Starting phenix.real_space_refine on Sun Jul 5 08:04:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8kd5_37125/07_2026/8kd5_37125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd5_37125/07_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_37125/07_2026/8kd5_37125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd5_37125/07_2026/8kd5_37125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kd5_37125/07_2026/8kd5_37125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd5_37125/07_2026/8kd5_37125.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8kd5_37125/07_2026/8kd5_37125.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8kd5_37125/07_2026/8kd5_37125.cif" } 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-dev-6108/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: 5.13, per 1000 atoms: 0.19 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: 2.30 Conformation dependent library (CDL) restraints added in 843.0 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: 3.29 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: 6.51 Time building geometry restraints manager: 3.06 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: 10.050 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.450 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.580 ------------------------------------------------------------------------------- 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 : 0.825 14.828 39298 Z= 0.570 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 0.82470 / 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 : 0.889 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: 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: 0.5682 time to fit residues: 215.6751 Evaluate side-chains 291 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 4.9990 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** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 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 = 0.4177 r_free = 0.4177 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105806 restraints weight = 58080.053| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.35 r_work: 0.3469 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28107 Z= 0.251 Angle : 0.721 11.078 39298 Z= 0.386 Chirality : 0.048 0.241 4343 Planarity : 0.006 0.082 3879 Dihedral : 26.876 172.996 6228 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.35 % Allowed : 25.69 % Favored : 68.96 % 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: -0.64 (0.16), residues: 2450 helix: 0.31 (0.14), residues: 1359 sheet: 0.37 (0.63), residues: 87 loop : -1.49 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 88 TYR 0.032 0.002 TYR P 88 PHE 0.020 0.002 PHE Q 25 TRP 0.036 0.002 TRP B 775 HIS 0.011 0.002 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (28105) covalent geometry : angle 0.72072 / 0.39 (39296) SS BOND : bond 0.00976 / 0.61 ( 1) SS BOND : angle 3.41594 / 1.45 ( 2) hydrogen bonds : bond 0.05109 / 3.37 ( 1340) hydrogen bonds : angle 4.08043 / 2.81 ( 3600) metal coordination : bond 0.01065 / 0.67 ( 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 466 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 347 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: D 280 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.5635 (tm-30) REVERT: D 291 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8243 (mmtt) REVERT: D 350 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7491 (tm-30) REVERT: F 256 MET cc_start: 0.5729 (tpp) cc_final: 0.5103 (pmt) REVERT: F 368 MET cc_start: 0.3821 (ttt) cc_final: 0.3566 (ppp) REVERT: O 63 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7757 (mmp80) REVERT: O 115 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8727 (mmtm) REVERT: R 76 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8112 (ttp80) REVERT: U 29 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8890 (ttm170) REVERT: U 73 ASN cc_start: 0.7490 (p0) cc_final: 0.7275 (p0) REVERT: A 105 ASN cc_start: 0.8999 (t0) cc_final: 0.8760 (t0) REVERT: A 118 GLU cc_start: 0.8576 (mp0) cc_final: 0.8366 (mp0) REVERT: A 306 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: A 316 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7354 (ptp90) REVERT: A 325 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: B 773 MET cc_start: 0.5467 (ppp) cc_final: 0.4698 (ppp) REVERT: B 813 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 825 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 1185 ASP cc_start: 0.8225 (t70) cc_final: 0.8000 (t0) REVERT: B 1244 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8272 (mmtp) REVERT: B 1317 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.6167 (pt) REVERT: E 500 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6833 (pttt) REVERT: E 501 LYS cc_start: 0.6647 (mmtt) cc_final: 0.6381 (mmtm) REVERT: E 544 GLU cc_start: 0.8370 (mp0) cc_final: 0.7959 (mp0) REVERT: E 559 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7316 (ptmt) outliers start: 119 outliers final: 37 residues processed: 416 average time/residue: 0.6146 time to fit residues: 298.3501 Evaluate side-chains 345 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU 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 63 ARG Chi-restraints excluded: chain O residue 73 GLU 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 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 171 ILE 