Starting phenix.real_space_refine on Sun May 25 10:53:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd4_37124/05_2025/8kd4_37124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd4_37124/05_2025/8kd4_37124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd4_37124/05_2025/8kd4_37124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd4_37124/05_2025/8kd4_37124.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd4_37124/05_2025/8kd4_37124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd4_37124/05_2025/8kd4_37124.cif" } resolution = 2.93 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= 0.002 sd= 0.011 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 Zn 1 6.06 5 P 328 5.49 5 S 91 5.16 5 C 16152 2.51 5 N 4810 2.21 5 O 5682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27064 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1883 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "F" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1639 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 2 Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2611 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 3 Chain: "G" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.71, per 1000 atoms: 0.58 Number of scatterers: 27064 At special positions: 0 Unit cell: (138.45, 161.88, 186.02, 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 S 91 16.00 P 328 15.00 O 5682 8.00 N 4810 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 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: 6.29 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4742 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 17 sheets defined 58.2% alpha, 3.5% beta 140 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 11.04 Creating SS restraints... Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 Processing helix chain 'D' and resid 273 through 293 removed outlier: 4.419A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 317 removed outlier: 4.456A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 4.027A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.995A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 4.034A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.370A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.574A pdb=" N VAL F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.500A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 328 through 343 removed outlier: 4.186A pdb=" N LEU F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Proline residue: F 339 - end of helix removed outlier: 3.735A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 367 removed outlier: 3.957A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.544A pdb=" N LEU O 70 " --> pdb=" O PRO O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.705A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.025A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.344A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.687A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.542A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 120 Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.628A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.619A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 25 through 29 removed outlier: 3.807A pdb=" N ILE T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 3.824A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.039A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.524A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.527A pdb=" N VAL V 38 " --> pdb=" O TYR V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.716A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.067A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.202A pdb=" N TYR A 32 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.306A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 4.018A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.502A pdb=" N ASN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 94' Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.548A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.689A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.736A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.866A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.751A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.529A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.601A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.711A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.945A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.604A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.896A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.884A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 3.923A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 removed outlier: 4.290A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.606A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.199A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 4.059A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 4.039A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.877A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1185 Processing helix chain 'B' and resid 1202 through 1216 Processing helix chain 'B' and resid 1221 through 1230 Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.849A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1236 through 1240' Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.596A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.518A pdb=" N TYR B1286 " --> pdb=" O ASP B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1307 through 1309 No H-bonds generated for 'chain 'B' and resid 1307 through 1309' Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.855A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 308 Processing helix chain 'E' and resid 321 through 330 removed outlier: 3.734A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.479A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 360 removed outlier: 4.162A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.503A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 407 " --> pdb=" O ASP E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'G' and resid 322 through 326 removed outlier: 3.597A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.995A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 541 through 569 Processing sheet with id=AA1, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.704A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.076A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.339A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.826A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.010A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'A' and