Starting phenix.real_space_refine on Sat Aug 8 08:49:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2026/8kd3_37123.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 328 5.49 5 S 100 5.16 5 C 16471 2.51 5 N 4897 2.21 5 O 5779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27576 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2620 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 3 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1647 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 2 Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1043 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} 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: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 848 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.20 Number of scatterers: 27576 At special positions: 0 Unit cell: (137.03, 161.17, 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 100 16.00 P 328 15.00 O 5779 8.00 N 4897 7.00 C 16471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS G 263 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 306 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 765.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4866 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 18 sheets defined 56.7% alpha, 3.6% beta 139 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.295A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.933A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.838A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.011A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.564A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.569A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.566A 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 'B' and resid 665 through 677 removed outlier: 4.618A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 5.174A 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: 3.550A 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 759 through 764 removed outlier: 3.674A pdb=" N THR B 763 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 764 " --> pdb=" O LYS B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 764' Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.711A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 839 removed outlier: 3.667A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.023A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.963A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 3.996A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 removed outlier: 4.035A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.808A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.085A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.632A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 3.916A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.867A 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 1221 through 1230 Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.803A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.583A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (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 1309 No H-bonds generated for 'chain 'B' and resid 1307 through 1309' Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.587A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 293 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.517A pdb=" N ILE D 325 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 removed outlier: 4.038A 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 removed outlier: 3.503A pdb=" N HIS D 369 " --> pdb=" O TRP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.905A 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 removed outlier: 3.712A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.118A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.984A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.566A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.808A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 3.972A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.371A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 263 No H-bonds generated for 'chain 'F' and resid 261 through 263' Processing helix chain 'F' and resid 275 through 292 removed outlier: 4.318A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 328 through 338 removed outlier: 4.310A pdb=" N LEU F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 348 through 368 removed outlier: 3.709A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.729A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN G 329 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.828A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.999A 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 570 removed outlier: 3.568A pdb=" N GLN G 570 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.680A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.538A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.756A 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: 3.929A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 removed outlier: 3.573A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) 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 74 removed outlier: 4.346A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.581A 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 Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 119 Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.582A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.757A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.914A 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 24 through 29 removed outlier: 3.794A pdb=" N GLN T 27 " --> pdb=" O ASP T 24 " (cutoff:3.500A) removed outlier: 3.911A 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: 3.790A pdb=" N GLU T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.812A 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 36 Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.179A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.561A 