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 860 MET 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 Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 87 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 257 optimal weight: 0.4980 chunk 261 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 304 ASN ** 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 = 0.4161 r_free = 0.4161 target = 0.135272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.103594 restraints weight = 58031.258| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.19 r_work: 0.3452 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2446 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= 0.147 Angle : 0.590 10.214 39298 Z= 0.322 Chirality : 0.041 0.217 4343 Planarity : 0.004 0.068 3879 Dihedral : 26.915 172.928 6227 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.87 % Allowed : 27.08 % Favored : 69.05 % 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: -0.10 (0.17), residues: 2450 helix: 0.82 (0.14), residues: 1362 sheet: 0.46 (0.63), residues: 84 loop : -1.35 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 71 TYR 0.020 0.001 TYR A 347 PHE 0.036 0.001 PHE F 362 TRP 0.021 0.001 TRP B 775 HIS 0.007 0.001 HIS B1221 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (28105) covalent geometry : angle 0.59009 / 0.32 (39296) SS BOND : bond 0.00790 / 0.49 ( 1) SS BOND : angle 2.62892 / 1.14 ( 2) hydrogen bonds : bond 0.04154 / 2.71 ( 1340) hydrogen bonds : angle 3.81413 / 2.64 ( 3600) metal coordination : bond 0.00274 / 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 404 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 318 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 103 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: D 291 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8302 (mmtt) REVERT: D 350 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7471 (tm-30) REVERT: F 256 MET cc_start: 0.5616 (tpp) cc_final: 0.5009 (pmt) REVERT: F 317 GLN cc_start: 0.4995 (OUTLIER) cc_final: 0.4686 (pm20) REVERT: F 347 MET cc_start: 0.1996 (pp-130) cc_final: 0.1751 (pp-130) REVERT: F 368 MET cc_start: 0.3813 (ttt) cc_final: 0.3608 (ppp) REVERT: O 115 LYS cc_start: 0.8941 (mmtp) cc_final: 0.8687 (mmtm) REVERT: U 29 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8816 (ttm170) REVERT: A 105 ASN cc_start: 0.9151 (t0) cc_final: 0.8794 (t0) REVERT: A 118 GLU cc_start: 0.8532 (mp0) cc_final: 0.8288 (mp0) REVERT: A 325 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: A 373 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6137 (mpp) REVERT: B 773 MET cc_start: 0.5644 (ppp) cc_final: 0.5011 (ppp) REVERT: B 809 LYS cc_start: 0.7847 (tttt) cc_final: 0.7496 (tttm) REVERT: B 813 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 825 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 860 MET cc_start: 0.6477 (mpp) cc_final: 0.5822 (mpt) REVERT: B 868 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7831 (mtt-85) REVERT: B 1020 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8587 (tp) REVERT: B 1244 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8267 (mmtp) REVERT: B 1285 ILE cc_start: 0.8685 (mm) cc_final: 0.8380 (mp) REVERT: B 1317 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.6066 (pt) REVERT: E 500 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6877 (pttt) REVERT: E 501 LYS cc_start: 0.6635 (mmtt) cc_final: 0.6379 (mmtm) REVERT: E 544 GLU cc_start: 0.8315 (mp0) cc_final: 0.7853 (mp0) outliers start: 86 outliers final: 31 residues processed: 375 average time/residue: 0.5924 time to fit residues: 260.6285 Evaluate side-chains 329 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 R residue 75 SER 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 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 699 LEU 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 993 ASP Chi-restraints excluded: chain B residue 1020 LEU 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 546 SER Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain E residue 558 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 235 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS D 389 ASN ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS Q 38 ASN R 64 ASN T 25 ASN V 60 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.127537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094383 restraints weight = 56290.504| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.23 r_work: 0.3264 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 28107 Z= 0.236 Angle : 0.683 16.145 39298 Z= 0.364 Chirality : 0.045 0.635 4343 Planarity : 0.005 0.060 3879 Dihedral : 27.180 174.209 6225 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.08 % Allowed : 25.19 % Favored : 69.73 % Cbeta Deviations : 0.04 % 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: -0.09 (0.17), residues: 2450 helix: 0.84 (0.14), residues: 1360 sheet: -0.06 (0.58), residues: 89 loop : -1.31 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 30 TYR 0.023 0.002 TYR A 347 PHE 0.020 0.002 PHE G 551 TRP 0.027 0.002 TRP B 775 HIS 0.009 0.001 HIS B1221 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (28105) covalent geometry : angle 0.67852 / 0.36 (39296) SS BOND : bond 0.01616 / 1.01 ( 1) SS BOND : angle 10.52232 / 3.66 ( 2) hydrogen bonds : bond 0.04841 / 3.17 ( 1340) hydrogen bonds : angle 3.85877 / 2.66 ( 3600) metal coordination : bond 0.00573 / 0.36 ( 