Starting phenix.real_space_refine on Sat Aug 8 07:06:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd5_37125/08_2026/8kd5_37125.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 319 5.49 5 S 91 5.16 5 C 16088 2.51 5 N 4778 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26908 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 2 Chain: "F" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1573 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: "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: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3277 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "Y" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3261 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} 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: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4519 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 12, 'TRANS': 526} 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: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 724 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} 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: 4.91, per 1000 atoms: 0.18 Number of scatterers: 26908 At special positions: 0 Unit cell: (139.87, 152.65, 188.15, 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 319 15.00 O 5631 8.00 N 4778 7.00 C 16088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 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: 1.85 Conformation dependent library (CDL) restraints added in 921.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 19 sheets defined 59.0% alpha, 3.8% beta 133 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'D' and resid 98 through 112 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.911A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 293 removed outlier: 4.425A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 316 removed outlier: 4.505A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.525A pdb=" N ARG D 324 " --> pdb=" O VAL D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 343 removed outlier: 3.914A 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 400 Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.796A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 4.408A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.192A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.721A pdb=" N VAL F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.374A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 313 Processing helix chain 'F' and resid 329 through 338 removed outlier: 4.319A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.817A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 369 removed outlier: 3.889A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS F 369 " --> pdb=" O TRP F 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 63 through 76 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: 3.734A 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: 3.790A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.020A 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 removed outlier: 3.606A pdb=" N LEU Q 83 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.622A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 removed outlier: 3.538A pdb=" N TYR R 80 " --> pdb=" O ARG R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 99 Processing helix chain 'R' and resid 101 through 120 removed outlier: 3.521A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.567A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.640A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.893A 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: 3.826A 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: 4.036A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.538A 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: 3.511A pdb=" N VAL V 38 " --> pdb=" O TYR V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.642A 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: 4.133A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS V 106 " --> pdb=" O GLU V 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.830A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.846A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.670A pdb=" N LEU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.868A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 104' Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.645A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.747A 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 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.723A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.524A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.794A 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: 4.459A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.928A 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: 3.628A 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 Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.788A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.937A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.504A pdb=" N TYR B 871 " --> pdb=" O ILE B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.749A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 4.026A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 removed outlier: 4.194A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.744A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.084A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.787A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 3.879A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 4.121A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1184 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1230 removed outlier: 3.829A pdb=" N PHE B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.797A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.585A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) removed