Starting phenix.real_space_refine on Sun Nov 17 20:11:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihn_35450/11_2024/8ihn_35450.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihn_35450/11_2024/8ihn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihn_35450/11_2024/8ihn_35450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihn_35450/11_2024/8ihn_35450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihn_35450/11_2024/8ihn_35450.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihn_35450/11_2024/8ihn_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.58, per 1000 atoms: 0.59 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: 3.85 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: 1.43 Creating SS restraints... Processing helix chain 'K' and resid 661 through 666 removed outlier: 3.775A pdb=" N GLU K 665 " --> pdb=" O SER K 661 " (cutoff:3.500A) Processing helix chain 'K' and resid 667 through 677 Processing helix chain 'K' and resid 678 through 694 removed outlier: 3.773A pdb=" N GLU K 684 " --> pdb=" O HIS K 680 " (cutoff:3.500A) Processing helix chain 'K' and resid 698 through 711 removed outlier: 3.868A pdb=" N PHE K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR K 709 " --> pdb=" O LYS K 705 " (cutoff:3.500A) Processing helix chain 'K' and resid 713 through 725 removed outlier: 3.605A pdb=" N TRP K 719 " --> pdb=" O GLU K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 765 removed outlier: 3.852A pdb=" N MET K 765 " --> pdb=" O ASP K 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 771 through 778 removed outlier: 3.538A pdb=" N TRP K 775 " --> pdb=" O ASP K 771 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 776 " --> pdb=" O ASP K 772 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 790 Processing helix chain 'K' and resid 805 through 841 removed outlier: 3.507A pdb=" N TYR K 820 " --> pdb=" O GLU K 816 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR K 827 " --> pdb=" O SER K 823 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 834 " --> pdb=" O CYS K 830 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) Processing helix chain 'K' and resid 842 through 848 removed outlier: 3.896A pdb=" N ASN K 848 " --> pdb=" O ASN K 844 " (cutoff:3.500A) Processing helix chain 'K' and resid 852 through 857 removed outlier: 4.021A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) Processing helix chain 'K' and resid 861 through 871 removed outlier: 3.702A pdb=" N ILE K 867 " --> pdb=" O TYR K 863 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 869 " --> pdb=" O LYS K 865 " (cutoff:3.500A) Processing helix chain 'K' and resid 874 through 886 removed outlier: 4.282A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 879 " --> pdb=" O ARG K 875 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 880 " --> pdb=" O GLY K 876 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 929 Proline residue: K 892 - end of helix removed outlier: 3.529A pdb=" N GLU K 911 " --> pdb=" O ARG K 907 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 914 " --> pdb=" O ARG K 910 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K 927 " --> pdb=" O VAL K 923 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 928 " --> pdb=" O PHE K 924 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP K 929 " --> pdb=" O PHE K 925 " (cutoff:3.500A) Processing helix chain 'K' and resid 929 through 934 removed outlier: 3.796A pdb=" N LEU K 933 " --> pdb=" O ASP K 929 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR K 934 " --> pdb=" O HIS K 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 929 through 934' Processing helix chain 'K' and resid 934 through 943 removed outlier: 3.962A pdb=" N LYS K 940 " --> pdb=" O LYS K 936 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS K 941 " --> pdb=" O GLN K 937 " (cutoff:3.500A) Processing helix chain 'K' and resid 946 through 965 removed outlier: 3.727A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE K 955 " --> pdb=" O GLU K 951 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS K 963 " --> pdb=" O GLN K 959 " (cutoff:3.500A) Processing helix chain 'K' and resid 982 through 999 removed outlier: 4.153A pdb=" N TYR K 986 " --> pdb=" O LYS K 982 