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 435 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 322 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7777 (mmm) cc_final: 0.6688 (mpt) REVERT: D 103 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: D 291 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8484 (mmtt) REVERT: D 350 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7672 (tm-30) REVERT: F 256 MET cc_start: 0.5680 (tpp) cc_final: 0.5077 (pmt) REVERT: F 317 GLN cc_start: 0.4931 (OUTLIER) cc_final: 0.4612 (pm20) REVERT: F 347 MET cc_start: 0.1791 (pp-130) cc_final: 0.1473 (pp-130) REVERT: O 115 LYS cc_start: 0.9097 (mmtp) cc_final: 0.8847 (mmtm) REVERT: Q 73 ASN cc_start: 0.8058 (p0) cc_final: 0.7855 (m110) REVERT: A 118 GLU cc_start: 0.8641 (mp0) cc_final: 0.8374 (mp0) REVERT: A 306 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7688 (tmm) REVERT: A 325 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: A 373 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6758 (mpp) REVERT: B 809 LYS cc_start: 0.8301 (tttt) cc_final: 0.7897 (tttm) REVERT: B 813 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 825 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8037 (mm) REVERT: B 860 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.5834 (mpt) REVERT: B 868 ARG cc_start: 0.8416 (tpp80) cc_final: 0.7950 (mtt-85) REVERT: B 1185 ASP cc_start: 0.8322 (t70) cc_final: 0.8092 (t0) REVERT: B 1187 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6911 (mm) REVERT: B 1285 ILE cc_start: 0.8723 (mm) cc_final: 0.8430 (mp) REVERT: B 1317 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6504 (pt) REVERT: E 500 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7002 (pttt) REVERT: E 501 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6429 (mptp) REVERT: E 523 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7390 (pt) REVERT: E 554 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8395 (tmtm) REVERT: E 559 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7161 (ptmt) REVERT: G 303 CYS cc_start: 0.2439 (OUTLIER) cc_final: 0.1647 (p) REVERT: G 552 PHE cc_start: 0.8042 (t80) cc_final: 0.7826 (m-10) outliers start: 113 outliers final: 41 residues processed: 394 average time/residue: 0.6749 time to fit residues: 306.7875 Evaluate side-chains 329 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 317 GLN 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 43 LYS 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 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 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 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 667 THR Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU 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 1244 LYS 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 523 ILE 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 Chi-restraints excluded: chain G residue 303 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 254 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Q 38 ASN R 46 HIS U 104 GLN V 60 ASN V 106 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** 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** B1143 ASN ** B1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 ASN E 519 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.122291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086905 restraints weight = 56358.479| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.00 r_work: 0.3188 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 28107 Z= 0.270 Angle : 0.722 10.221 39298 Z= 0.384 Chirality : 0.047 0.226 4343 Planarity : 0.005 0.056 3879 Dihedral : 27.540 175.294 6225 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.31 % Allowed : 25.64 % Favored : 69.05 % 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: -0.25 (0.16), residues: 2450 helix: 0.72 (0.14), residues: 1359 sheet: -0.89 (0.54), residues: 97 loop : -1.30 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 424 TYR 0.028 0.002 TYR A 347 PHE 0.037 0.002 PHE F 362 TRP 0.027 0.002 TRP B1151 HIS 0.010 0.001 HIS R 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.27 (28105) covalent geometry : angle 0.71947 / 0.38 (39296) SS BOND : bond 0.02596 / 1.62 ( 1) SS BOND : angle 8.96496 / 3.55 ( 2) hydrogen bonds : bond 0.04630 / 3.01 ( 1340) hydrogen bonds : angle 3.96614 / 2.72 ( 3600) metal coordination : bond 0.00648 / 0.40 ( 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 430 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 312 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7585 (mmm) cc_final: 0.6715 (mpt) REVERT: D 82 GLN cc_start: 0.6941 (pp30) cc_final: 0.6563 (pt0) REVERT: D 291 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8668 (mmtt) REVERT: D 308 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7991 (mm-30) REVERT: D 350 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7754 (tm-30) REVERT: F 256 MET cc_start: 0.5762 (tpp) cc_final: 0.5137 (pmt) REVERT: F 317 GLN cc_start: 0.4813 (OUTLIER) cc_final: 0.4565 (pm20) REVERT: F 347 MET cc_start: 0.1918 (pp-130) cc_final: 0.1546 (pp-130) REVERT: O 115 LYS cc_start: 0.9181 (mmtp) cc_final: 0.8933 (mmtm) REVERT: R 105 LYS cc_start: 0.8712 (pttm) cc_final: 0.8507 (ptpp) REVERT: U 64 GLU cc_start: 0.8622 (tt0) cc_final: 0.8243 (tp30) REVERT: V 46 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8572 (m170) REVERT: A 60 