resid 62 through 64 removed outlier: 5.900A pdb=" N VAL A 21 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 977 through 978 removed outlier: 3.946A pdb=" N PHE B 977 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B1312 " --> pdb=" O PHE B 977 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 272 through 274 Processing sheet with id=AB6, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AB7, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AB8, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.602A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 983 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 16.86 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6715 1.34 - 1.46: 7613 1.46 - 1.58: 13159 1.58 - 1.70: 654 1.70 - 1.82: 144 Bond restraints: 28285 Sorted by residual: bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.708 -0.216 5.00e-02 4.00e+02 1.86e+01 bond pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.40e-02 5.10e+03 1.32e+01 bond pdb=" CG PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.503 1.402 0.101 3.40e-02 8.65e+02 8.76e+00 bond pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.00e+00 bond pdb=" C ASN B1004 " pdb=" N PRO B1005 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 7.94e+00 ... (remaining 28280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 39243 3.41 - 6.82: 273 6.82 - 10.24: 39 10.24 - 13.65: 18 13.65 - 17.06: 6 Bond angle restraints: 39579 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 96.38 15.62 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N PRO D 319 " pdb=" CD PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 103.20 93.25 9.95 1.50e+00 4.44e-01 4.40e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.58 -11.48 2.00e+00 2.50e-01 3.29e+01 angle pdb=" CA GLU E 507 " pdb=" CB GLU E 507 " pdb=" CG GLU E 507 " ideal model delta sigma weight residual 114.10 124.92 -10.82 2.00e+00 2.50e-01 2.93e+01 angle pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " pdb=" CG LEU F 297 " ideal model delta sigma weight residual 116.30 133.36 -17.06 3.50e+00 8.16e-02 2.38e+01 ... (remaining 39574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 14091 35.18 - 70.36: 2029 70.36 - 105.54: 47 105.54 - 140.72: 2 140.72 - 175.89: 1 Dihedral angle restraints: 16170 sinusoidal: 8831 harmonic: 7339 Sorted by residual: dihedral pdb=" CA LEU B1184 " pdb=" C LEU B1184 " pdb=" N ASP B1185 " pdb=" CA ASP B1185 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET D 347 " pdb=" C MET D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4131 0.086 - 0.173: 228 0.173 - 0.259: 6 0.259 - 0.345: 4 0.345 - 0.432: 1 Chirality restraints: 4370 Sorted by residual: chirality pdb=" CG LEU B 825 " pdb=" CB LEU B 825 " pdb=" CD1 LEU B 825 " pdb=" CD2 LEU B 825 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" C PRO D 319 " pdb=" CB PRO D 319 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL F 364 " pdb=" CA VAL F 364 " pdb=" CG1 VAL F 364 " pdb=" CG2 VAL F 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4367 not shown) Planarity restraints: 3885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.059 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO D 319 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.018 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 775 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 492 " 0.015 2.00e-02 2.50e+03 1.76e-02 7.75e+00 pdb=" CG TRP E 492 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP E 492 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 492 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 492 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 492 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 492 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 492 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 492 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 492 " -0.001 2.00e-02 2.50e+03 ... (remaining 3882 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 236 2.60 - 3.17: 21330 3.17 - 3.75: 48536 3.75 - 4.32: 62990 4.32 - 4.90: 95594 Nonbonded interactions: 228686 Sorted by model distance: nonbonded pdb=" CD2 LEU B 883 " pdb=" OG1 THR B 890 " model vdw 2.023 3.460 nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.036 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.122 3.880 nonbonded pdb=" OG SER A 123 " pdb=" OD2 ASP A 165 " model vdw 2.222 3.040 nonbonded pdb=" OG SER D 392 " pdb=" OE1 GLU A 156 " model vdw 2.227 3.040 ... (remaining 228681 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 'D' and (resid 11 through 24 or resid 80 through 112 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 37 through 133) selection = (chain 'S' and resid 37 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } 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: 11.150 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: 0.040 Extract box with map and model: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 76.630 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.150 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.004 0.216 28287 Z= 0.181 Angle : 0.809 17.062 39581 Z= 0.429 Chirality : 0.042 0.432 4370 Planarity : 0.005 0.095 3885 Dihedral : 24.504 175.895 11425 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 0.59 % Allowed : 32.67 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.15), residues: 2447 helix: -0.45 (0.13), residues: 1312 sheet: 0.18 (0.64), residues: 85 loop : -1.70 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 775 HIS 0.011 0.001 HIS B 785 PHE 0.020 0.001 PHE B 708 TYR 0.038 0.002 TYR A 176 ARG 0.021 0.001 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.15073 ( 1351) hydrogen bonds : angle 5.61158 ( 3631) metal coordination : bond 0.00067 ( 1) SS BOND : bond 0.00050 ( 1) SS BOND : angle 1.11361 ( 2) covalent geometry : bond 0.00388 (28285) covalent geometry : angle 0.80882 (39579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 354 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 ILE cc_start: 0.8233 (pt) cc_final: 0.7910 (pt) REVERT: D 349 LEU cc_start: 0.8262 (mm) cc_final: 0.8057 (tp) REVERT: F 95 ASP cc_start: 0.3396 (p0) cc_final: 0.2587 (t70) REVERT: F 233 VAL cc_start: 0.2420 (t) cc_final: 0.2121 (m) REVERT: F 234 ASP cc_start: 0.5247 (t70) cc_final: 0.4881 (m-30) REVERT: F 296 MET cc_start: 0.3920 (mmm) cc_final: 0.3703 (mpp) REVERT: U 74 LYS cc_start: 0.7930 (mptp) cc_final: 0.7626 (mptt) REVERT: U 90 ASP cc_start: 0.7919 (t0) cc_final: 0.7697 (t0) REVERT: U 95 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7458 (tttt) REVERT: A 316 ARG cc_start: 0.7054 (mtm110) cc_final: 0.6845 (ttp-110) REVERT: B 670 GLU cc_start: 0.7535 (mp0) cc_final: 0.7122 (pt0) REVERT: B 684 GLU cc_start: 0.8307 (tp30) cc_final: 0.8009 (tp30) REVERT: B 799 ARG cc_start: 0.7430 (mmm160) cc_final: 0.7116 (mtt-85) REVERT: B 813 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6522 (mm-30) REVERT: B 907 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7867 (pmm-80) REVERT: E 545 ASN cc_start: 0.7508 (t0) cc_final: 0.7273 (t0) REVERT: G 560 MET cc_start: 0.8508 (mpt) cc_final: 0.7893 (ptp) REVERT: G 565 LYS cc_start: 0.6179 (mptt) cc_final: 0.5907 (tptp) outliers start: 13 outliers final: 8 residues processed: 361 average time/residue: 1.1631 time to fit residues: 498.2243 Evaluate side-chains 319 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 310 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 886 HIS Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 1306 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN O 68 GLN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS E 314 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102306 restraints weight = 58726.993| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.03 r_work: 0.3460 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 28287 Z= 0.204 Angle : 0.627 13.960 39581 Z= 0.339 Chirality : 0.039 0.200 4370 Planarity : 0.004 0.051 3885 Dihedral : 26.650 177.505 6328 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.00 % Allowed : 26.63 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.16), residues: 2447 helix: 0.41 (0.14), residues: 1356 sheet: 0.28 (0.59), residues: 96 loop : -1.50 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 775 HIS 0.010 0.001 HIS T 75 PHE 0.018 0.002 PHE E 341 TYR 0.036 0.002 TYR P 88 ARG 0.013 0.001 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1351) hydrogen bonds : angle 3.90830 ( 3631) metal coordination : bond 0.00337 ( 1) SS BOND : bond 0.00536 ( 1) SS BOND : angle 1.82273 ( 2) covalent geometry : bond 0.00458 (28285) covalent geometry : angle 0.62665 (39579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 375 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 275 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: D 278 LEU cc_start: 0.8308 (tp) cc_final: 0.8068 (tp) REVERT: D 341 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5899 (pp) REVERT: F 95 ASP cc_start: 0.3210 (p0) cc_final: 0.2539 (t70) REVERT: F 233 VAL cc_start: 0.2783 (t) cc_final: 0.2527 (m) REVERT: F 234 ASP cc_start: 0.5503 (t70) cc_final: 0.4848 (m-30) REVERT: F 256 MET cc_start: 0.1802 (OUTLIER) cc_final: 0.1230 (pp-130) REVERT: O 129 ARG cc_start: 0.8414 (tpt90) cc_final: 0.8171 (tpt90) REVERT: P 53 GLU cc_start: 0.8638 (tp30) cc_final: 0.8436 (tp30) REVERT: R 39 TYR cc_start: 0.8630 (t80) cc_final: 0.8304 (t80) REVERT: R 46 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7688 (m170) REVERT: R 110 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: R 113 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8271 (ptpp) REVERT: T 91 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8877 (tttt) REVERT: U 95 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8697 (ttmm) REVERT: V 61 SER cc_start: 0.9205 (t) cc_final: 0.9002 (m) REVERT: V 105 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8340 (mttp) REVERT: A 47 MET cc_start: 0.7055 (ptt) cc_final: 0.6849 (ptt) REVERT: A 88 ARG cc_start: 0.8400 (mtm110) cc_final: 0.7996 (mtm180) REVERT: A 165 ASP cc_start: 0.8260 (p0) cc_final: 0.8024 (p0) REVERT: A 263 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: B 684 GLU cc_start: 0.8601 (tp30) cc_final: 0.8343 (tp30) REVERT: B 755 TYR cc_start: 0.6761 (m-10) cc_final: 0.6462 (m-10) REVERT: B 817 TYR cc_start: 0.8436 (m-80) cc_final: 0.7955 (m-80) REVERT: B 825 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (mm) REVERT: B 910 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7604 (tmt170) REVERT: B 918 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 1136 PHE cc_start: 0.5247 (OUTLIER) cc_final: 0.4821 (m-10) REVERT: B 1187 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7183 (mm) REVERT: B 1257 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7510 (mtm) REVERT: E 271 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.7242 (m) REVERT: E 375 GLU cc_start: 0.8851 (pm20) cc_final: 0.8576 (pm20) REVERT: E 512 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6052 (pt) REVERT: E 549 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8316 (t80) outliers start: 111 outliers final: 34 residues processed: 437 average time/residue: 1.3175 time to fit residues: 671.4434 Evaluate side-chains 362 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 44 GLN Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 886 HIS Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN O 68 GLN S 108 ASN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS B1221 HIS B1254 HIS ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN E 410 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.133769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101898 restraints weight = 58088.169| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.14 r_work: 0.3340 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28287 Z= 0.162 Angle : 0.586 13.071 39581 Z= 0.317 Chirality : 0.037 0.187 4370 Planarity : 0.004 0.058 3885 Dihedral : 26.607 176.051 6314 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.96 % Allowed : 26.86 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.17), residues: 2447 helix: 0.79 (0.14), residues: 1351 sheet: 0.41 (0.61), residues: 86 loop : -1.38 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 775 HIS 0.006 0.001 HIS A 43 PHE 0.018 0.001 PHE B 708 TYR 0.031 0.002 TYR B1145 ARG 0.021 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1351) hydrogen bonds : angle 3.77681 ( 3631) metal coordination : bond 0.00191 ( 1) SS BOND : bond 0.00413 ( 1) SS BOND : angle 1.45127 ( 2) covalent geometry : bond 0.00364 (28285) covalent geometry : angle 0.58603 (39579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 325 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 275 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6696 (mp10) REVERT: D 277 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: D 278 LEU cc_start: 0.8384 (tp) cc_final: 0.8166 (tp) REVERT: F 95 ASP cc_start: 0.3082 (p0) cc_final: 0.2454 (t70) REVERT: F 256 MET cc_start: 0.1120 (OUTLIER) cc_final: 0.0753 (pp-130) REVERT: F 270 GLU cc_start: 0.1271 (OUTLIER) cc_final: 