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1022 removed outlier: 3.780A pdb=" N GLU K1008 " --> pdb=" O ASN K1004 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG K1009 " --> pdb=" O PRO K1005 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K1014 " --> pdb=" O LEU K1010 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K1015 " --> pdb=" O LYS K1011 " (cutoff:3.500A) Processing helix chain 'K' and resid 1025 through 1040 Processing helix chain 'K' and resid 1064 through 1069 Processing helix chain 'K' and resid 1070 through 1080 removed outlier: 4.345A pdb=" N LYS K1076 " --> pdb=" O SER K1072 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K1077 " --> pdb=" O ARG K1073 " (cutoff:3.500A) Processing helix chain 'K' and resid 1141 through 1175 removed outlier: 3.669A pdb=" N PHE K1147 " --> pdb=" O ASN K1143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE K1154 " --> pdb=" O HIS K1150 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET K1164 " --> pdb=" O GLU K1160 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU K1166 " --> pdb=" O LYS K1162 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG K1167 " --> pdb=" O GLN K1163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K1170 " --> pdb=" O GLU K1166 " (cutoff:3.500A) Processing helix chain 'K' and resid 1178 through 1183 Processing helix chain 'K' and resid 1189 through 1195 Processing helix chain 'K' and resid 1202 through 1216 removed outlier: 3.801A pdb=" N ARG K1213 " --> pdb=" O ARG K1209 " (cutoff:3.500A) Processing helix chain 'K' and resid 1220 through 1233 removed outlier: 3.547A pdb=" N LEU K1228 " --> pdb=" O PHE K1224 " (cutoff:3.500A) Processing helix chain 'K' and resid 1241 through 1258 removed outlier: 3.593A pdb=" N LEU K1256 " --> pdb=" O HIS K1252 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET K1257 " --> pdb=" O ALA K1253 " (cutoff:3.500A) Processing helix chain 'K' and resid 1259 through 1275 removed outlier: 3.786A pdb=" N LYS K1271 " --> pdb=" O ALA K1267 " (cutoff:3.500A) Processing helix chain 'K' and resid 1279 through 1294 removed outlier: 3.559A pdb=" N ILE K1284 " --> pdb=" O ALA K1280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS K1293 " --> pdb=" O GLN K1289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET K1294 " --> pdb=" O VAL K1290 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 removed outlier: 3.939A pdb=" N GLY L 30 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 55 removed outlier: 4.223A pdb=" N ARG L 46 " --> pdb=" O PRO L 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 72 through 77 removed outlier: 3.932A pdb=" N PHE L 77 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 89 removed outlier: 3.682A pdb=" N ARG L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.652A pdb=" N LEU L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 115 through 136 removed outlier: 3.802A pdb=" N GLY L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY L 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 174 removed outlier: 3.605A pdb=" N LEU L 168 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 195 Processing helix chain 'L' and resid 226 through 230 removed outlier: 3.587A pdb=" N LYS L 230 " --> pdb=" O GLY L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 262 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 287 through 300 removed outlier: 4.330A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 330 removed outlier: 3.642A pdb=" N ARG L 320 " --> pdb=" O ARG L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 381 removed outlier: 3.585A pdb=" N LYS L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 414 Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 318 through 330 removed outlier: 3.524A pdb=" N ILE M 322 " --> pdb=" O THR M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 335 No H-bonds generated for 'chain 'M' and resid 333 through 335' Processing helix chain 'M' and resid 336 through 343 Processing helix chain 'M' and resid 354 through 359 Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.732A pdb=" N THR M 405 " --> pdb=" O ASN M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 434 removed outlier: 3.685A pdb=" N ASN M 433 " --> pdb=" O HIS M 430 " (cutoff:3.500A) Processing helix chain 