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 Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.782A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 removed outlier: 3.511A pdb=" N ILE V 91 " --> pdb=" O THR V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.023A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.272A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 756 through 757 removed outlier: 4.156A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 974 through 978 removed outlier: 5.070A pdb=" N LEU B 975 " --> pdb=" O ILE B1314 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B1314 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 977 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B1312 " --> pdb=" O PHE B 977 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA7, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA8, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.833A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.704A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.905A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.212A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.399A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'S' and resid 83 through 84 removed outlier: 7.190A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.028A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'U' and resid 77 through 78 983 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7213 1.34 - 1.46: 7823 1.46 - 1.58: 12964 1.58 - 1.70: 656 1.70 - 1.82: 153 Bond restraints: 28809 Sorted by residual: bond pdb=" C1' DT X 66 " pdb=" N1 DT X 66 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+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 1.40e+01 bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.37e+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 1.29e+01 bond pdb=" N ASP E 288 " pdb=" CA ASP E 288 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 ... (remaining 28804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 40008 3.48 - 6.96: 226 6.96 - 10.44: 35 10.44 - 13.92: 9 13.92 - 17.40: 7 Bond angle restraints: 40285 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 97.32 14.68 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PRO B 853 " pdb=" N PRO B 853 " pdb=" CD PRO B 853 " ideal model delta sigma weight residual 112.00 102.60 9.40 1.40e+00 5.10e-01 4.51e+01 angle pdb=" CB MET D 107 " pdb=" CG MET D 107 " pdb=" SD MET D 107 " ideal model delta sigma weight residual 112.70 130.10 -17.40 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.29 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 128.61 -15.91 3.00e+00 1.11e-01 2.81e+01 ... (remaining 40280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14402 35.15 - 70.29: 2026 70.29 - 105.44: 60 105.44 - 140.59: 2 140.59 - 175.74: 1 Dihedral angle restraints: 16491 sinusoidal: 8965 harmonic: 7526 Sorted by residual: dihedral pdb=" CB CYS G 263 " pdb=" SG CYS G 263 " pdb=" SG CYS G 266 " pdb=" CB CYS G 266 " ideal model delta sinusoidal sigma weight residual 93.00 46.45 46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C MET D 107 " pdb=" N MET D 107 " pdb=" CA MET D 107 " pdb=" CB MET D 107 " ideal model delta harmonic sigma weight residual -122.60 -132.87 10.27 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 16488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4098 0.081 - 0.161: 323 0.161 - 0.242: 17 0.242 - 0.323: 3 0.323 - 0.403: 1 Chirality restraints: 4442 Sorted by residual: chirality pdb=" CA ILE E 395 " pdb=" N ILE E 395 " pdb=" C ILE E 395 " pdb=" CB ILE E 395 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.07e+00 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 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA MET D 107 " pdb=" N MET D 107 " pdb=" C MET D 107 " pdb=" CB MET D 107 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 4439 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 852 " -0.095 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 853 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 853 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 853 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.073 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 319 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 88 " -0.023 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" CG TYR P 88 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR P 88 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR P 88 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR P 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 88 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR P 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR P 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 5 2.01 - 2.73: 1570 2.73 - 3.45: 38270 3.45 - 4.18: 72964 4.18 - 4.90: 117351 Nonbonded interactions: 230160 Sorted by model distance: nonbonded pdb=" OE2 GLU B 885 " pdb=" CD2 HIS B 886 " model vdw 1.281 3.260 nonbonded pdb=" NE2 HIS O 113 " pdb=" OD1 ASP S 123 " model vdw 1.391 3.120 nonbonded pdb=" OD1 ASP B 872 " pdb=" O ILE E 54 " model vdw 1.709 3.040 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 1.813 3.880 nonbonded pdb=" OE2 GLU B 816 " pdb=" OD1 ASP E 47 " model vdw 1.850 3.040 ... (remaining 230155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 11 through 24 or resid 80 through 113 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 36 through 133) selection = (chain 'S' and resid 36 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 14.200 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: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 29.010 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 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 0.185 28814 Z= 0.410 Angle : 0.850 17.397 40291 Z= 0.595 Chirality : 0.047 0.403 4442 Planarity : 0.006 0.137 3978 Dihedral : 24.414 175.735 11616 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.13 % Allowed : 30.60 % Favored : 69.27 % 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: -1.28 (0.16), residues: 2507 helix: -0.20 (0.13), residues: 1350 sheet: 0.83 (0.61), residues: 93 loop : -1.83 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG U 71 TYR 0.066 0.001 TYR P 88 PHE 0.023 0.001 PHE B 985 TRP 0.046 0.001 TRP F 365 HIS 0.005 0.001 HIS R 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.41 (28809) covalent geometry : angle 0.85032 / 0.60 (40285) SS BOND : bond 0.00522 / 0.26 ( 3) SS BOND : angle 0.90434 / 0.56 ( 6) hydrogen bonds : bond 0.10934 / 7.00 ( 1350) hydrogen bonds : angle 4.89267 / 3.48 ( 3635) metal coordination : bond 0.00030 / 0.02 ( 1) Misc. bond : bond 0.06595 / 3.