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6467 (ptpp) REVERT: A 118 GLU cc_start: 0.8701 (mp0) cc_final: 0.8443 (mp0) REVERT: A 306 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7830 (tmm) REVERT: A 325 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: A 373 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7967 (mtt) REVERT: B 812 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: B 825 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8090 (mm) REVERT: B 860 MET cc_start: 0.6596 (mpp) cc_final: 0.5912 (mpt) REVERT: B 868 ARG cc_start: 0.8489 (tpp80) cc_final: 0.8007 (mtt-85) REVERT: B 910 ARG cc_start: 0.8212 (ttp80) cc_final: 0.8003 (ttp80) REVERT: B 1187 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6926 (mm) REVERT: B 1285 ILE cc_start: 0.8837 (mm) cc_final: 0.8534 (mp) REVERT: B 1317 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7283 (pp) REVERT: E 501 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6549 (mptp) REVERT: E 517 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8721 (p0) REVERT: E 542 ILE cc_start: 0.8538 (mm) cc_final: 0.8230 (tt) REVERT: E 554 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8547 (tmtm) outliers start: 118 outliers final: 37 residues processed: 401 average time/residue: 0.6749 time to fit residues: 311.5544 Evaluate side-chains 330 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 317 GLN 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 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 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 46 HIS Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 60 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 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 812 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 1244 LYS Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 517 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 O 76 GLN Q 38 ASN U 38 ASN V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088160 restraints weight = 56106.333| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.98 r_work: 0.3212 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28107 Z= 0.170 Angle : 0.656 10.708 39298 Z= 0.350 Chirality : 0.043 0.270 4343 Planarity : 0.004 0.054 3879 Dihedral : 27.473 174.451 6225 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.18 % Allowed : 26.68 % Favored : 69.14 % 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: 0.83 (0.14), residues: 1358 sheet: -0.62 (0.57), residues: 89 loop : -1.27 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 30 TYR 0.020 0.002 TYR V 37 PHE 0.073 0.002 PHE F 362 TRP 0.023 0.002 TRP B 775 HIS 0.011 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (28105) covalent geometry : angle 0.65646 / 0.35 (39296) SS BOND : bond 0.00189 / 0.12 ( 1) SS BOND : angle 0.85704 / 0.30 ( 2) hydrogen bonds : bond 0.03972 / 2.55 ( 1340) hydrogen bonds : angle 3.85610 / 2.65 ( 3600) metal coordination : bond 0.00398 / 0.25 ( 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 379 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 286 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7588 (mmm) cc_final: 0.6853 (mpt) REVERT: D 291 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8666 (mmtt) REVERT: D 308 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7979 (mm-30) REVERT: D 350 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7721 (tm-30) REVERT: D 384 ASP cc_start: 0.8280 (p0) cc_final: 0.8078 (p0) REVERT: F 256 MET cc_start: 0.5797 (tpp) cc_final: 0.5177 (pmt) REVERT: F 317 GLN cc_start: 0.4829 (OUTLIER) cc_final: 0.4577 (pm20) REVERT: O 59 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: O 115 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8917 (mmtm) REVERT: P 85 ASP cc_start: 0.8668 (p0) cc_final: 0.8421 (p0) REVERT: U 64 GLU cc_start: 0.8583 (tt0) cc_final: 0.8203 (tp30) REVERT: V 46 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8530 (m170) REVERT: V 54 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8519 (ttpp) REVERT: A 60 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6414 (ptpp) REVERT: A 118 GLU cc_start: 0.8697 (mp0) cc_final: 0.8457 (mp0) REVERT: A 138 LYS cc_start: 0.7562 (tppt) cc_final: 0.7216 (tptp) REVERT: A 211 TYR cc_start: 0.8186 (t80) cc_final: 0.7890 (t80) REVERT: A 306 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7752 (tmm) REVERT: A 325 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: A 373 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7923 (mtt) REVERT: B 825 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8060 (mm) REVERT: B 860 MET cc_start: 0.6598 (mpp) cc_final: 0.5878 (mpt) REVERT: B 868 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8019 (mtt-85) REVERT: B 1244 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8514 (mptp) REVERT: B 1285 ILE cc_start: 0.8834 (mm) cc_final: 0.8528 (mp) REVERT: E 316 MET cc_start: 0.1446 (mpm) cc_final: 0.1127 (mpp) REVERT: E 500 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7131 (pttt) REVERT: E 501 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6509 (mptp) REVERT: E 542 ILE cc_start: 0.8464 (mm) cc_final: 0.8183 (tt) REVERT: E 554 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8527 (tmtm) outliers start: 93 outliers final: 41 residues processed: 352 average time/residue: 0.7093 time to fit residues: 288.0140 Evaluate side-chains 328 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR 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 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 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 56 LYS 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 46 HIS 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 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 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 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS 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 360 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 261 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Q 38 ASN S 85 GLN U 38 ASN U 104 GLN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 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** E 519 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091023 restraints weight = 56008.833| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.13 r_work: 0.3206 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28107 Z= 0.159 Angle : 0.639 9.396 39298 Z= 0.344 Chirality : 0.042 0.214 4343 Planarity : 0.004 0.050 3879 Dihedral : 27.397 174.516 6225 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.05 % Allowed : 26.72 % Favored : 69.23 % 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: -0.00 (0.17), residues: 2450 helix: 0.95 (0.14), residues: 1358 sheet: -0.66 (0.57), residues: 89 loop : -1.25 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 30 TYR 0.022 0.001 TYR V 37 PHE 0.047 0.002 PHE G 552 TRP 0.032 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (28105) covalent geometry : angle 0.63932 / 0.34 (39296) SS BOND : bond 0.00304 / 0.19 ( 1) SS BOND : angle 0.52837 / 0.25 ( 2) hydrogen bonds : bond 0.03820 / 2.45 ( 1340) hydrogen bonds : angle 3.79966 / 2.62 ( 3600) metal coordination : bond 0.00331 / 0.21 ( 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 381 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 291 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7703 (mmm) cc_final: 0.7042 (mpt) REVERT: D 291 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8686 (mmtt) REVERT: D 308 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8002 (mm-30) REVERT: D 350 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7789 (tm-30) REVERT: F 256 MET cc_start: 0.5736 (tpp) cc_final: 0.5145 (pmt) REVERT: F 317 GLN cc_start: 0.4829 (OUTLIER) cc_final: 0.4569 (pm20) REVERT: F 347 MET cc_start: 0.1988 (OUTLIER) cc_final: 0.1119 (pp-130) REVERT: O 59 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: O 115 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8941 (mmtm) REVERT: R 105 LYS cc_start: 0.8757 (pttm) cc_final: 0.8482 (ptpp) REVERT: S 42 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7983 (ptm-80) REVERT: V 32 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: V 46 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8486 (m170) REVERT: V 54 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8541 (ttpp) REVERT: V 61 SER cc_start: 0.9423 (OUTLIER) cc_final: 0.9223 (m) REVERT: V 82 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8486 (mmtt) REVERT: A 118 GLU cc_start: 0.8787 (mp0) cc_final: 0.8512 (mp0) REVERT: A 138 LYS cc_start: 0.7691 (tppt) cc_final: 0.7257 (tptp) REVERT: A 210 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8397 (ptmm) REVERT: A 260 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: A 306 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7808 (tmm) REVERT: A 325 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: A 373 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7928 (mtt) REVERT: B 813 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8247 (mp0) REVERT: B 825 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8115 (mm) REVERT: B 860 MET cc_start: 0.6582 (mpp) cc_final: 0.5829 (mpt) REVERT: B 868 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7966 (mtt-85) REVERT: B 910 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8034 (ttp80) REVERT: B 1187 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6862 (mm) REVERT: B 1244 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8498 (mptp) REVERT: B 1285 ILE cc_start: 0.8860 (mm) cc_final: 0.8546 (mp) REVERT: E 272 PHE cc_start: 0.7107 (m-80) cc_final: 0.6890 (m-80) REVERT: E 316 MET cc_start: 0.1492 (mpm) cc_final: 0.1179 (mpp) REVERT: E 500 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7209 (pttt) REVERT: E 501 LYS cc_start: 0.7041 (mmtt) cc_final: 0.6721 (mmtm) REVERT: E 542 ILE cc_start: 0.8390 (mm) cc_final: 0.8089 (tt) REVERT: E 554 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8488 (tmtm) REVERT: E 559 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6973 (ptmt) outliers start: 90 outliers final: 40 residues processed: 350 average time/residue: 0.7395 time to fit residues: 297.8525 Evaluate side-chains 330 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 347 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 45 VAL 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 56 LYS 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 V residue 32 GLU Chi-restraints excluded: chain V residue 46 HIS 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 189 HIS Chi-restraints excluded: chain A residue 210 LYS 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 A residue 422 ARG Chi-restraints excluded: chain B residue 667 THR 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 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 1244 LYS 