'M' and resid 544 through 577 removed outlier: 3.702A pdb=" N ILE M 574 " --> pdb=" O GLN M 570 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 241 removed outlier: 3.724A pdb=" N VAL N 233 " --> pdb=" O LYS N 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR N 240 " --> pdb=" O TRP N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 269 removed outlier: 3.965A pdb=" N GLN N 267 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU N 268 " --> pdb=" O GLU N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 297 removed outlier: 3.527A pdb=" N GLN N 275 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN N 277 " --> pdb=" O GLY N 273 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY N 294 " --> pdb=" O ASP N 290 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN N 295 " --> pdb=" O LYS N 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 297 " --> pdb=" O LEU N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 301 No H-bonds generated for 'chain 'N' and resid 299 through 301' Processing helix chain 'N' and resid 302 through 317 removed outlier: 3.653A pdb=" N LYS N 315 " --> pdb=" O LYS N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 326 removed outlier: 3.546A pdb=" N ILE N 325 " --> pdb=" O VAL N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 337 removed outlier: 3.586A pdb=" N LEU N 331 " --> pdb=" O GLY N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 345 removed outlier: 3.628A pdb=" N THR N 345 " --> pdb=" O LEU N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 369 Processing helix chain 'N' and resid 369 through 374 removed outlier: 3.601A pdb=" N TYR N 373 " --> pdb=" O HIS N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 400 removed outlier: 3.534A pdb=" N GLY N 396 " --> pdb=" O SER N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 315 through 330 Processing helix chain 'O' and resid 337 through 344 removed outlier: 4.118A pdb=" N ASP O 344 " --> pdb=" O LEU O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 354 through 361 removed outlier: 4.070A pdb=" N PHE O 361 " --> pdb=" O ILE O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 544 through 577 removed outlier: 3.918A pdb=" N LYS O 554 " --> pdb=" O ASP O 550 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET O 560 " --> pdb=" O TYR O 556 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL O 561 " --> pdb=" O LYS O 557 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU O 577 " --> pdb=" O LEU O 573 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 242 Processing helix chain 'P' and resid 253 through 265 Processing helix chain 'P' and resid 266 through 268 No H-bonds generated for 'chain 'P' and resid 266 through 268' Processing helix chain 'P' and resid 271 through 296 removed outlier: 3.861A pdb=" N ASP P 290 " --> pdb=" O LYS P 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS P 291 " --> pdb=" O LEU P 287 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY P 294 " --> pdb=" O ASP P 290 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 317 removed outlier: 3.595A pdb=" N LEU P 304 " --> pdb=" O ARG P 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN P 305 " --> pdb=" O LEU P 301 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU P 308 " --> pdb=" O LEU P 304 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU P 309 " --> pdb=" O GLN P 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P 310 " --> pdb=" O TYR P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 321 through 326 removed outlier: 3.730A pdb=" N ILE P 325 " --> pdb=" O VAL P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 345 removed outlier: 3.805A pdb=" N LEU P 331 " --> pdb=" O GLY P 327 " (cutoff:3.500A) Proline residue: P 339 - end of helix removed outlier: 3.639A pdb=" N SER P 343 " --> pdb=" O PRO P 339 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER P 344 " --> pdb=" O GLU P 340 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR P 345 " --> pdb=" O LEU P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 370 removed outlier: 3.509A pdb=" N THR P 359 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET P 368 " --> pdb=" O VAL P 364 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS P 369 " --> pdb=" O TRP