outlier: 3.618A 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 Processing helix chain 'B' and resid 1307 through 1310 Processing helix chain 'E' and resid 52 through 57 Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.641A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.146A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.556A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.553A 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 304 through 312 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.699A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.824A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.975A 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 245 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.677A 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: 6.252A 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: 7.439A 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: 6.931A 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: 7.025A 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 233 through 238 removed outlier: 8.095A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.264A 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: 7.724A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 21 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 66 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 756 through 757 removed outlier: 4.081A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id=AB6, first strand: chain 'E' and resid 272 through 275 removed outlier: 4.115A pdb=" N CYS E 275 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 280 " --> pdb=" O CYS E 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AB9, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.632A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.514A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 992 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 2.49 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: 7634 1.34 - 1.47: 8286 1.47 - 1.59: 11407 1.59 - 1.72: 636 1.72 - 1.85: 142 Bond restraints: 28105 Sorted by residual: bond pdb=" C1' DT X 66 " pdb=" N1 DT X 66 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" C3' DC X 34 " pdb=" C2' DC X 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DT Y -17 " pdb=" C2' DT Y -17 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DA Y 67 " pdb=" C2' DA Y 67 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG X 64 " pdb=" C2' DG X 64 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 ... (remaining 28100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 38928 2.97 - 5.93: 286 5.93 - 8.90: 62 8.90 - 11.86: 15 11.86 - 14.83: 5 Bond angle restraints: 39296 Sorted by residual: angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.61 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" CB LYS B 962 " pdb=" CG LYS B 962 " pdb=" CD LYS B 962 " ideal model delta sigma weight residual 111.30 122.72 -11.42 2.30e+00 1.89e-01 2.47e+01 angle pdb=" CB MET S 90 " pdb=" CG MET S 90 " pdb=" SD MET S 90 " ideal model delta sigma weight residual 112.70 127.53 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN F 305 " pdb=" CB GLN F 305 " pdb=" CG GLN F 305 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" N3 DT Y -42 " pdb=" C4 DT Y -42 " pdb=" O4 DT Y -42 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 ... (remaining 39291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 14067 35.18 - 70.36: 1981 70.36 - 105.55: 51 105.55 - 140.73: 2 140.73 - 175.91: 1 Dihedral angle restraints: 16102 sinusoidal: 8750 harmonic: 7352 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 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA MET F 347 " pdb=" C MET F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA HIS E 302 " pdb=" C HIS E 302 " pdb=" N CYS E 303 " pdb=" CA CYS E 303 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 16099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3363 0.052 - 0.103: 838 0.103 - 0.155: 128 0.155 - 0.207: 12 0.207 - 0.259: 2 Chirality restraints: 4343 Sorted by residual: chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL B 777 " pdb=" CA VAL B 777 " pdb=" CG1 VAL B 777 " pdb=" CG2 VAL B 777 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU F 338 " pdb=" CB LEU F 338 " pdb=" CD1 LEU F 338 " pdb=" CD2 LEU F 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4340 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 321 " -0.088 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO D 322 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 292 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO E 293 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.015 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP B 775 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.002 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 345 2.62 - 3.19: 21665 3.19 - 3.76: 48180 3.76 - 4.33: 62272 4.33 - 4.90: 94710 Nonbonded interactions: 227172 Sorted by model distance: nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.044 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.139 3.880 nonbonded pdb=" O ASN B1165 " pdb=" OG1 THR B1169 " model vdw 2.221 3.040 nonbonded pdb=" O LYS D 243 " pdb=" OG1 THR D 390 " model vdw 2.234 3.040 nonbonded pdb=" O ILE E 395 " pdb=" NZ LYS E 397 " model vdw 2.260 3.120 ... (remaining 227167 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 'O' and resid 36 through 133) selection = chain 'S' } 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=0.00 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: 10.