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 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: 0.8980 chunk 123 optimal weight: 9.9990 chunk 232 optimal weight: 0.5980 chunk 111 optimal weight: 50.0000 chunk 1 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN Q 38 ASN R 46 HIS R 60 ASN R 64 ASN S 108 ASN U 38 ASN U 104 GLN 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** ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088415 restraints weight = 56366.484| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.97 r_work: 0.3220 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28107 Z= 0.160 Angle : 0.636 10.041 39298 Z= 0.341 Chirality : 0.042 0.218 4343 Planarity : 0.004 0.053 3879 Dihedral : 27.371 174.197 6225 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.42 % Allowed : 27.67 % 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: 0.04 (0.17), residues: 2450 helix: 0.96 (0.14), residues: 1362 sheet: -0.80 (0.57), residues: 88 loop : -1.18 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 30 TYR 0.026 0.001 TYR V 37 PHE 0.048 0.002 PHE F 362 TRP 0.038 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (28105) covalent geometry : angle 0.63590 / 0.34 (39296) SS BOND : bond 0.00155 / 0.10 ( 1) SS BOND : angle 0.46013 / 0.20 ( 2) hydrogen bonds : bond 0.03835 / 2.47 ( 1340) hydrogen bonds : angle 3.78671 / 2.61 ( 3600) metal coordination : bond 0.00352 / 0.22 ( 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 365 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7827 (mmm) cc_final: 0.6817 (mpt) REVERT: D 103 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6800 (pp20) REVERT: D 291 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8700 (mmtt) REVERT: D 308 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7947 (mm-30) REVERT: D 350 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7734 (tm-30) REVERT: F 256 MET cc_start: 0.5788 (tpp) cc_final: 0.5183 (pmt) REVERT: F 317 GLN cc_start: 0.4816 (OUTLIER) cc_final: 0.4554 (pm20) REVERT: F 347 MET cc_start: 0.1989 (pp-130) cc_final: 0.1179 (pp-130) REVERT: O 59 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: O 94 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8424 (mm-30) REVERT: R 105 LYS cc_start: 0.8740 (pttm) cc_final: 0.8469 (ptpp) REVERT: S 42 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7989 (ptm-80) REVERT: V 32 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: V 54 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: V 82 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8559 (mmtm) REVERT: A 60 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6586 (ptpp) REVERT: A 118 GLU cc_start: 0.8721 (mp0) cc_final: 0.8466 (mp0) REVERT: A 138 LYS cc_start: 0.7672 (tppt) cc_final: 0.7307 (tptp) REVERT: A 210 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8383 (ptmm) REVERT: A 260 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: A 306 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7770 (tmm) REVERT: A 325 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 373 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7930 (mtt) REVERT: B 825 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8122 (mm) REVERT: B 860 MET cc_start: 0.6590 (mpp) cc_final: 0.5839 (mpt) REVERT: B 868 ARG cc_start: 0.8412 (tpp80) cc_final: 0.7938 (mtt-85) REVERT: B 1019 SER cc_start: 0.9032 (p) cc_final: 0.8621 (m) REVERT: B 1187 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6841 (mm) REVERT: B 1244 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8522 (mptp) REVERT: E 272 PHE cc_start: 0.7088 (m-80) cc_final: 0.6842 (m-80) REVERT: E 500 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7187 (pttt) REVERT: E 501 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6577 (mptp) REVERT: E 542 ILE cc_start: 0.8364 (mm) cc_final: 0.8105 (tt) REVERT: E 554 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8552 (tmtm) outliers start: 76 outliers final: 37 residues processed: 342 average time/residue: 0.7252 time to fit residues: 284.1680 Evaluate side-chains 326 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 344 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 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 75 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS 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 32 GLU 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 210 LYS 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 A residue 422 ARG Chi-restraints excluded: chain B residue 667 THR 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 1194 MET Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS 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 373 SER Chi-restraints excluded: chain E residue 398 LEU 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 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 176 optimal weight: 0.0570 chunk 223 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN Q 38 ASN R 46 HIS R 60 ASN R 64 ASN R 106 HIS U 38 ASN U 104 GLN V 46 HIS 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** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.120836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085752 restraints weight = 56119.201| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.97 r_work: 0.3163 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28107 Z= 0.220 Angle : 0.682 10.743 39298 Z= 0.363 Chirality : 0.044 0.222 4343 Planarity : 