P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 391 through 400 Processing sheet with id=AA1, first strand: chain 'K' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'K' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'L' and resid 63 through 64 removed outlier: 7.942A pdb=" N TYR L 64 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR L 23 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA L 142 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL L 267 " --> pdb=" O MET L 306 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL L 308 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU L 269 " --> pdb=" O VAL L 308 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU L 181 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN L 270 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE L 183 " --> pdb=" O GLN L 270 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL L 234 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR L 205 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL L 236 " --> pdb=" O THR L 205 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER L 207 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU L 238 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS L 209 " --> pdb=" O LEU L 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 272 through 274 Processing sheet with id=AA5, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'M' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'M' and resid 473 through 477 Processing sheet with id=AA8, first strand: chain 'M' and resid 504 through 506 removed outlier: 6.870A pdb=" N LEU M 504 " --> pdb=" O ILE M 539 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN M 541 " --> pdb=" O LEU M 504 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR M 506 " --> pdb=" O GLN M 541 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASP M 543 " --> pdb=" O TYR M 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'O' and resid 262 through 263 Processing sheet with id=AB2, first strand: chain 'O' and resid 272 through 274 Processing sheet with id=AB3, first strand: chain 'P' and resid 245 through 246 673 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 4.41 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: 2.190 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.410 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.840 ------------------------------------------------------------------------------- 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 14909 Z= 0.349 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 *********************** 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 : 1.899 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: 0.2693 time to fit residues: 89.9735 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 : 1.842 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.0990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14909 Z= 0.245 Angle : 0.577 7.000 20184 Z= 0.315 Chirality : 0.041 0.162 2236 Planarity : 0.004 0.042 2620 Dihedral : 5.230 51.934 2039 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % 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: -0.27 (0.18), residues: 1877 helix: 0.66 (0.17), residues: 939 sheet: -0.26 (0.56), residues: 91 loop : -1.10 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 966 HIS 0.014 0.001 HIS M 479 PHE 0.013 0.001 PHE K1269 TYR 0.024 0.002 TYR O 556 ARG 0.006 0.000 ARG O 564 *********************** 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 223 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: L 306 MET cc_start: 0.9041 (ttp) cc_final: 0.8822 (ttm) REVERT: M 323 GLU cc_start: 0.8316 (tt0) cc_final: 0.8081 (tt0) REVERT: M 343 ILE cc_start: 0.9035 (tp) cc_final: 0.8749 (tp) REVERT: M 373 SER cc_start: 0.9250 (p) cc_final: 0.8932 (t) REVERT: M 374 ASP cc_start: 0.8291 (t0) cc_final: 0.7983 (m-30) REVERT: M 560 MET cc_start: 0.8445 (tpt) cc_final: 0.8012 (tpt) REVERT: N 267 GLN cc_start: 0.8438 (pt0) cc_final: 0.8128 (pp30) REVERT: N 307 ASP cc_start: 0.8549 (t70) cc_final: 0.8335 (t0) REVERT: N 326 TYR cc_start: 0.8781 (m-80) cc_final: 0.8391 (m-80) REVERT: N 358 GLN cc_start: 0.7206 (tp-100) cc_final: 0.6801 (tm-30) REVERT: N 373 TYR cc_start: 0.8814 (m-10) cc_final: 