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28107 Z= 0.390 Angle : 0.828 14.828 39298 Z= 0.574 Chirality : 0.045 0.259 4343 Planarity : 0.005 0.131 3879 Dihedral : 24.457 175.912 11345 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.29 % Favored : 95.59 % Rotamer: Outliers : 0.54 % Allowed : 32.75 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 2450 helix: -0.12 (0.13), residues: 1323 sheet: 0.76 (0.67), residues: 81 loop : -1.75 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 88 TYR 0.032 0.001 TYR A 176 PHE 0.038 0.001 PHE E 326 TRP 0.041 0.001 TRP B 775 HIS 0.017 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.39 (28105) covalent geometry : angle 0.82816 / 0.57 (39296) SS BOND : bond 0.00187 / 0.12 ( 1) SS BOND : angle 0.88978 / 0.38 ( 2) hydrogen bonds : bond 0.15766 / 10.37 ( 1340) hydrogen bonds : angle 5.53322 / 3.79 ( 3600) metal coordination : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 315 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 291 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7906 (mmtt) REVERT: D 350 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 256 MET cc_start: 0.5695 (tpp) cc_final: 0.5075 (pmt) REVERT: P 84 MET cc_start: 0.8088 (tpp) cc_final: 0.7885 (tpp) REVERT: Q 95 LYS cc_start: 0.7854 (ttmp) cc_final: 0.7254 (tptt) REVERT: R 30 ARG cc_start: 0.5740 (mtp-110) cc_final: 0.5044 (mtp-110) REVERT: U 74 LYS cc_start: 0.7341 (mppt) cc_final: 0.7077 (mppt) REVERT: V 60 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: B 726 TYR cc_start: 0.6199 (t80) cc_final: 0.5780 (t80) REVERT: B 757 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8121 (ttp80) REVERT: B 773 MET cc_start: 0.5049 (ppp) cc_final: 0.4287 (ppp) REVERT: B 813 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 1185 ASP cc_start: 0.8091 (t70) cc_final: 0.7787 (t0) REVERT: B 1288 LEU cc_start: 0.7932 (tm) cc_final: 0.7617 (tm) REVERT: E 282 PHE cc_start: 0.6906 (m-10) cc_final: 0.6197 (m-10) outliers start: 12 outliers final: 3 residues processed: 319 average time/residue: 0.5845 time to fit residues: 222.0695 Evaluate side-chains 292 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain B residue 785 HIS Chi-restraints excluded: chain E residue 540 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 50.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN F 263 HIS F 267 GLN F 305 GLN O 39 HIS O 108 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 331 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1190 GLN ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105747 restraints weight = 58080.784| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.33 r_work: 0.3470 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 28107 Z= 0.243 Angle : 0.716 11.494 39298 Z= 0.385 Chirality : 0.047 0.294 4343 Planarity : 0.005 0.082 3879 Dihedral : 26.800 173.691 6228 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.31 % Allowed : 25.51 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2450 helix: 0.42 (0.14), residues: 1358 sheet: 0.37 (0.63), residues: 87 loop : -1.49 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 30 TYR 0.033 0.002 TYR P 88 PHE 0.020 0.002 PHE Q 25 TRP 0.037 0.002 TRP B 775 HIS 0.009 0.002 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (28105) covalent geometry : angle 0.71556 / 0.39 (39296) SS BOND : bond 0.01064 / 0.67 ( 1) SS BOND : angle 3.34535 / 1.42 ( 2) hydrogen bonds : bond 0.05086 / 3.36 ( 1340) hydrogen bonds : angle 4.03386 / 2.79 ( 3600) metal coordination : bond 0.00718 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 346 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 280 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5643 (tm-30) REVERT: D 291 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8281 (mmtt) REVERT: D 350 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 256 MET cc_start: 0.5754 (tpp) cc_final: 0.5126 (pmt) REVERT: F 368 MET cc_start: 0.3802 (ttt) cc_final: 0.3552 (ppp) REVERT: O 115 LYS cc_start: 0.8962 (mmtp) cc_final: 0.8731 (mmtm) REVERT: Q 36 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7981 (pttp) REVERT: R 76 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8056 (ttp80) REVERT: U 29 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8887 (ttm170) REVERT: U 73 ASN cc_start: 0.7500 (p0) cc_final: 0.7286 (p0) REVERT: A 105 ASN cc_start: 0.9038 (t0) cc_final: 0.8783 (t0) REVERT: A 306 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7692 (tmm) REVERT: A 316 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7353 (ptp90) REVERT: A 325 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: B 773 MET cc_start: 0.5493 (ppp) cc_final: 0.4709 (ppp) REVERT: B 813 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 825 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8166 (mm) REVERT: B 868 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7884 (mtt-85) REVERT: B 1185 ASP cc_start: 0.8216 (t70) cc_final: 0.7991 (t0) REVERT: B 1244 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8289 (mmtp) REVERT: B 1317 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.6160 (pt) REVERT: E 500 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6833 (pttt) REVERT: E 501 LYS cc_start: 0.6641 (mmtt) cc_final: 0.6377 (mmtm) REVERT: E 544 GLU cc_start: 0.8378 (mp0) cc_final: 0.7978 (mp0) outliers start: 118 outliers final: 35 residues processed: 417 average time/residue: 0.6640 time to fit residues: 323.2525 Evaluate side-chains 345 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 785 HIS Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1288 LEU Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN F 305 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS ** Q 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN V 60 ASN A 31 ASN A 54 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103560 restraints weight = 57912.847| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.33 r_work: 0.3439 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28107 Z= 0.150 Angle : 0.603 10.302 39298 Z= 0.327 Chirality : 0.041 0.237 4343 Planarity : 0.004 0.066 3879 Dihedral : 26.881 173.534 6227 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.91 % Allowed : 26.90 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2450 