0.0047 (pm20) REVERT: O 59 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: Q 56 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: R 39 TYR cc_start: 0.8586 (t80) cc_final: 0.8187 (t80) REVERT: R 46 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7787 (m170) REVERT: S 45 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8678 (p) REVERT: S 83 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: T 91 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8811 (tttt) REVERT: V 105 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8370 (mttp) REVERT: A 52 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 88 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7881 (mtm180) REVERT: A 252 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7611 (mm-30) REVERT: A 263 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: A 306 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8098 (tmm) REVERT: A 373 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.6535 (mpp) REVERT: B 684 GLU cc_start: 0.8464 (tp30) cc_final: 0.8115 (tp30) REVERT: B 817 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 825 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 910 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7586 (tmt170) REVERT: B 918 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: B 1016 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7506 (t80) REVERT: B 1136 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.4837 (m-10) REVERT: B 1222 GLN cc_start: 0.8052 (pt0) cc_final: 0.7842 (pm20) REVERT: B 1257 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: E 282 PHE cc_start: 0.6695 (m-80) cc_final: 0.6429 (m-80) REVERT: E 359 GLU cc_start: 0.7535 (pp20) cc_final: 0.7292 (pp20) REVERT: E 375 GLU cc_start: 0.8819 (pm20) cc_final: 0.8600 (pm20) REVERT: E 512 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6338 (pt) REVERT: E 549 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8265 (t80) outliers start: 110 outliers final: 38 residues processed: 392 average time/residue: 1.4600 time to fit residues: 661.6052 Evaluate side-chains 351 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 291 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain S residue 83 ARG Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 501 LYS Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 110 optimal weight: 0.0470 chunk 53 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 99 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.7692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN S 76 GLN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.130880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.098930 restraints weight = 57816.011| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.14 r_work: 0.3274 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28287 Z= 0.169 Angle : 0.584 13.700 39581 Z= 0.317 Chirality : 0.037 0.187 4370 Planarity : 0.004 0.054 3885 Dihedral : 26.628 176.861 6312 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.14 % Allowed : 26.95 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.17), residues: 2447 helix: 0.91 (0.14), residues: 1359 sheet: 0.02 (0.57), residues: 90 loop : -1.28 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 775 HIS 0.007 0.001 HIS A 189 PHE 0.025 0.001 PHE G 551 TYR 0.022 0.002 TYR B1145 ARG 0.014 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1351) hydrogen bonds : angle 3.67290 ( 3631) metal coordination : bond 0.00225 ( 1) SS BOND : bond 0.00382 ( 1) SS BOND : angle 1.43055 ( 2) covalent geometry : bond 0.00379 (28285) covalent geometry : angle 0.58365 (39579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 346 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 278 LEU cc_start: 0.8459 (tp) cc_final: 0.8227 (tp) REVERT: D 354 LEU cc_start: 0.8566 (tm) cc_final: 0.8336 (pp) REVERT: F 95 ASP cc_start: 0.3016 (p0) cc_final: 0.2402 (t70) REVERT: F 270 GLU cc_start: 0.1214 (OUTLIER) cc_final: 0.0130 (pm20) REVERT: Q 56 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: R 39 TYR cc_start: 0.8604 (t80) cc_final: 0.8206 (t80) REVERT: R 90 GLU cc_start: 0.8769 (mp0) cc_final: 0.8484 (mp0) REVERT: T 91 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8806 (tttt) REVERT: V 105 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8397 (mttp) REVERT: A 52 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 88 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8080 (mtm180) REVERT: A 189 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.5484 (p90) REVERT: A 204 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8103 (ttt) REVERT: A 211 TYR cc_start: 0.8191 (t80) cc_final: 0.7915 (t80) REVERT: A 252 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: A 373 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.6753 (mpp) REVERT: B 670 GLU cc_start: 0.7971 (mp0) cc_final: 0.7547 (pt0) REVERT: B 684 GLU cc_start: 0.8460 (tp30) cc_final: 0.8066 (tp30) REVERT: B 817 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: B 825 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8751 (mm) REVERT: B 881 ASP cc_start: 0.8600 (t0) cc_final: 0.7802 (p0) REVERT: B 910 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7581 (tmt170) REVERT: B 918 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: B 1016 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 1136 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5045 (m-10) REVERT: B 1187 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7136 (mm) REVERT: B 1289 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6717 (pt0) REVERT: E 282 PHE cc_start: 0.6835 (m-80) cc_final: 0.6555 (m-80) REVERT: E 359 GLU cc_start: 0.7584 (pp20) cc_final: 0.7338 (pp20) REVERT: E 375 GLU cc_start: 0.8800 (pm20) cc_final: 0.8560 (pm20) REVERT: E 512 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6635 (pt) REVERT: E 549 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8312 (t80) REVERT: E 556 TYR cc_start: 0.8283 (m-10) cc_final: 0.7786 (m-10) outliers start: 114 outliers final: 41 residues processed: 412 average time/residue: 1.3719 time to fit residues: 656.1752 Evaluate side-chains 354 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1248 SER Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 181 optimal weight: 0.0000 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN S 85 GLN T 25 ASN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 76 GLN A 382 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 GLN ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092974 restraints weight = 56353.559| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.05 r_work: 0.3150 