0.8306 (m-10) REVERT: P 220 ILE cc_start: 0.8230 (mm) cc_final: 0.7984 (mp) REVERT: P 268 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8973 (mm-30) REVERT: P 270 GLU cc_start: 0.8953 (pm20) cc_final: 0.8321 (pm20) REVERT: P 394 TYR cc_start: 0.7541 (t80) cc_final: 0.7317 (t80) outliers start: 14 outliers final: 10 residues processed: 216 average time/residue: 0.2458 time to fit residues: 82.4759 Evaluate side-chains 201 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 O residue 319 LEU 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 94 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 M 479 HIS N 223 GLN ** O 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14909 Z= 0.205 Angle : 0.514 7.922 20184 Z= 0.279 Chirality : 0.040 0.147 2236 Planarity : 0.004 0.069 2620 Dihedral : 4.859 45.969 2039 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.29 % Allowed : 9.90 % Favored : 88.81 % 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: 0.18 (0.19), residues: 1877 helix: 1.08 (0.17), residues: 951 sheet: -0.33 (0.57), residues: 92 loop : -0.92 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 966 HIS 0.012 0.001 HIS M 479 PHE 0.022 0.001 PHE M 262 TYR 0.020 0.001 TYR M 356 ARG 0.006 0.000 ARG O 564 *********************** 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 218 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: K 961 ASN cc_start: 0.7826 (t0) cc_final: 0.7626 (t0) REVERT: M 343 ILE cc_start: 0.9079 (tp) cc_final: 0.8839 (tp) REVERT: M 373 SER cc_start: 0.9209 (p) cc_final: 0.8856 (t) REVERT: M 416 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8826 (mt) REVERT: M 560 MET cc_start: 0.8459 (tpt) cc_final: 0.7998 (tpt) REVERT: N 267 GLN cc_start: 0.8416 (pt0) cc_final: 0.8080 (pp30) REVERT: N 307 ASP cc_start: 0.8494 (t70) cc_final: 0.8259 (t0) REVERT: N 326 TYR cc_start: 0.8715 (m-80) cc_final: 0.8360 (m-80) REVERT: N 358 GLN cc_start: 0.7346 (tp-100) cc_final: 0.6796 (tm-30) REVERT: O 556 TYR cc_start: 0.9001 (t80) cc_final: 0.8602 (t80) REVERT: O 560 MET cc_start: 0.8608 (mpp) cc_final: 0.8129 (mpp) REVERT: P 220 ILE cc_start: 0.8301 (mm) cc_final: 0.8052 (mp) REVERT: P 223 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7613 (tm-30) REVERT: P 268 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8991 (mm-30) REVERT: P 270 GLU cc_start: 0.8979 (pm20) cc_final: 0.8292 (pm20) REVERT: P 288 TYR cc_start: 0.9234 (t80) cc_final: 0.8806 (t80) REVERT: P 401 MET cc_start: 0.4341 (mmm) cc_final: 0.4028 (mmm) outliers start: 19 outliers final: 14 residues processed: 211 average time/residue: 0.2445 time to fit residues: 79.3047 Evaluate side-chains 202 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 416 ILE 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 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 168 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 114 optimal weight: 0.0980 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 M 479 HIS N 223 GLN O 583 GLN P 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14909 Z= 0.204 Angle : 0.497 8.633 20184 Z= 0.265 Chirality : 0.039 0.149 2236 Planarity : 0.004 0.069 2620 Dihedral : 4.564 34.183 2039 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.36 % Allowed : 12.47 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 948 sheet: -0.19 (0.58), residues: 91 loop : -0.82 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 966 HIS 0.016 0.001 HIS M 479 PHE 0.021 0.001 PHE M 262 TYR 0.016 0.001 TYR M 356 ARG 0.005 0.000 ARG O 564 *********************** 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 213 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: N 242 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8563 (t0) REVERT: N 267 GLN cc_start: 0.8406 (pt0) cc_final: 0.8076 (pp30) REVERT: N 307 ASP cc_start: 0.8470 (t70) cc_final: 0.8231 (t0) REVERT: N 354 LEU cc_start: 0.9034 (tp) cc_final: 0.8712 (tt) REVERT: N 358 GLN cc_start: 0.7606 (tp-100) cc_final: 0.6789 (tm-30) REVERT: N 373 TYR cc_start: 0.8672 (m-10) cc_final: 0.7793 (m-10) REVERT: O 556 TYR cc_start: 0.9015 (t80) cc_final: 0.8563 (t80) REVERT: O 560 MET cc_start: 0.8323 (mpp) cc_final: 0.7957 (mpp) REVERT: P 223 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7392 (tm-30) REVERT: P 270 GLU cc_start: 0.8980 (pm20) cc_final: 0.8699 (pm20) REVERT: P 288 TYR cc_start: 0.9209 (t80) cc_final: 0.9009 (t80) REVERT: P 401 MET cc_start: 0.4142 (mmm) cc_final: 0.3806 (mmm) outliers start: 20 outliers final: 14 residues processed: 203 average time/residue: 0.2501 time to fit residues: 78.6068 Evaluate side-chains 197 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 M residue 324 SER Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 242 ASP Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1221 HIS N 223 GLN P 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14909 Z= 0.386 Angle : 0.574 6.943 20184 Z= 0.306 Chirality : 0.042 0.159 2236 Planarity : 0.004 0.075 2620 Dihedral : 4.783 29.210 2039 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.90 % Allowed : 13.97 % Favored : 84.14 % 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: 0.30 (0.19), residues: 1877 helix: 1.20 (0.17), residues: 947 sheet: -0.40 (0.57), residues: 97 loop : -0.87 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 966 HIS 0.004 0.001 HIS N 330 PHE 0.018 0.002 PHE K 819 TYR 0.018 0.002 TYR K 675 ARG 0.006 0.001 ARG O 564 *********************** 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 211 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: N 267 GLN cc_start: 0.8449 (pt0) cc_final: 0.8102 (pp30) REVERT: N 307 ASP cc_start: 0.8516 (t70) cc_final: 0.8274 (t0) REVERT: N 358 GLN cc_start: 0.7957 (tp-100) cc_final: 0.6789 (tm-30) REVERT: N 373 TYR cc_start: 0.8752 (m-10) cc_final: 0.8003 (m-10) REVERT: O 556 TYR cc_start: 0.9081 (t80) cc_final: 0.8806 (t80) REVERT: P 270 GLU cc_start: 0.8979 (pm20) cc_final: 0.8719 (pm20) REVERT: P 288 TYR cc_start: 0.9227 (t80) cc_final: 0.9002 (t80) outliers start: 28 outliers final: 20 residues processed: 201 average time/residue: 0.2435 time to fit residues: 75.2959 Evaluate side-chains 196 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 269 LEU Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 452 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 300 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 547 ILE Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 373 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14909 Z= 0.174 Angle : 0.493 7.167 20184 Z= 0.263 Chirality : 0.039 0.168 2236 Planarity : 0.004 0.075 2620 Dihedral : 4.433 24.774 2038 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.83 % Allowed : 14.92 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.19), residues: 1877 helix: 1.46 (0.17), residues: 949 sheet: -0.22 (0.60), residues: 91 loop : -0.80 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 PHE 0.017 0.001 PHE M 262 TYR 0.015 0.001 TYR M 356 ARG 0.006 0.000 ARG P 247 *********************** 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 215 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.809 Fit side-chains REVERT: K 792 ASP cc_start: 0.8289 (t70) cc_final: 0.7969 (t70) REVERT: M 416 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8904 (mt) REVERT: N 267 GLN cc_start: 0.8406 (pt0) cc_final: 0.8075 (pp30) REVERT: N 307 ASP cc_start: 0.8456 (t70) cc_final: 0.8221 (t0) REVERT: N 354 LEU cc_start: 0.9053 (tp) cc_final: 0.8769 (tt) REVERT: N 358 GLN cc_start: 0.7930 (tp-100) cc_final: 0.6822 (tm-30) REVERT: N 373 TYR cc_start: 0.8619 (m-10) cc_final: 0.7898 (m-10) REVERT: O 560 MET cc_start: 0.8654 (mpp) cc_final: 0.8144 (mpp) REVERT: P 270 GLU cc_start: 0.8955 (pm20) cc_final: 0.8734 (pm20) REVERT: P 288 TYR cc_start: 0.9218 (t80) cc_final: 0.8924 (t80) outliers start: 27 outliers final: 20 residues processed: 205 average time/residue: 0.2323 time to fit residues: 74.2686 Evaluate side-chains 198 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 416 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 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 175 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14909 Z= 0.184 Angle : 0.496 7.159 20184 Z= 0.263 Chirality : 0.039 0.176 2236 Planarity : 0.004 0.066 2620 Dihedral : 4.326 24.280 2038 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.03 % Allowed : 15.46 % Favored : 82.51 % 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: 0.66 (0.19), residues: 1877 helix: 1.59 (0.17), residues: 