helix: 0.88 (0.14), residues: 1362 sheet: 0.45 (0.63), residues: 84 loop : -1.34 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 71 TYR 0.021 0.001 TYR A 347 PHE 0.038 0.001 PHE F 362 TRP 0.021 0.001 TRP B 775 HIS 0.008 0.001 HIS B1221 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (28105) covalent geometry : angle 0.60319 / 0.33 (39296) SS BOND : bond 0.00806 / 0.50 ( 1) SS BOND : angle 2.58784 / 1.12 ( 2) hydrogen bonds : bond 0.04138 / 2.70 ( 1340) hydrogen bonds : angle 3.80359 / 2.63 ( 3600) metal coordination : bond 0.00267 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 326 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7269 (mmm) cc_final: 0.6672 (mpt) REVERT: D 103 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6872 (pp20) REVERT: D 291 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8332 (mmtt) REVERT: D 325 ILE cc_start: 0.7205 (tp) cc_final: 0.7001 (pt) REVERT: D 350 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7506 (tm-30) REVERT: F 256 MET cc_start: 0.5648 (tpp) cc_final: 0.5016 (pmt) REVERT: F 317 GLN cc_start: 0.4977 (OUTLIER) cc_final: 0.4646 (pm20) REVERT: F 347 MET cc_start: 0.1981 (pp-130) cc_final: 0.1763 (pp-130) REVERT: O 115 LYS cc_start: 0.8975 (mmtp) cc_final: 0.8706 (mmtm) REVERT: U 29 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8758 (ttm170) REVERT: A 105 ASN cc_start: 0.9159 (t0) cc_final: 0.8752 (t0) REVERT: A 325 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: A 373 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6160 (mpp) REVERT: B 773 MET cc_start: 0.5668 (ppp) cc_final: 0.5039 (ppp) REVERT: B 809 LYS cc_start: 0.7845 (tttt) cc_final: 0.7488 (tttm) REVERT: B 812 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: B 813 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 825 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8203 (mm) REVERT: B 868 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7852 (mtt-85) REVERT: B 1185 ASP cc_start: 0.8180 (t70) cc_final: 0.7959 (t0) REVERT: B 1244 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8238 (mmtp) REVERT: B 1285 ILE cc_start: 0.8677 (mm) cc_final: 0.8366 (mp) REVERT: B 1317 ILE cc_start: 0.6315 (OUTLIER) cc_final: 0.6098 (pt) REVERT: E 272 PHE cc_start: 0.6872 (m-80) cc_final: 0.6670 (m-80) REVERT: E 341 PHE cc_start: 0.7587 (t80) cc_final: 0.7220 (t80) REVERT: E 500 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6885 (pttt) REVERT: E 501 LYS cc_start: 0.6626 (mmtt) cc_final: 0.6367 (mmtm) REVERT: E 544 GLU cc_start: 0.8327 (mp0) cc_final: 0.7851 (mp0) outliers start: 87 outliers final: 28 residues processed: 383 average time/residue: 0.6827 time to fit residues: 304.7115 Evaluate side-chains 330 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 555 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 235 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 265 optimal weight: 30.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS Q 38 ASN R 64 ASN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 HIS ** B1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.128964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096259 restraints weight = 56483.395| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.13 r_work: 0.3304 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28107 Z= 0.206 Angle : 0.661 15.622 39298 Z= 0.352 Chirality : 0.044 0.507 4343 Planarity : 0.005 0.059 3879 Dihedral : 27.050 174.400 6225 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.81 % Allowed : 25.51 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2450 helix: 0.96 (0.14), residues: 1363 sheet: 0.04 (0.62), residues: 84 loop : -1.32 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 757 TYR 0.023 0.002 TYR A 347 PHE 0.027 0.002 PHE G 326 TRP 0.028 0.002 TRP B 775 HIS 0.028 0.002 HIS F 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (28105) covalent geometry : angle 0.65770 / 0.35 (39296) SS BOND : bond 0.05902 / 3.69 ( 1) SS BOND : angle 8.89683 / 3.47 ( 2) hydrogen bonds : bond 0.04505 / 2.95 ( 1340) hydrogen bonds : angle 3.78529 / 2.61 ( 3600) metal coordination : bond 0.00478 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 316 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7366 (mmm) cc_final: 0.6491 (mpp) REVERT: D 103 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6789 (pp20) REVERT: D 291 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8558 (mmtt) REVERT: D 325 ILE cc_start: 0.7542 (tp) cc_final: 0.7295 (pt) REVERT: D 350 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7708 (tm-30) REVERT: F 256 MET cc_start: 0.5769 (tpp) cc_final: 0.5144 (pmt) REVERT: F 317 GLN cc_start: 0.4947 (OUTLIER) cc_final: 0.4633 (pm20) REVERT: O 115 LYS cc_start: 0.9185 (mmtp) cc_final: 0.8949 (mmtm) REVERT: Q 73 ASN cc_start: 0.8165 (p0) cc_final: 0.7850 (m110) REVERT: U 29 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.9050 (ttm170) REVERT: A 306 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7855 (tmm) REVERT: A 325 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: A 373 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.6815 (mpp) REVERT: B 809 LYS cc_start: 0.8279 (tttt) cc_final: 0.7920 (tttm) REVERT: B 813 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 825 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8099 (mm) REVERT: B 868 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7990 (mtt-85) REVERT: B 910 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7928 (ttp80) REVERT: B 1185 ASP cc_start: 0.8357 (t70) cc_final: 0.8096 (t0) REVERT: B 1187 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6980 (mm) REVERT: B 1285 ILE cc_start: 0.8710 (mm) cc_final: 0.8410 (mp) REVERT: B 1317 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6441 (pt) REVERT: E 272 PHE cc_start: 0.7046 (m-10) cc_final: 0.6809 (m-80) REVERT: E 500 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7036 (pttt) REVERT: E 501 LYS cc_start: 0.6851 (mmtt) cc_final: 0.6555 (mmtm) REVERT: E 544 GLU cc_start: 0.8473 (mp0) cc_final: 0.8009 (mp0) REVERT: E 554 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8423 (tmtm) REVERT: G 303 CYS cc_start: 0.2724 (OUTLIER) cc_final: 0.1925 (p) outliers start: 107 outliers final: 41 residues processed: 386 average time/residue: 0.7142 time to fit residues: 319.1299 Evaluate side-chains 333 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O 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 116 LEU Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 555 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 0.2980 chunk 186 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 275 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN U 104 GLN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.128045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095738 restraints weight = 56877.514| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.21 r_work: 0.3284 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28107 Z= 0.165 Angle : 0.622 9.375 39298 Z= 0.333 Chirality : 0.042 0.234 4343 Planarity : 0.004 0.053 3879 Dihedral : 27.111 173.897 6225 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.55 % Allowed : 27.04 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2450 helix: 1.04 (0.14), residues: 1357 sheet: -0.09 (0.61), residues: 84 loop : -1.24 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 30 TYR 0.019 0.001 TYR A 347 PHE 0.043 0.002 PHE F 362 TRP 0.021 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (28105) covalent geometry : angle 0.62170 / 0.33 (39296) SS BOND : bond 0.00863 / 0.54 ( 1) SS BOND : angle 3.16139 / 1.21 ( 2) hydrogen bonds : bond 0.03867 / 2.50 ( 1340) hydrogen bonds : angle 3.75784 / 2.59 ( 3600) metal coordination : bond 0.00359 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 312 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7170 (mmm) cc_final: 0.6522 (mpt) REVERT: D 103 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: D 291 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8518 (mmtt) REVERT: D 350 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 256 MET cc_start: 0.5719 (tpp) cc_final: 0.5119 (pmt) REVERT: F 270 GLU cc_start: 0.1741 (OUTLIER) cc_final: 0.1515 (pt0) REVERT: F 317 GLN cc_start: 0.4952 (OUTLIER) cc_final: 0.4648 (pm20) REVERT: F 347 MET cc_start: 0.1827 (pp-130) cc_final: 0.1606 (pp-130) REVERT: O 115 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8832 (mmtm) REVERT: Q 73 ASN cc_start: 0.7997 (p0) cc_final: 0.7783 (m110) REVERT: U 29 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8998 (ttm170) REVERT: V 54 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8403 (ttpp) REVERT: A 306 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7694 (tmm) REVERT: A 325 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 373 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6644 (mpp) REVERT: B 809 LYS cc_start: 0.8285 (tttt) cc_final: 0.7895 (tttm) REVERT: B 813 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8513 (mt-10) REVERT: B 825 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8128 (mm) REVERT: B 868 ARG cc_start: 0.8418 (tpp80) cc_final: 0.7922 (mtt-85) REVERT: B 1185 ASP cc_start: 0.8278 (t70) cc_final: 0.8034 (t0) REVERT: B 1285 ILE cc_start: 0.8726 (mm) cc_final: 0.8413 (mp) REVERT: B 1317 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6398 (pp) REVERT: E 500 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7073 (pttt) REVERT: E 501 LYS cc_start: 0.6849 (mmtt) cc_final: 0.6570 (mmtm) REVERT: E 554 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8372 (tmtm) REVERT: E 559 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7062 (ptmt) outliers start: 79 outliers final: 30 residues processed: 369 average time/residue: 0.7014 time to fit residues: 299.6198 Evaluate side-chains 326 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain G residue 555 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Q 38 ASN ** S 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN U 104 GLN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1143 ASN ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 517 ASN E 519 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.125875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093366 restraints weight = 56439.390| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.19 r_work: 0.3241 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28107 Z= 0.181 Angle : 0.643 9.432 39298 Z= 0.343 Chirality : 0.043 0.289 4343 Planarity : 0.004 0.051 3879 Dihedral : 27.156 174.363 6225 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.63 % Allowed : 26.05 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2450 helix: 1.02 (0.14), residues: 1358 sheet: -0.32 (0.57), residues: 89 loop : -1.20 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 30 TYR 0.023 0.002 TYR A 58 PHE 0.016 0.001 PHE B1147 TRP 0.033 0.002 TRP B 775 HIS 0.009 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (28105) covalent geometry : angle 0.64305 / 0.34 (39296) SS BOND : bond 0.00222 / 0.14 ( 1) SS BOND : angle 0.81057 / 0.28 ( 2) hydrogen bonds : bond 0.04102 / 2.66 ( 1340) hydrogen bonds : angle 3.77278 / 2.60 ( 3600) metal coordination : bond 0.00434 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 301 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7344 (mmm) cc_final: 0.6650 (mpt) REVERT: D 82 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6724 (pp30) REVERT: D 103 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6814 (pp20) REVERT: D 291 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8536 (mmtt) REVERT: D 350 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7650 (tm-30) REVERT: F 256 MET cc_start: 0.5758 (tpp) cc_final: 0.5158 (pmt) REVERT: O 115 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8865 (mmtm) REVERT: P 85 ASP cc_start: 0.8640 (p0) cc_final: 0.8389 (p0) REVERT: V 54 