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28287 Z= 0.242 Angle : 0.640 13.968 39581 Z= 0.348 Chirality : 0.041 0.237 4370 Planarity : 0.004 0.060 3885 Dihedral : 26.907 177.967 6312 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 5.09 % Allowed : 27.53 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.17), residues: 2447 helix: 0.76 (0.14), residues: 1352 sheet: -0.28 (0.56), residues: 90 loop : -1.20 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 775 HIS 0.009 0.001 HIS A 189 PHE 0.018 0.002 PHE B 708 TYR 0.024 0.002 TYR A 176 ARG 0.017 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1351) hydrogen bonds : angle 3.79506 ( 3631) metal coordination : bond 0.00314 ( 1) SS BOND : bond 0.00392 ( 1) SS BOND : angle 1.44034 ( 2) covalent geometry : bond 0.00550 (28285) covalent geometry : angle 0.64036 (39579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 333 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 275 GLN cc_start: 0.6902 (mm110) cc_final: 0.6254 (mp10) REVERT: F 24 GLU cc_start: 0.5023 (mt-10) cc_final: 0.4693 (mm-30) REVERT: F 95 ASP cc_start: 0.2827 (p0) cc_final: 0.2250 (t70) REVERT: F 270 GLU cc_start: 0.1165 (OUTLIER) cc_final: 0.0140 (pm20) REVERT: Q 56 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: R 90 GLU cc_start: 0.8812 (mp0) cc_final: 0.8598 (mp0) REVERT: T 91 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8824 (tttt) REVERT: V 105 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8526 (mttp) REVERT: A 52 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 88 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8202 (mtm180) REVERT: A 189 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6223 (p90) REVERT: A 252 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: A 316 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7898 (ptm-80) REVERT: A 373 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7111 (mpp) REVERT: B 670 GLU cc_start: 0.8078 (mp0) cc_final: 0.7099 (mp0) REVERT: B 817 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: B 825 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 910 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7691 (tmt170) REVERT: B 918 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: B 982 LYS cc_start: 0.7533 (mttt) cc_final: 0.7003 (mtmm) REVERT: B 1016 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7675 (t80) REVERT: B 1136 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5268 (m-10) REVERT: B 1187 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7183 (mm) REVERT: B 1289 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: E 262 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7218 (t80) REVERT: E 282 PHE cc_start: 0.6949 (m-80) cc_final: 0.6704 (m-80) REVERT: E 369 ARG cc_start: 0.8107 (pmm-80) cc_final: 0.7835 (mtm-85) REVERT: E 375 GLU cc_start: 0.8862 (pm20) cc_final: 0.8605 (pm20) REVERT: E 512 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7318 (pt) REVERT: E 548 LYS cc_start: 0.8258 (ptmt) cc_final: 0.8030 (pptt) REVERT: E 549 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8259 (t80) REVERT: E 556 TYR cc_start: 0.8410 (m-10) cc_final: 0.7974 (m-10) REVERT: G 548 LYS cc_start: 0.4345 (mmmt) cc_final: 0.3993 (mmmt) outliers start: 113 outliers final: 44 residues processed: 410 average time/residue: 1.4115 time to fit residues: 671.4469 Evaluate side-chains 362 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 120 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 243 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN F 82 GLN S 76 GLN T 25 ASN U 38 ASN V 46 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 76 GLN ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN B1289 GLN E 314 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.126055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.093514 restraints weight = 56336.665| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.15 r_work: 0.3172 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28287 Z= 0.179 Angle : 0.610 13.831 39581 Z= 0.329 Chirality : 0.038 0.193 4370 Planarity : 0.004 0.058 3885 Dihedral : 26.877 176.567 6312 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.06 % Allowed : 28.39 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.17), residues: 2447 helix: 0.85 (0.14), residues: 1360 sheet: -0.56 (0.55), residues: 90 loop : -1.13 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 261 HIS 0.008 0.001 HIS A 189 PHE 0.022 0.001 PHE B 708 TYR 0.021 0.001 TYR F 281 ARG 0.014 0.001 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1351) hydrogen bonds : angle 3.73727 ( 3631) metal coordination : bond 0.00251 ( 1) SS BOND : bond 0.00398 ( 1) SS BOND : angle 1.49363 ( 2) covalent geometry : bond 0.00404 (28285) covalent geometry : angle 0.60972 (39579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 330 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7974 (pp30) cc_final: 0.7696 (pm20) REVERT: D 107 MET cc_start: 0.5053 (tmm) cc_final: 0.4504 (pmm) REVERT: D 275 GLN cc_start: 0.6889 (mm110) cc_final: 0.6186 (mp10) REVERT: F 24 GLU cc_start: 0.5024 (mt-10) cc_final: 0.4676 (mm-30) REVERT: F 95 ASP cc_start: 0.2724 (p0) cc_final: 0.2154 (t70) REVERT: F 256 MET cc_start: 0.1579 (OUTLIER) cc_final: 0.1146 (pp-130) REVERT: F 270 GLU cc_start: 0.0991 (OUTLIER) cc_final: 0.0104 (pm20) REVERT: Q 56 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: R 90 GLU cc_start: 0.8781 (mp0) cc_final: 0.8560 (mp0) REVERT: T 91 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8879 (tttt) REVERT: V 105 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8507 (mttp) REVERT: A 52 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 97 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6226 (t80) REVERT: A 140 ASP cc_start: 0.7843 (t0) cc_final: 0.7332 (t0) REVERT: A 189 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6140 (p90) REVERT: A 204 MET cc_start: 0.8918 (tpp) cc_final: 0.8484 (ttt) REVERT: A 252 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: B 670 GLU cc_start: 0.8064 (mp0) cc_final: 0.7087 (mp0) REVERT: B 684 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 825 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 881 ASP cc_start: 0.8670 (t0) cc_final: 0.8203 (m-30) REVERT: B 910 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7722 (tmt170) REVERT: B 918 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: B 982 LYS cc_start: 0.7403 (mttt) cc_final: 0.6906 (mtmm) REVERT: B 1016 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 1136 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.5205 (m-10) REVERT: B 1289 