943 sheet: -0.20 (0.60), residues: 91 loop : -0.82 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 966 HIS 0.003 0.001 HIS K 930 PHE 0.014 0.001 PHE M 262 TYR 0.030 0.001 TYR O 556 ARG 0.007 0.000 ARG O 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.910 Fit side-chains REVERT: K 792 ASP cc_start: 0.8269 (t70) cc_final: 0.7831 (t0) REVERT: M 416 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8882 (mt) REVERT: N 267 GLN cc_start: 0.8382 (pt0) cc_final: 0.8045 (pp30) REVERT: N 307 ASP cc_start: 0.8414 (t70) cc_final: 0.8177 (t0) REVERT: N 354 LEU cc_start: 0.9060 (tp) cc_final: 0.8800 (tt) REVERT: N 358 GLN cc_start: 0.8011 (tp-100) cc_final: 0.6725 (tm-30) REVERT: N 373 TYR cc_start: 0.8623 (m-10) cc_final: 0.7901 (m-10) REVERT: P 270 GLU cc_start: 0.8952 (pm20) cc_final: 0.8730 (pm20) REVERT: P 288 TYR cc_start: 0.9209 (t80) cc_final: 0.8878 (t80) REVERT: P 401 MET cc_start: 0.3257 (mmm) cc_final: 0.2942 (mmt) outliers start: 30 outliers final: 22 residues processed: 206 average time/residue: 0.2616 time to fit residues: 84.8752 Evaluate side-chains 198 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 416 ILE Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 L 31 ASN N 223 GLN O 329 GLN O 583 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14909 Z= 0.168 Angle : 0.491 7.461 20184 Z= 0.259 Chirality : 0.039 0.178 2236 Planarity : 0.003 0.061 2620 Dihedral : 4.211 24.501 2038 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.63 % Allowed : 16.68 % Favored : 81.69 % 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: 0.76 (0.19), residues: 1877 helix: 1.68 (0.17), residues: 943 sheet: -0.21 (0.59), residues: 91 loop : -0.77 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.008 0.000 ARG O 564 *********************** 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 215 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.782 Fit side-chains REVERT: K 792 ASP cc_start: 0.8243 (t70) cc_final: 0.7840 (t0) REVERT: K 987 ASP cc_start: 0.8110 (m-30) cc_final: 0.7886 (m-30) REVERT: M 416 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8857 (mt) REVERT: N 267 GLN cc_start: 0.8364 (pt0) cc_final: 0.8026 (pp30) REVERT: N 307 ASP cc_start: 0.8401 (t70) cc_final: 0.8157 (t0) REVERT: N 353 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: N 354 LEU cc_start: 0.9028 (tp) cc_final: 0.8809 (tt) REVERT: N 358 GLN cc_start: 0.8010 (tp-100) cc_final: 0.6670 (tm-30) REVERT: N 373 TYR cc_start: 0.8586 (m-10) cc_final: 0.7882 (m-10) REVERT: P 223 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7626 (tm-30) REVERT: P 264 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7817 (mm-30) REVERT: P 270 GLU cc_start: 0.8920 (pm20) cc_final: 0.8709 (pm20) REVERT: P 288 TYR cc_start: 0.9190 (t80) cc_final: 0.8858 (t80) REVERT: P 373 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7310 (p90) outliers start: 24 outliers final: 19 residues processed: 206 average time/residue: 0.2460 time to fit residues: 79.2634 Evaluate side-chains 205 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 407 ILE Chi-restraints excluded: chain M residue 416 ILE Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 235 ASP 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 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 173 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 329 GLN O 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14909 Z= 0.259 Angle : 0.528 7.488 20184 Z= 0.280 Chirality : 0.040 0.171 2236 Planarity : 0.004 0.059 2620 Dihedral : 4.341 24.132 2038 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.90 % Allowed : 16.95 % Favored : 81.15 % 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: 0.66 (0.19), residues: 1877 helix: 1.61 (0.17), residues: 941 sheet: -0.43 (0.55), residues: 97 loop : -0.81 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 PHE 0.012 0.001 PHE K 819 TYR 0.031 0.001 TYR O 556 ARG 0.009 0.000 ARG O 564 *********************** 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 210 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.775 Fit side-chains REVERT: K 792 ASP cc_start: 0.8283 (t70) cc_final: 0.7670 (t0) REVERT: M 416 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8919 (mt) REVERT: N 267 GLN