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8410 (ttpp) REVERT: A 306 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7637 (tmm) REVERT: A 325 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: A 373 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: B 825 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 860 MET cc_start: 0.6654 (mpp) cc_final: 0.5973 (mpt) REVERT: B 868 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7927 (mtt-85) REVERT: B 910 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7896 (ttp80) REVERT: B 1180 PHE cc_start: 0.3055 (OUTLIER) cc_final: 0.2781 (t80) REVERT: B 1185 ASP cc_start: 0.8297 (t70) cc_final: 0.8090 (t0) REVERT: B 1187 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6843 (mm) REVERT: B 1285 ILE cc_start: 0.8755 (mm) cc_final: 0.8446 (mp) REVERT: E 316 MET cc_start: 0.1436 (mpm) cc_final: 0.1100 (mpp) REVERT: E 500 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7125 (pttt) REVERT: E 501 LYS cc_start: 0.6922 (mmtt) cc_final: 0.6634 (mmtm) REVERT: E 554 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8365 (tmtm) REVERT: E 559 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7048 (ptmt) outliers start: 103 outliers final: 45 residues processed: 374 average time/residue: 0.7293 time to fit residues: 314.8979 Evaluate side-chains 335 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 278 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 261 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 93 optimal weight: 0.0070 chunk 115 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN U 38 ASN U 104 GLN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090955 restraints weight = 56274.637| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.99 r_work: 0.3265 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28107 Z= 0.165 Angle : 0.641 10.540 39298 Z= 0.341 Chirality : 0.042 0.230 4343 Planarity : 0.004 0.049 3879 Dihedral : 27.172 174.130 6225 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.87 % Allowed : 27.22 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2450 helix: 1.05 (0.14), residues: 1357 sheet: -0.43 (0.57), residues: 89 loop : -1.21 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 30 TYR 0.025 0.001 TYR A 58 PHE 0.046 0.001 PHE F 362 TRP 0.034 0.001 TRP B 775 HIS 0.009 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (28105) covalent geometry : angle 0.64145 / 0.34 (39296) SS BOND : bond 0.00145 / 0.09 ( 1) SS BOND : angle 0.53173 / 0.25 ( 2) hydrogen bonds : bond 0.03824 / 2.46 ( 1340) hydrogen bonds : angle 3.73838 / 2.58 ( 3600) metal coordination : bond 0.00391 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7342 (mmm) cc_final: 0.6592 (mpt) REVERT: D 103 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6867 (pp20) REVERT: D 291 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8616 (mmtt) REVERT: D 350 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7663 (tm-30) REVERT: F 256 MET cc_start: 0.5826 (tpp) cc_final: 0.5225 (pmt) REVERT: F 317 GLN cc_start: 0.4954 (OUTLIER) cc_final: 0.4632 (pm20) REVERT: F 347 MET cc_start: 0.1722 (pp-130) cc_final: 0.0786 (pp-130) REVERT: O 115 LYS cc_start: 0.9155 (mmtp) cc_final: 0.8953 (mmtm) REVERT: V 54 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8536 (ttpp) REVERT: V 82 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8498 (mmtt) REVERT: A 60 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6047 (ptpp) REVERT: A 138 LYS cc_start: 0.7517 (tppt) cc_final: 0.7198 (tptp) REVERT: A 306 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7779 (tmm) REVERT: A 325 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: A 373 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7798 (mtm) REVERT: B 825 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 868 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7926 (mtt-85) REVERT: B 1185 ASP cc_start: 0.8377 (t70) cc_final: 0.8158 (t0) REVERT: B 1187 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6877 (mm) REVERT: B 1285 ILE cc_start: 0.8785 (mm) cc_final: 0.8471 (mp) REVERT: E 272 PHE cc_start: 0.7036 (m-80) cc_final: 0.6784 (m-80) REVERT: E 500 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7140 (pttt) REVERT: E 501 LYS cc_start: 0.6968 (mmtt) cc_final: 0.6661 (mmtm) REVERT: E 542 ILE cc_start: 0.8390 (mm) cc_final: 0.8101 (tt) REVERT: E 554 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8471 (tmtm) REVERT: E 559 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6988 (ptmt) outliers start: 86 outliers final: 44 residues processed: 343 average time/residue: 0.7508 time to fit residues: 296.9759 Evaluate side-chains 330 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 212 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 199 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 111 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 147 optimal weight: 0.0270 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Q 38 ASN ** S 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN U 104 GLN U 110 ASN V 46 HIS V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090097 restraints weight = 56612.885| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.99 r_work: 0.3250 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28107 Z= 0.170 Angle : 0.647 9.869 39298 Z= 0.343 Chirality : 0.042 0.231 4343 Planarity : 0.004 0.049 3879 Dihedral : 27.175 173.996 6225 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.33 % Allowed : 27.49 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2450 helix: 1.03 (0.14), residues: 1364 sheet: -0.55 (0.57), residues: 89 loop : -1.18 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 30 TYR 0.028 0.002 TYR V 37 PHE 0.024 0.001 PHE G 326 TRP 0.040 0.001 TRP B 775 HIS 0.009 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (28105) covalent geometry : angle 0.64746 / 0.34 (39296) SS BOND : bond 0.00150 / 0.09 ( 1) SS BOND : angle 0.50901 / 0.22 ( 2) hydrogen bonds : bond 0.03867 / 2.49 ( 1340) hydrogen