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: E 262 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7208 (t80) REVERT: E 282 PHE cc_start: 0.6983 (m-80) cc_final: 0.6706 (m-80) REVERT: E 369 ARG cc_start: 0.8131 (pmm-80) cc_final: 0.7865 (mtm-85) REVERT: E 375 GLU cc_start: 0.8879 (pm20) cc_final: 0.8618 (pm20) REVERT: E 549 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: E 556 TYR cc_start: 0.8469 (m-10) cc_final: 0.8126 (m-10) REVERT: G 548 LYS cc_start: 0.4468 (mmmt) cc_final: 0.4120 (mmmt) outliers start: 90 outliers final: 40 residues processed: 392 average time/residue: 1.5063 time to fit residues: 678.0098 Evaluate side-chains 350 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 165 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN O 39 HIS S 76 GLN T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 76 GLN A 177 HIS ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 GLN E 410 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.125048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092628 restraints weight = 56159.231| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.12 r_work: 0.3146 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28287 Z= 0.194 Angle : 0.628 15.145 39581 Z= 0.337 Chirality : 0.039 0.192 4370 Planarity : 0.004 0.068 3885 Dihedral : 26.878 177.267 6312 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.78 % Allowed : 27.99 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.17), residues: 2447 helix: 0.84 (0.14), residues: 1367 sheet: -0.66 (0.55), residues: 90 loop : -1.10 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 261 HIS 0.008 0.001 HIS A 189 PHE 0.026 0.001 PHE E 341 TYR 0.023 0.002 TYR A 176 ARG 0.016 0.001 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 1351) hydrogen bonds : angle 3.71678 ( 3631) metal coordination : bond 0.00267 ( 1) SS BOND : bond 0.00364 ( 1) SS BOND : angle 1.41151 ( 2) covalent geometry : bond 0.00438 (28285) covalent geometry : angle 0.62780 (39579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 310 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: D 82 GLN cc_start: 0.8119 (pp30) cc_final: 0.7804 (pm20) REVERT: D 107 MET cc_start: 0.5044 (tmm) cc_final: 0.4591 (pmm) REVERT: D 275 GLN cc_start: 0.6887 (mm110) cc_final: 0.6210 (mp10) REVERT: D 295 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.7061 (m-40) REVERT: F 24 GLU cc_start: 0.5021 (mt-10) cc_final: 0.4623 (mm-30) REVERT: F 95 ASP cc_start: 0.2608 (p0) cc_final: 0.2058 (t70) REVERT: F 256 MET cc_start: 0.1591 (OUTLIER) cc_final: 0.1158 (pp-130) REVERT: F 270 GLU cc_start: 0.1083 (OUTLIER) cc_final: 0.0105 (pm20) REVERT: Q 56 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: R 32 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: S 42 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8244 (mtp-110) REVERT: T 91 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8841 (tttt) REVERT: V 105 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8520 (mttp) REVERT: A 52 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8203 (mp) REVERT: A 97 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6422 (t80) REVERT: A 140 ASP cc_start: 0.7898 (t0) cc_final: 0.7369 (t0) REVERT: A 165 ASP cc_start: 0.8324 (p0) cc_final: 0.7977 (p0) REVERT: A 189 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6314 (p90) REVERT: A 252 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: A 263 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: A 316 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7992 (ptm-80) REVERT: B 670 GLU cc_start: 0.8087 (mp0) cc_final: 0.7115 (mp0) REVERT: B 684 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 765 MET cc_start: 0.5716 (mmt) cc_final: 0.4797 (ppp) REVERT: B 799 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7040 (mtt-85) REVERT: B 811 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8241 (tt0) REVERT: B 825 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8761 (mm) REVERT: B 881 ASP cc_start: 0.8670 (t0) cc_final: 0.8204 (m-30) REVERT: B 910 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7704 (tmt170) REVERT: B 918 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: B 982 LYS cc_start: 0.7386 (mttt) cc_final: 0.6893 (mtmm) REVERT: B 1014 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 1016 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 1136 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5227 (m-10) REVERT: B 1160 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: B 1187 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 1289 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6886 (pt0) REVERT: E 262 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7213 (t80) REVERT: E 282 PHE cc_start: 0.7007 (m-80) cc_final: 0.6549 (m-80) REVERT: E 375 GLU cc_start: 0.8889 (pm20) cc_final: 0.8622 (pm20) REVERT: E 556 TYR cc_start: 0.8491 (m-10) cc_final: 0.8055 (m-10) REVERT: G 548 LYS cc_start: 0.4472 (mmmt) cc_final: 0.4095 (mmmt) outliers start: 106 outliers final: 47 residues processed: 383 average time/residue: 1.4299 time to fit residues: 632.7185 Evaluate side-chains 366 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 120 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN R 60 ASN T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 76 GLN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 GLN E 469 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.124710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092065 restraints weight = 56169.005| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.15 r_work: 0.3144 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28287 Z= 0.189 Angle : 0.636 14.422 39581 Z= 0.339 Chirality : 0.039 0.198 4370 Planarity : 0.004 0.051 3885 Dihedral : 26.868 176.732 6312 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.10 % Allowed : 28.75 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.17), residues: 2447 helix: 0.85 (0.14), residues: 1373 sheet: -0.75 (0.53), residues: 98 loop : -1.12 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 261 HIS 0.009 0.001 HIS A 43 PHE 0.036 0.001 PHE G 551 TYR 0.026 0.002 TYR P 88 ARG 0.013 0.001 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 1351) hydrogen bonds : angle 3.71940 ( 3631) metal coordination : bond 0.00266 ( 1) SS BOND : bond 0.00355 ( 1) SS BOND : angle 1.39160 ( 2) covalent geometry : bond 0.00429 (28285) covalent geometry : angle 0.63629 (39579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 312 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.8159 (pp30) cc_final: 0.7911 (pm20) REVERT: D 275 GLN cc_start: 0.6874 (mm110) cc_final: 0.6198 (mp10) REVERT: D 295 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: F 24 GLU cc_start: 0.5133 (mt-10) cc_final: 0.4707 (mm-30) REVERT: F 95 ASP cc_start: 0.2557 (p0) cc_final: 0.2043 (t70) REVERT: F 256 MET cc_start: 0.1625 (OUTLIER) cc_final: 0.1146 (pp-130) REVERT: F 270 GLU cc_start: 0.1092 (OUTLIER) cc_final: 0.0128 (pm20) REVERT: Q 56 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: S 42 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8340 (mtp-110) REVERT: S 131 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8633 (mtt180) REVERT: T 91 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8834 (tttt) REVERT: V 105 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8504 (mttp) REVERT: A 52 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 60 LYS cc_start: 0.6793 (mttm) cc_final: 0.6534 (ptpt) REVERT: A 88 ARG cc_start: 0.8445 (mtm110) cc_final: 0.7897 (mtm180) REVERT: A 97 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6381 (t80) REVERT: A 140 ASP cc_start: 0.7881 (t0) cc_final: 0.7454 (t0) REVERT: A 165 ASP cc_start: 0.8286 (p0) cc_final: 0.7906 (p0) REVERT: A 189 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6324 (p90) REVERT: A 252 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: A 316 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8017 (ptm-80) REVERT: B 670 GLU cc_start: 0.8080 (mp0) cc_final: 0.7112 (mp0) REVERT: B 684 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 755 TYR cc_start: 0.7753 (m-80) cc_final: 0.7505 (m-80) REVERT: B 765 MET cc_start: 0.5678 (mmt) cc_final: 0.4792 (ppp) REVERT: B 825 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8835 (mm) REVERT: B 881 ASP cc_start: 0.8678 (t0) cc_final: 0.8217 (m-30) REVERT: B 910 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7707 (tmt170) REVERT: B 918 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: B 982 LYS cc_start: 0.7380 (mttt) cc_final: 0.6884 (mtmm) REVERT: B 1016 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7893 (t80) REVERT: B 1136 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5262 (m-10) REVERT: B 1160 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 1187 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7269 (mm) REVERT: B 1289 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: E 262 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7228 (t80) REVERT: E 282 PHE cc_start: 0.7006 (m-80) cc_final: 0.6541 (m-80) REVERT: E 344 ASP cc_start: 0.7877 (m-30) cc_final: 0.7190 (OUTLIER) REVERT: E 375 GLU cc_start: 0.8886 (pm20) cc_final: 0.8631 (pm20) REVERT: E 549 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8201 (t80) REVERT: E 556 TYR cc_start: 0.8550 (m-10) cc_final: 0.8107 (m-10) REVERT: G 548 LYS cc_start: 0.4459 (mmmt) cc_final: 0.4077 (mmmt) outliers start: 91 outliers final: 45 residues processed: 375 average time/residue: 1.4175 time to fit residues: 614.6026 Evaluate side-chains 358 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 294 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 77 optimal weight: 0.6980 chunk 271 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 217 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN Q 104 GLN R 46 HIS R 60 ASN S 39 HIS T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN A 330 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.124717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091925 restraints weight = 56417.416| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.10 r_work: 0.3150 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28287 Z= 0.180 Angle : 0.634 14.450 39581 Z= 0.339 Chirality : 0.039 0.210 4370 Planarity : 0.004 0.078 3885 Dihedral : 26.858 176.578 6312 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.83 % Allowed : 28.93 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.17), residues: 2447 helix: 0.84 (0.14), residues: 1381 sheet: -0.53 (0.56), residues: 88 loop : -1.09 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 261 HIS 0.008 0.001 HIS A 43 PHE 0.037 0.001 PHE G 551 TYR 0.028 0.002 TYR P 88 ARG 0.019 0.001 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 1351) hydrogen bonds : angle 3.69522 ( 3631) metal coordination : bond 0.00238 ( 1) SS BOND : bond 0.00339 ( 1) SS BOND : angle 1.37578 ( 2) covalent geometry : bond 0.00406 (28285) covalent geometry : angle 0.63439 (39579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.8166 (pp30) cc_final: 0.7937 (pm20) REVERT: D 275 GLN cc_start: 0.6882 (mm110) cc_final: 0.6198 (mp10) REVERT: D 295 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6937 (m-40) REVERT: F 24 GLU cc_start: 0.5282 (mt-10) cc_final: 0.4867 (mm-30) REVERT: F 95 ASP cc_start: 0.2539 (p0) cc_final: 0.2030 (t70) REVERT: F 256 MET cc_start: 0.1683 (OUTLIER) cc_final: 0.1184 (pp-130) REVERT: F 270 GLU cc_start: 0.0968 (OUTLIER) cc_final: 0.0119 (pm20) REVERT: Q 56 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: S 131 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8626 (mtt180) REVERT: T 91 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8831 (tttt) REVERT: V 105 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8481 (mttp) REVERT: A 60 LYS cc_start: 0.6891 (mttm) cc_final: 0.6613 (ptpt) REVERT: A 88 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8108 (mtm180) REVERT: A 97 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6512 (t80) REVERT: A 140 ASP cc_start: 0.7917 (t0) cc_final: 0.7413 (t0) REVERT: A 165 ASP cc_start: 0.8279 (p0) cc_final: 0.7911 (p0) REVERT: A 189 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6297 (p90) REVERT: A 252 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: B 670 GLU cc_start: 0.8057 (mp0) cc_final: 0.7141 (mp0) REVERT: B 684 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 755 TYR cc_start: 0.7751 (m-80) cc_final: 0.7512 (m-80) REVERT: B 765 MET cc_start: 0.5524 (mmt) cc_final: 0.4931 (pp-130) REVERT: B 799 ARG cc_start: 0.7717 (mmm160) cc_final: 0.7142 (mtt-85) REVERT: B 825 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8848 (mm) REVERT: B 881 ASP cc_start: 0.8675 (t0) cc_final: 0.8227 (m-30) REVERT: B 910 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7748 (tmt170) REVERT: B 918 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 982 LYS cc_start: 0.7375 (mttt) cc_final: 0.6866 (mtmm) REVERT: B 1136 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5242 (m-10) REVERT: B 1160 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: B 1187 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 1289 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6965 (pt0) REVERT: E 262 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7214 (t80) REVERT: E 282 PHE