cc_start: 0.8402 (pt0) cc_final: 0.8077 (pp30) REVERT: N 307 ASP cc_start: 0.8466 (t70) cc_final: 0.8211 (t0) REVERT: N 335 ILE cc_start: 0.9081 (mm) cc_final: 0.8812 (mt) REVERT: N 353 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: N 354 LEU cc_start: 0.9051 (tp) cc_final: 0.8788 (tt) REVERT: N 373 TYR cc_start: 0.8654 (m-10) cc_final: 0.7955 (m-10) REVERT: P 223 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7646 (tm-30) REVERT: P 236 TRP cc_start: 0.8990 (t60) cc_final: 0.8524 (t60) REVERT: P 270 GLU cc_start: 0.8958 (pm20) cc_final: 0.8750 (pm20) REVERT: P 288 TYR cc_start: 0.9214 (t80) cc_final: 0.8906 (t80) outliers start: 28 outliers final: 22 residues processed: 201 average time/residue: 0.2648 time to fit residues: 83.2056 Evaluate side-chains 201 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 957 VAL Chi-restraints excluded: chain K residue 993 ASP Chi-restraints excluded: chain K residue 1215 ILE Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 416 ILE Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 561 VAL Chi-restraints excluded: chain N residue 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 108 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 329 GLN O 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14909 Z= 0.177 Angle : 0.507 7.877 20184 Z= 0.269 Chirality : 0.039 0.180 2236 Planarity : 0.004 0.057 2620 Dihedral : 4.249 23.891 2038 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.63 % Allowed : 17.22 % Favored : 81.15 % 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: 1.67 (0.17), residues: 943 sheet: -0.37 (0.57), residues: 91 loop : -0.79 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 966 HIS 0.003 0.001 HIS M 480 PHE 0.011 0.001 PHE M 262 TYR 0.019 0.001 TYR L 176 ARG 0.010 0.000 ARG O 564 ********************** 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 207 residues out of total 1743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.698 Fit side-chains REVERT: K 792 ASP cc_start: 0.8282 (t70) cc_final: 0.7639 (t0) REVERT: K 987 ASP cc_start: 0.8102 (m-30) cc_final: 0.7879 (m-30) REVERT: M 416 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8880 (mt) REVERT: M 564 ARG cc_start: 0.8536 (mmt180) cc_final: 0.8269 (mmp-170) REVERT: N 267 GLN cc_start: 0.8360 (pt0) cc_final: 0.8002 (pp30) REVERT: N 307 ASP cc_start: 0.8411 (t70) cc_final: 0.8169 (t0) REVERT: N 335 ILE cc_start: 0.9066 (mm) cc_final: 0.8782 (mt) REVERT: N 353 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: N 354 LEU cc_start: 0.9028 (tp) cc_final: 0.8795 (tt) REVERT: N 373 TYR cc_start: 0.8574 (m-10) cc_final: 0.7868 (m-10) REVERT: P 236 TRP cc_start: 0.8974 (t60) cc_final: 0.8523 (t60) REVERT: P 288 TYR cc_start: 0.9186 (t80) cc_final: 0.8873 (t80) outliers start: 24 outliers final: 21 residues processed: 198 average time/residue: 0.2482 time to fit residues: 77.2887 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 : 1.822 ------------------------------------------------------------------------------- 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 375 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 416 ILE Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 487 VAL Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain 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 45 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 131 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104898 restraints weight = 27856.661| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.37 r_work: 0.3301 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14909 Z= 0.195 Angle : 0.514 7.799 20184 Z= 0.273 Chirality : 0.039 0.169 2236 Planarity : 0.004 0.057 2620 Dihedral : 4.190 23.586 2038 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.97 % Allowed : 17.15 % Favored : 80.88 % 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: 0.76 (0.19), residues: 1877 helix: 1.71 (0.17), residues: 937 sheet: -0.39 (0.57), residues: 91 loop : -0.77 (0.21), residues: 849 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 0.011 0.001 PHE M 262 TYR 0.037 0.001 TYR O 556 ARG 0.010 0.000 ARG O 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.03 seconds wall clock time: 54 minutes 29.37 seconds (3269.37 seconds total)