bonds : angle 3.74039 / 2.58 ( 3600) metal coordination : bond 0.00373 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7454 (mmm) cc_final: 0.6720 (mpt) REVERT: D 82 GLN cc_start: 0.7026 (pp30) cc_final: 0.6772 (pp30) REVERT: D 103 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: D 291 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8642 (mmtt) REVERT: D 350 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7660 (tm-30) REVERT: F 256 MET cc_start: 0.5836 (tpp) cc_final: 0.5226 (pmt) REVERT: F 317 GLN cc_start: 0.4818 (OUTLIER) cc_final: 0.4560 (pm20) REVERT: F 347 MET cc_start: 0.1869 (pp-130) cc_final: 0.1001 (pp-130) REVERT: O 59 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: O 115 LYS cc_start: 0.9166 (mmtp) cc_final: 0.8884 (mmtm) REVERT: P 85 ASP cc_start: 0.8678 (p0) cc_final: 0.8411 (p0) REVERT: V 54 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: V 82 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8502 (mmtt) REVERT: A 60 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6212 (ptpp) REVERT: A 138 LYS cc_start: 0.7552 (tppt) cc_final: 0.7200 (tptp) REVERT: A 306 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7773 (tmm) REVERT: A 325 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: A 373 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7860 (mtm) REVERT: B 809 LYS cc_start: 0.8546 (tttt) cc_final: 0.8312 (tttm) REVERT: B 825 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 868 ARG cc_start: 0.8395 (tpp80) cc_final: 0.7913 (mtt-85) REVERT: B 910 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7958 (ttp80) REVERT: B 1185 ASP cc_start: 0.8417 (t70) cc_final: 0.8208 (t0) REVERT: B 1187 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6890 (mm) REVERT: B 1285 ILE cc_start: 0.8792 (mm) cc_final: 0.8469 (mp) REVERT: E 272 PHE cc_start: 0.7011 (m-80) cc_final: 0.6755 (m-80) REVERT: E 316 MET cc_start: 0.1502 (mpm) cc_final: 0.1185 (mpp) REVERT: E 500 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7170 (pttt) REVERT: E 501 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6668 (mmtm) REVERT: E 542 ILE cc_start: 0.8435 (mm) cc_final: 0.8182 (tt) REVERT: E 554 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8533 (tmtm) REVERT: E 559 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6897 (ptmt) outliers start: 74 outliers final: 44 residues processed: 333 average time/residue: 0.7671 time to fit residues: 293.6204 Evaluate side-chains 331 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O 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 114 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 110 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 3 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN S 85 GLN U 38 ASN U 104 GLN V 60 ASN V 106 HIS ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.119280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083519 restraints weight = 55984.597| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.97 r_work: 0.3121 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 28107 Z= 0.330 Angle : 0.783 11.718 39298 Z= 0.410 Chirality : 0.051 0.581 4343 Planarity : 0.005 0.051 3879 Dihedral : 27.527 176.240 6225 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.73 % Allowed : 27.35 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2450 helix: 0.69 (0.14), residues: 1367 sheet: -1.04 (0.57), residues: 86 loop : -1.23 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 30 TYR 0.036 0.002 TYR A 58 PHE 0.021 0.002 PHE D 362 TRP 0.050 0.002 TRP B 775 HIS 0.014 0.002 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.33 (28105) covalent geometry : angle 0.78277 / 0.41 (39296) SS BOND : bond 0.00157 / 0.10 ( 1) SS BOND : angle 0.56288 / 0.25 ( 2) hydrogen bonds : bond 0.05446 / 3.55 ( 1340) hydrogen bonds : angle 3.95551 / 2.72 ( 3600) metal coordination : bond 0.01009 / 0.63 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 305 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7587 (mmm) cc_final: 0.6825 (mpt) REVERT: D 82 GLN cc_start: 0.7158 (pp30) cc_final: 0.6934 (pp30) REVERT: D 103 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6766 (pp20) REVERT: D 291 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8789 (mmtt) REVERT: D 308 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8073 (mm-30) REVERT: D 350 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7821 (tm-30) REVERT: F 256 MET cc_start: 0.5840 (tpp) cc_final: 0.5225 (pmt) REVERT: F 317 GLN cc_start: 0.4807 (OUTLIER) cc_final: 0.4576 (pm20) REVERT: F 347 MET cc_start: 0.2041 (OUTLIER) cc_final: 0.1200 (pp-130) REVERT: F 358 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: O 59 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: O 115 LYS cc_start: 0.9208 (mmtp) cc_final: 0.8947 (mmtm) REVERT: P 85 ASP cc_start: 0.8851 (p0) cc_final: 0.8636 (p0) REVERT: V 54 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8571 (ttpp) REVERT: V 82 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8560 (mmtt) REVERT: A 60 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6974 (ptpp) REVERT: A 98 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7914 (pttt) REVERT: A 138 LYS cc_start: 0.7850 (tppt) cc_final: 0.7487 (tptp) REVERT: A 211 TYR cc_start: 0.8442 (t80) cc_final: 0.8197 (t80) REVERT: A 260 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 306 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7792 (tmm) REVERT: A 373 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8147 (mtt) REVERT: B 707 ASP cc_start: 0.7600 (m-30) cc_final: 0.7348 (t0) REVERT: B 825 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8016 (mm) REVERT: B 860 MET cc_start: 0.6794 (mpp) cc_final: 0.6081 (mpt) REVERT: B 868 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8017 (mtt-85) REVERT: B 1187 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6826 (mm) REVERT: B 1285 ILE cc_start: 0.8868 (mm) cc_final: 0.8539 (mp) REVERT: E 272 PHE cc_start: 0.7113 (m-80) cc_final: 0.6911 (m-80) REVERT: E 316 MET cc_start: 0.1342 (mpm) cc_final: 0.0987 (mpp) REVERT: E 501 LYS cc_start: 0.7240 (mmtt) cc_final: 0.6713 (mptp) REVERT: E 542 ILE cc_start: 0.8679 (mm) cc_final: 0.8459 (tt) REVERT: E 554 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8605 (tmtm) REVERT: E 559 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7069 (ptmt) outliers start: 83 outliers final: 47 residues processed: 365 average time/residue: 0.7540 time to fit residues: 316.8425 Evaluate side-chains 343 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O 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 114 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 237 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 35 optimal weight: 0.0870 chunk 212 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 93 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN O 76 GLN Q 38 ASN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 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 = 0.3965 r_free = 0.3965 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087231 restraints weight = 56197.753| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.97 r_work: 0.3201 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 28107 Z= 0.152 Angle : 0.695 12.153 39298 Z= 0.367 Chirality : 0.044 0.235 4343 Planarity : 0.004 0.055 3879 Dihedral : 27.441 173.757 6225 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.38 % Allowed : 29.15 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2450 helix: 0.80 (0.14), residues: 1368 sheet: -0.81 (0.60), residues: 78 loop : -1.21 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 30 TYR 0.031 0.002 TYR A 58 PHE 0.091 0.002 PHE F 362 TRP 0.055 0.002 TRP B 775 HIS 0.007 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (28105) covalent geometry : angle 0.69547 / 0.37 (39296) SS BOND : bond 0.00145 / 0.09 ( 1) SS BOND : angle 0.53482 / 0.24 ( 2) hydrogen bonds : bond 0.03887 / 2.48 ( 1340) hydrogen bonds : angle 3.86579 / 2.67 ( 3600) metal coordination : bond 0.00285 / 0.18 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 285 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7545 (mmm) cc_final: 0.6837 (mpt) REVERT: D 103 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6830 (pp20) REVERT: D 291 LYS cc_start: 0.9094 (mtpt) cc_final: 0.8740 (mmtt) REVERT: D 308 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8009 (mm-30) REVERT: D 350 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7765 (tm-30) REVERT: F 256 MET cc_start: 0.5788 (tpp) cc_final: 0.5185 (pmt) REVERT: F 347 MET cc_start: 0.1976 (OUTLIER) cc_final: 0.1233 (pp-130) REVERT: O 59 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: O 115 LYS cc_start: 0.9157 (mmtp) cc_final: 0.8940 (mmtm) REVERT: P 85 ASP cc_start: 0.8703 (p0) cc_final: 0.8492 (p0) REVERT: R 105 LYS cc_start: 0.8721 (pttm) cc_final: 0.8480 (ptpp) REVERT: V 54 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8535 (ttpp) REVERT: V 82 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8525 (mmtt) REVERT: A 138 LYS cc_start: 0.7876 (tppt) cc_final: 0.7487 (tptp) REVERT: A 211 TYR cc_start: 0.8225 (t80) cc_final: 0.7979 (t80) REVERT: A 260 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 306 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: A 373 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7919 (mtt) REVERT: B 825 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 860 MET cc_start: 0.6862 (mpp) cc_final: 0.6132 (mpt) REVERT: B 868 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7906 (mtt-85) REVERT: B 910 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8012 (ttp80) REVERT: B 1019 SER cc_start: 0.9043 (p) cc_final: 0.8627 (m) REVERT: B 1187 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6880 (mm) REVERT: E 272 PHE cc_start: 0.6979 (m-80) cc_final: 0.6741 (m-80) REVERT: E 316 MET cc_start: 0.1334 (mpm) cc_final: 0.0990 (mpp) REVERT: E 501 LYS cc_start: 0.7026 (mmtt) cc_final: 0.6591 (mptp) REVERT: E 542 ILE cc_start: 0.8575 (mm) cc_final: 0.8365 (tt) REVERT: E 559 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7020 (ptmt) outliers start: 53 outliers final: 30 residues processed: 320 average time/residue: 0.7723 time to fit residues: 284.1579 Evaluate side-chains 316 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain R residue 32 GLU Chi-restraints excluded: chain R residue 46 HIS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 68 GLN Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 54 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 126 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 chunk 224 optimal weight: 0.5980 chunk 214 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 268 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN U 38 ASN U 104 GLN V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086512 restraints weight = 55904.985| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.97 r_work: 0.3187 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28107 Z= 0.181 Angle : 0.692 11.214 39298 Z= 0.367 Chirality : 0.044 0.234 4343 Planarity : 0.004 0.050 3879 Dihedral : 27.360 174.699 6225 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.47 % Allowed : 29.51 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2450 helix: 0.83 (0.14), residues: 1368 sheet: -0.87 (0.59), residues: 78 loop : -1.18 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 30 TYR 0.035 0.002 TYR V 37 PHE 0.044 0.002 PHE F 362 TRP 0.060 0.002 TRP B 775 HIS 0.009 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (28105) covalent geometry : angle 0.69233 / 0.37 (39296) SS BOND : bond 0.00147 / 0.09 ( 1) SS BOND : angle 0.55237 / 0.25 ( 2) hydrogen bonds : bond 0.04076 / 2.62 ( 1340) hydrogen bonds : angle 3.85243 / 2.65 ( 3600) metal coordination : bond 0.00428 / 0.27 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11553.00 seconds wall clock time: 197 minutes 22.98 seconds (11842.98 seconds total)