cc_start: 0.6999 (m-80) cc_final: 0.6538 (m-80) REVERT: E 344 ASP cc_start: 0.7830 (m-30) cc_final: 0.7125 (OUTLIER) REVERT: E 375 GLU cc_start: 0.8875 (pm20) cc_final: 0.8639 (pm20) REVERT: E 549 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8158 (t80) REVERT: E 556 TYR cc_start: 0.8573 (m-10) cc_final: 0.8175 (m-10) REVERT: G 548 LYS cc_start: 0.4525 (mmmt) cc_final: 0.4293 (mmmt) REVERT: G 551 PHE cc_start: 0.7580 (t80) cc_final: 0.7349 (t80) outliers start: 85 outliers final: 46 residues processed: 367 average time/residue: 1.4335 time to fit residues: 609.7066 Evaluate side-chains 351 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 97 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN Q 104 GLN R 46 HIS R 60 ASN T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 76 GLN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 ASN ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.125558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089422 restraints weight = 56118.120| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.96 r_work: 0.3227 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28287 Z= 0.157 Angle : 0.636 16.062 39581 Z= 0.339 Chirality : 0.038 0.214 4370 Planarity : 0.004 0.072 3885 Dihedral : 26.795 175.917 6312 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.38 % Allowed : 29.56 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.17), residues: 2447 helix: 0.85 (0.14), residues: 1382 sheet: -0.44 (0.59), residues: 80 loop : -1.08 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 261 HIS 0.011 0.001 HIS R 46 PHE 0.034 0.001 PHE G 551 TYR 0.032 0.002 TYR B 675 ARG 0.018 0.001 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1351) hydrogen bonds : angle 3.69659 ( 3631) metal coordination : bond 0.00187 ( 1) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.38609 ( 2) covalent geometry : bond 0.00350 (28285) covalent geometry : angle 0.63589 (39579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 317 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5154 (m-80) REVERT: D 275 GLN cc_start: 0.6920 (mm110) cc_final: 0.6225 (mp10) REVERT: D 295 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6756 (m-40) REVERT: F 22 MET cc_start: 0.1384 (mmm) cc_final: 0.0624 (mtt) REVERT: F 24 GLU cc_start: 0.5468 (mt-10) cc_final: 0.4977 (mm-30) REVERT: F 95 ASP cc_start: 0.2503 (p0) cc_final: 0.2047 (t70) REVERT: F 256 MET cc_start: 0.1751 (OUTLIER) cc_final: 0.1286 (pp-130) REVERT: F 270 GLU cc_start: 0.1053 (OUTLIER) cc_final: 0.0122 (pm20) REVERT: Q 56 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: S 131 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8703 (mtt180) REVERT: T 91 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8904 (tttt) REVERT: V 105 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8562 (mttp) REVERT: A 60 LYS cc_start: 0.6898 (mttm) cc_final: 0.6589 (ptpt) REVERT: A 88 ARG cc_start: 0.8535 (mtm110) cc_final: 0.8208 (mtm180) REVERT: A 97 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6580 (t80) REVERT: A 140 ASP cc_start: 0.8006 (t0) cc_final: 0.7544 (t0) REVERT: A 165 ASP cc_start: 0.8382 (p0) cc_final: 0.8006 (p0) REVERT: A 189 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6186 (p90) REVERT: A 252 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8034 (mm-30) REVERT: B 670 GLU cc_start: 0.8030 (mp0) cc_final: 0.7071 (mp0) REVERT: B 684 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8202 (mm-30) REVERT: B 755 TYR cc_start: 0.7748 (m-80) cc_final: 0.7500 (m-80) REVERT: B 765 MET cc_start: 0.5538 (mmt) cc_final: 0.5031 (pp-130) REVERT: B 799 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7166 (mtt-85) REVERT: B 825 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8897 (mm) REVERT: B 881 ASP cc_start: 0.8594 (t0) cc_final: 0.8163 (m-30) REVERT: B 910 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7769 (tmt170) REVERT: B 918 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 982 LYS cc_start: 0.7390 (mttt) cc_final: 0.6873 (mtmm) REVERT: B 1016 TYR cc_start: 0.7771 (t80) cc_final: 0.7505 (t80) REVERT: B 1136 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.5339 (m-10) REVERT: B 1187 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7304 (mm) REVERT: B 1228 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 1289 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: E 282 PHE cc_start: 0.7013 (m-80) cc_final: 0.6676 (m-80) REVERT: E 344 ASP cc_start: 0.7901 (m-30) cc_final: 0.7189 (t0) REVERT: E 375 GLU cc_start: 0.8920 (pm20) cc_final: 0.8592 (pm20) REVERT: E 556 TYR cc_start: 0.8582 (m-10) cc_final: 0.8145 (m-10) REVERT: G 548 LYS cc_start: 0.4582 (mmmt) cc_final: 0.4190 (mmmt) outliers start: 75 outliers final: 39 residues processed: 369 average time/residue: 1.4799 time to fit residues: 636.5838 Evaluate side-chains 352 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain F residue 81 TYR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 79 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 24 ASP Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 62 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1278 THR Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain G residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 13 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 211 optimal weight: 0.0050 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN Q 104 GLN R 46 HIS R 60 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.125515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093131 restraints weight = 56413.679| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.14 r_work: 0.3173 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 28287 Z= 0.202 Angle : 0.817 61.570 39581 Z= 0.450 Chirality : 0.044 1.338 4370 Planarity : 0.005 0.142 3885 Dihedral : 26.793 175.918 6312 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.29 % Allowed : 29.83 % Favored : 66.88 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.17), residues: 2447 helix: 0.85 (0.14), residues: 1383 sheet: -0.44 (0.59), residues: 80 loop : -1.09 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 261 HIS 0.205 0.003 HIS R 46 PHE 0.032 0.001 PHE G 551 TYR 0.038 0.002 TYR D 288 ARG 0.015 0.000 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 1351) hydrogen bonds : angle 3.69588 ( 3631) metal coordination : bond 0.00175 ( 1) SS BOND : bond 0.00344 ( 1) SS BOND : angle 1.37782 ( 2) covalent geometry : bond 0.00425 (28285) covalent geometry : angle 0.81734 (39579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20714.67 seconds wall clock time: 359 minutes 13.75 seconds (21553.75 seconds total)