc_start: 0.8489 (m-10) cc_final: 0.7806 (m-10) REVERT: O 556 TYR cc_start: 0.9086 (t80) cc_final: 0.8535 (t80) REVERT: O 560 MET cc_start: 0.8140 (mpp) cc_final: 0.7889 (mpp) REVERT: P 288 TYR cc_start: 0.9328 (t80) cc_final: 0.9114 (t80) REVERT: P 323 ILE cc_start: 0.8613 (tt) cc_final: 0.8405 (tp) outliers start: 29 outliers final: 20 residues processed: 207 average time/residue: 0.2259 time to fit residues: 73.2238 Evaluate side-chains 200 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 114 ASP Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 334 LYS 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 252 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 79 optimal weight: 0.0980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 31 ASN N 223 GLN O 329 GLN O 583 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.135661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108905 restraints weight = 27946.688| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.46 r_work: 0.3360 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14910 Z= 0.096 Angle : 0.471 7.219 20184 Z= 0.248 Chirality : 0.038 0.138 2236 Planarity : 0.003 0.073 2620 Dihedral : 4.136 26.027 2039 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.69 % Allowed : 14.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1877 helix: 1.75 (0.17), residues: 945 sheet: 0.03 (0.59), residues: 91 loop : -0.75 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 966 HIS 0.003 0.001 HIS M 448 PHE 0.014 0.001 PHE M 262 TYR 0.016 0.001 TYR M 356 ARG 0.007 0.000 ARG P 247 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 673) hydrogen bonds : angle 3.76131 ( 1953) metal coordination : bond 0.00184 ( 1) covalent geometry : bond 0.00213 (14909) covalent geometry : angle 0.47054 (20184) *********************** 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 220 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.572 Fit side-chains REVERT: K 792 ASP cc_start: 0.8333 (t70) cc_final: 0.7949 (t0) REVERT: K 961 ASN cc_start: 0.7569 (t0) cc_final: 0.7328 (t0) REVERT: N 307 ASP cc_start: 0.8597 (t70) cc_final: 0.8367 (t0) REVERT: N 335 ILE cc_start: 0.9124 (mm) cc_final: 0.8873 (mt) REVERT: N 358 GLN cc_start: 0.7733 (tp-100) cc_final: 0.6822 (tm-30) REVERT: N 373 TYR cc_start: 0.8507 (m-10) cc_final: 0.7794 (m-10) REVERT: P 288 TYR cc_start: 0.9336 (t80) cc_final: 0.9132 (t80) REVERT: P 323 ILE cc_start: 0.8660 (tt) cc_final: 0.8412 (tp) REVERT: P 326 TYR cc_start: 0.7993 (m-10) cc_final: 0.7752 (m-10) outliers start: 25 outliers final: 17 residues processed: 209 average time/residue: 0.2479 time to fit residues: 80.3298 Evaluate side-chains 198 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 373 TYR Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 149 optimal weight: 0.0870 chunk 179 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 479 HIS N 223 GLN O 329 GLN O 583 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.132233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106146 restraints weight = 27766.773| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.25 r_work: 0.3351 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14910 Z= 0.119 Angle : 0.505 10.609 20184 Z= 0.261 Chirality : 0.039 0.175 2236 Planarity : 0.004 0.063 2620 Dihedral : 4.098 24.215 2038 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.56 % Allowed : 15.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1877 helix: 1.80 (0.17), residues: 944 sheet: -0.09 (0.58), residues: 91 loop : -0.77 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 966 HIS 0.010 0.001 HIS M 479 PHE 0.013 0.001 PHE M 262 TYR 0.039 0.001 TYR O 556 ARG 0.007 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 673) hydrogen bonds : angle 3.78921 ( 1953) metal coordination : bond 0.00376 ( 1) covalent geometry : bond 0.00274 (14909) covalent geometry : angle 0.50545 (20184) *********************** 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 211 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.723 Fit side-chains REVERT: K 792 ASP cc_start: 0.8610 (t70) cc_final: 0.8208 (t0) REVERT: K 961 ASN cc_start: 0.7745 (t0) cc_final: 0.7499 (t0) REVERT: N 307 ASP cc_start: 0.8818 (t70) cc_final: 0.8582 (t0) REVERT: N 335 ILE cc_start: 0.9180 (mm) cc_final: 0.8920 (mt) REVERT: N 353 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: N 358 GLN cc_start: 0.8010 (tp-100) cc_final: 0.6775 (tm-30) REVERT: N 373 TYR cc_start: 0.8627 (m-10) cc_final: 0.7853 (m-10) REVERT: O 305 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8480 (pp20) REVERT: P 323 ILE cc_start: 0.8658 (tt) cc_final: 0.8387 (tp) REVERT: P 373 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7192 (p90) outliers start: 23 outliers final: 18 residues processed: 198 average time/residue: 0.2335 time to fit residues: 72.1151 Evaluate side-chains 204 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 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 N residue 301 LEU Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 373 TYR Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 116 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 136 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 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 = 0.3876 r_free = 0.3876 target = 0.135258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108472 restraints weight = 27765.097| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.40 r_work: 0.3365 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3202 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= 0.107 Angle : 0.496 9.400 20184 Z= 0.257 Chirality : 0.038 0.166 2236 Planarity : 0.003 0.055 2620 Dihedral : 4.006 24.243 2038 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.49 % Allowed : 15.25 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1877 helix: 1.83 (0.17), residues: 950 sheet: -0.10 (0.58), residues: 91 loop : -0.72 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 PHE 0.012 0.001 PHE M 262 TYR 0.016 0.001 TYR M 356 ARG 0.009 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 673) hydrogen bonds : angle 3.75337 ( 1953) metal coordination : bond 0.00260 ( 1) covalent geometry : bond 0.00245 (14909) covalent geometry : angle 0.49646 (20184) *********************** 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 212 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.979 Fit side-chains REVERT: K 792 ASP cc_start: 0.8360 (t70) cc_final: 0.7929 (t0) REVERT: K 961 ASN cc_start: 0.7512 (t0) cc_final: 0.7276 (t0) REVERT: N 307 ASP cc_start: 0.8552 (t70) cc_final: 0.8309 (t0) REVERT: N 335 ILE cc_start: 0.9138 (mm) cc_final: 0.8860 (mt) REVERT: N 353 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: N 358 GLN cc_start: 0.7797 (tp-100) cc_final: 0.6707 (tm-30) REVERT: N 373 TYR cc_start: 0.8414 (m-10) cc_final: 0.7702 (m-10) REVERT: P 236 TRP cc_start: 0.8814 (t60) cc_final: 0.8364 (t60) REVERT: P 288 TYR cc_start: 0.9177 (t80) cc_final: 0.8896 (t80) REVERT: P 323 ILE cc_start: 0.8561 (tt) cc_final: 0.8331 (tp) outliers start: 22 outliers final: 19 residues processed: 202 average time/residue: 0.2357 time to fit residues: 74.9145 Evaluate side-chains 203 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 407 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 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 = 0.3827 r_free = 0.3827 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104695 restraints weight = 28048.834| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.37 r_work: 0.3286 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14910 Z= 0.197 Angle : 0.563 9.751 20184 Z= 0.295 Chirality : 0.041 0.169 2236 Planarity : 0.004 0.049 2620 Dihedral : 4.300 23.928 2038 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.56 % Allowed : 16.07 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1877 helix: 1.68 (0.17), residues: 945 sheet: -0.38 (0.55), residues: 97 loop : -0.77 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 966 HIS 0.005 0.001 HIS M 480 PHE 0.015 0.001 PHE K 819 TYR 0.029 0.002 TYR O 556 ARG 0.011 0.001 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 673) hydrogen bonds : angle 3.97022 ( 1953) metal coordination : bond 0.00733 ( 1) covalent geometry : bond 0.00467 (14909) covalent geometry : angle 0.56314 (20184) ********************** 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 206 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.652 Fit side-chains REVERT: K 792 ASP cc_start: 0.8528 (t70) cc_final: 0.7943 (t0) REVERT: K 961 ASN cc_start: 0.7647 (t0) cc_final: 0.7403 (t0) REVERT: M 564 ARG cc_start: 0.8629 (mmt180) cc_final: 0.8354 (mmp-170) REVERT: N 307 ASP cc_start: 0.8612 (t70) cc_final: 0.8358 (t0) REVERT: N 335 ILE cc_start: 0.9180 (mm) cc_final: 0.8901 (mt) REVERT: N 353 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: N 373 TYR cc_start: 0.8612 (m-10) cc_final: 0.7890 (m-10) REVERT: P 236 TRP cc_start: 0.8849 (t60) cc_final: 0.8403 (t60) REVERT: P 288 TYR cc_start: 0.9275 (t80) cc_final: 0.9053 (t80) outliers start: 23 outliers final: 22 residues processed: 197 average time/residue: 0.2298 time to fit residues: 69.7404 Evaluate side-chains 202 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 437 ILE Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 353 GLN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 71 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.3843 r_free = 0.3843 target = 0.131727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105290 restraints weight = 28061.858| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.34 r_work: 0.3359 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14910 Z= 0.120 Angle : 0.511 9.412 20184 Z= 0.266 Chirality : 0.039 0.160 2236 Planarity : 0.003 0.049 2620 Dihedral : 4.104 23.825 2038 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.69 % Allowed : 15.73 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1877 helix: 1.82 (0.17), residues: 942 sheet: -0.20 (0.58), residues: 91 loop : -0.76 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 PHE 0.011 0.001 PHE M 262 TYR 0.017 0.001 TYR L 176 ARG 0.010 0.000 ARG O 564 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 673) hydrogen bonds : angle 3.81560 ( 1953) metal coordination : bond 0.00277 ( 1) covalent geometry : bond 0.00278 (14909) covalent geometry : angle 0.51104 (20184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6845.87 seconds wall clock time: 119 minutes 36.49 seconds (7176.49 seconds total)