0.004 0.049 3879 Dihedral : 27.461 174.384 6225 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.37 % Allowed : 27.58 % Favored : 69.05 % 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: 0.88 (0.14), residues: 1367 sheet: -0.71 (0.60), residues: 78 loop : -1.15 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 30 TYR 0.028 0.002 TYR V 37 PHE 0.048 0.002 PHE F 362 TRP 0.047 0.002 TRP B 775 HIS 0.013 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (28105) covalent geometry : angle 0.68190 / 0.36 (39296) SS BOND : bond 0.00192 / 0.12 ( 1) SS BOND : angle 0.53158 / 0.24 ( 2) hydrogen bonds : bond 0.04359 / 2.81 ( 1340) hydrogen bonds : angle 3.83819 / 2.64 ( 3600) metal coordination : bond 0.00599 / 0.37 ( 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 378 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7658 (mmm) cc_final: 0.6936 (mpt) REVERT: D 291 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8754 (mmtt) REVERT: D 308 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8036 (mm-30) REVERT: D 350 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7788 (tm-30) REVERT: F 89 ASP cc_start: 0.1319 (m-30) cc_final: 0.1045 (m-30) REVERT: F 256 MET cc_start: 0.5811 (tpp) cc_final: 0.5198 (pmt) REVERT: F 317 GLN cc_start: 0.4774 (OUTLIER) cc_final: 0.4495 (pm20) REVERT: F 347 MET cc_start: 0.2145 (OUTLIER) cc_final: 0.1420 (pp-130) REVERT: O 59 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: R 105 LYS cc_start: 0.8758 (pttm) cc_final: 0.8477 (ptpp) REVERT: S 59 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: V 54 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8578 (ttpp) REVERT: V 82 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8532 (mmtt) REVERT: A 60 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6949 (ptpp) REVERT: A 98 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7904 (pttt) REVERT: A 118 GLU cc_start: 0.8734 (mp0) cc_final: 0.8428 (mp0) REVERT: A 138 LYS cc_start: 0.7799 (tppt) cc_final: 0.7423 (tptp) REVERT: A 210 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8501 (ptmm) REVERT: A 260 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: A 293 ASN cc_start: 0.8572 (t0) cc_final: 0.8167 (t0) REVERT: A 306 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7751 (tmm) REVERT: A 325 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 825 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 860 MET cc_start: 0.6634 (mpp) cc_final: 0.5885 (mpt) REVERT: B 868 ARG cc_start: 0.8433 (tpp80) cc_final: 0.7942 (mtt-85) REVERT: B 910 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8065 (ttp80) REVERT: B 1019 SER cc_start: 0.9045 (p) cc_final: 0.8661 (m) REVERT: B 1187 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6814 (mm) REVERT: B 1244 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8531 (mptp) REVERT: B 1298 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6688 (mt-10) REVERT: E 272 PHE cc_start: 0.7030 (m-80) cc_final: 0.6773 (m-80) REVERT: E 316 MET cc_start: 0.1419 (mpm) cc_final: 0.1071 (mpp) REVERT: E 500 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7298 (pttt) REVERT: E 501 LYS cc_start: 0.7111 (mmtt) cc_final: 0.6618 (mptp) REVERT: E 542 ILE cc_start: 0.8467 (mm) cc_final: 0.8211 (tt) REVERT: E 554 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8556 (tmtm) outliers start: 75 outliers final: 39 residues processed: 350 average time/residue: 0.7521 time to fit residues: 301.5821 Evaluate side-chains 344 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 290 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 TYR Chi-restraints excluded: chain D residue 256 MET 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 O residue 59 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 117 VAL 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 75 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 59 GLU 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 61 SER Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 210 LYS 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 360 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 667 THR 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 1018 ILE Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1194 MET Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 398 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 237 optimal weight: 8.9990 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: 30.0000 chunk 212 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 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 ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3956 r_free = 0.3956 target = 0.121378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086524 restraints weight = 56074.567| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.96 r_work: 0.3185 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28107 Z= 0.177 Angle : 0.671 11.742 39298 Z= 0.357 Chirality : 0.043 0.223 4343 Planarity : 0.004 0.075 3879 Dihedral : 27.447 173.447 6225 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.61 % Allowed : 28.70 % Favored : 68.69 % 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: 0.90 (0.14), residues: 1367 sheet: -0.81 (0.59), residues: 78 loop : -1.14 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 30 TYR 0.032 0.002 TYR T 88 PHE 0.045 0.002 PHE F 362 TRP 0.054 0.002 TRP B 775 HIS 0.008 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (28105) covalent geometry : angle 0.67075 / 0.36 (39296) SS BOND : bond 0.00179 / 0.11 ( 1) SS BOND : angle 0.55305 / 0.25 ( 2) hydrogen bonds : bond 0.03909 / 2.51 ( 1340) hydrogen bonds : angle 3.84233 / 2.65 ( 3600) metal coordination : bond 0.00388 / 0.24 ( 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 348 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 MET cc_start: 0.7660 (mmm) cc_final: 0.7052 (mpt) REVERT: D 275 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7450 (mm-40) REVERT: D 291 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8765 (mmtt) REVERT: D 308 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7969 (mm-30) REVERT: D 350 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7774 (tm-30) REVERT: F 89 ASP cc_start: 0.1353 (m-30) cc_final: 0.1121 (m-30) REVERT: F 256 MET cc_start: 0.5795 (tpp) cc_final: 0.5200 (pmt) REVERT: F 317 GLN cc_start: 0.4741 (OUTLIER) cc_final: 0.4462 (pm20) REVERT: F 347 MET cc_start: 0.2060 (OUTLIER) cc_final: 0.1361 (pp-130) REVERT: O 59 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: R 105 LYS cc_start: 0.8708 (pttm) cc_final: 0.8438 (ptpp) REVERT: V 54 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8553 (ttpp) REVERT: V 82 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8554 (mmtm) REVERT: A 60 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6985 (ptpp) REVERT: A 118 GLU cc_start: 0.8715 (mp0) cc_final: 0.8443 (mp0) REVERT: A 138 LYS cc_start: 0.7869 (tppt) cc_final: 0.7410 (tmtt) REVERT: A 210 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8408 (ptmm) REVERT: A 260 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: A 293 ASN cc_start: 0.8611 (t0) cc_final: 0.8201 (t0) REVERT: A 306 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: A 325 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: B 825 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8097 (mm) REVERT: B 860 MET cc_start: 0.6631 (mpp) cc_final: 0.5869 (mpt) REVERT: B 868 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7924 (mtt-85) REVERT: B 910 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8074 (ttp80) REVERT: B 1019 SER cc_start: 0.9066 (p) cc_final: 0.8637 (m) REVERT: B 1187 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6824 (mm) REVERT: B 1244 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8527 (mptp) REVERT: E 272 PHE cc_start: 0.7029 (m-80) cc_final: 0.6774 (m-80) REVERT: E 316 MET cc_start: 0.1491 (mpm) cc_final: 0.1163 (mpp) REVERT: E 500 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7237 (pttt) REVERT: E 501 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6578 (mptp) REVERT: E 542 ILE cc_start: 0.8423 (mm) cc_final: 0.8180 (tt) REVERT: E 554 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8568 (tmtm) REVERT: E 559 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7098 (ptmt) REVERT: G 316 MET cc_start: 0.3427 (OUTLIER) cc_final: 0.2974 (tpt) outliers start: 58 outliers final: 35 residues processed: 332 average time/residue: 0.7514 time to fit residues: 286.0579 Evaluate side-chains 337 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 286 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain F residue 234 ASP 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 O residue 59 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 117 VAL 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 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 60 LYS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 210 LYS 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 422 ARG Chi-restraints excluded: chain B residue 667 THR 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 1194 MET Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1244 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 398 LEU 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 Chi-restraints excluded: chain G residue 316 MET 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: 0.0170 chunk 223 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- 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** ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN S 39 HIS U 38 ASN U 104 GLN 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** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.121156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088679 restraints weight = 55764.593| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.09 r_work: 0.3154 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28107 Z= 0.179 Angle : 0.667 11.131 39298 Z= 0.356 Chirality : 0.043 0.226 4343 Planarity : 0.004 0.061 3879 Dihedral : 27.414 173.679 6225 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.83 % Allowed : 28.52 % Favored : 68.65 % 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: 0.02 (0.17), residues: 2450 helix: 0.91 (0.14), residues: 1366 sheet: -0.91 (0.59), residues: 78 loop : -1.13 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 30 TYR 0.033 0.002 TYR V 37 PHE 0.044 0.002 PHE F 362 TRP 0.057 0.002 TRP B 775 HIS 0.012 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (28105) covalent geometry : angle 0.66725 / 0.36 (39296) SS BOND : bond 0.00190 / 0.12 ( 1) SS BOND : angle 0.57418 / 0.26 ( 2) hydrogen bonds : bond 0.03968 / 2.56 ( 1340) hydrogen bonds : angle 3.83427 / 2.65 ( 3600) metal coordination : bond 0.00435 / 0.27 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11229.63 seconds wall clock time: 207 minutes 19.68 seconds (12439.68 seconds total)