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.8387 (t) cc_final: 0.8034 (m) REVERT: D 107 MET cc_start: 0.7324 (ttt) cc_final: 0.7025 (mmp) REVERT: D 223 GLN cc_start: 0.6619 (pp30) cc_final: 0.6350 (pp30) REVERT: F 307 ASP cc_start: 0.4858 (t70) cc_final: 0.4589 (t70) REVERT: F 340 GLU cc_start: 0.4745 (pm20) cc_final: 0.4526 (tm-30) outliers start: 3 outliers final: 0 residues processed: 326 average time/residue: 0.4970 time to fit residues: 194.0454 Evaluate side-chains 280 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 HIS ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 HIS O 39 HIS ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN P 75 HIS Q 38 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN S 85 GLN S 93 GLN T 25 ASN U 38 ASN V 60 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.141369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.108601 restraints weight = 57496.861| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.27 r_work: 0.3471 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 28814 Z= 0.253 Angle : 0.741 12.895 40291 Z= 0.394 Chirality : 0.048 0.422 4442 Planarity : 0.006 0.076 3978 Dihedral : 26.772 172.243 6379 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.53 % Allowed : 24.14 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2507 helix: 0.23 (0.13), residues: 1383 sheet: 0.56 (0.58), residues: 96 loop : -1.65 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG U 71 TYR 0.042 0.003 TYR F 238 PHE 0.022 0.002 PHE A 215 TRP 0.022 0.002 TRP F 365 HIS 0.019 0.002 HIS B 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (28809) covalent geometry : angle 0.74008 / 0.39 (40285) SS BOND : bond 0.00522 / 0.26 ( 3) SS BOND : angle 2.60748 / 1.36 ( 6) hydrogen bonds : bond 0.05137 / 3.41 ( 1350) hydrogen bonds : angle 3.94684 / 2.74 ( 3635) metal coordination : bond 0.00755 / 0.40 ( 1) Misc. bond : bond 0.00726 / 0.38 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 348 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8942 (t0) cc_final: 0.8463 (t0) REVERT: A 204 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7793 (ttp) REVERT: A 306 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.7991 (tpp) REVERT: A 373 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.6975 (mpp) REVERT: B 982 LYS cc_start: 0.6350 (mttt) cc_final: 0.6133 (tttt) REVERT: B 1137 ASN cc_start: 0.7321 (m-40) cc_final: 0.7055 (m-40) REVERT: D 107 MET cc_start: 0.6982 (ttt) cc_final: 0.6712 (pp-130) REVERT: D 357 LYS cc_start: 0.8224 (tptt) cc_final: 0.7892 (ttmt) REVERT: D 368 MET cc_start: 0.6948 (mmm) cc_final: 0.6617 (mmp) REVERT: E 369 ARG cc_start: 0.7292 (pmm-80) cc_final: 0.7004 (pmm-80) REVERT: E 387 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6186 (t80) REVERT: E 435 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7902 (mmt90) REVERT: E 548 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7834 (ptpp) REVERT: F 94 TYR cc_start: 0.2559 (OUTLIER) cc_final: 0.1991 (p90) REVERT: F 96 ARG cc_start: 0.0371 (OUTLIER) cc_final: -0.0952 (mmt180) REVERT: F 237 GLU cc_start: 0.4564 (tp30) cc_final: 0.3474 (pm20) REVERT: F 373 TYR cc_start: 0.2483 (p90) cc_final: 0.2282 (p90) REVERT: P 40 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.7959 (ttp-170) REVERT: P 44 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8462 (tttt) REVERT: P 84 MET cc_start: 0.9001 (tpp) cc_final: 0.8800 (mmt) REVERT: Q 90 ASP cc_start: 0.8348 (t0) cc_final: 0.8076 (t70) outliers start: 126 outliers final: 36 residues processed: 432 average time/residue: 0.5604 time to fit residues: 282.9961 Evaluate side-chains 350 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1299 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 121 optimal weight: 0.0970 chunk 203 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 210 optimal weight: 0.5980 chunk 229 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 217 optimal weight: 0.7980 chunk 270 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN O 39 HIS O 68 GLN Q 73 ASN T 25 ASN V 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.111632 restraints weight = 57886.451| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.79 r_work: 0.3490 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28814 Z= 0.132 Angle : 0.580 13.663 40291 Z= 0.314 Chirality : 0.040 0.260 4442 Planarity : 0.004 0.060 3978 Dihedral : 26.803 168.512 6379 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.73 % Allowed : 26.21 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.16), residues: 2507 helix: 0.74 (0.14), residues: 1383 sheet: 0.20 (0.56), residues: 96 loop : -1.49 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 89 TYR 0.023 0.001 TYR B 692 PHE 0.014 0.001 PHE E 551 TRP 0.019 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (28809) covalent geometry : angle 0.57946 / 0.31 (40285) SS BOND : bond 0.00552 / 0.28 ( 3) SS BOND : angle 1.92769 / 0.99 ( 6) hydrogen bonds : bond 0.03808 / 2.54 ( 1350) hydrogen bonds : angle 3.68169 / 2.58 ( 3635) metal coordination : bond 0.00100 / 0.05 ( 1) Misc. bond : bond 0.00106 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 315 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 89 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7215 (t) REVERT: A 105 ASN cc_start: 0.8967 (t0) cc_final: 0.8509 (t0) REVERT: A 189 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.5579 (p-80) REVERT: A 248 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7806 (mmm-85) REVERT: B 701 ASP cc_start: 0.7075 (m-30) cc_final: 0.6875 (m-30) REVERT: B 982 LYS cc_start: 0.6322 (mtmt) cc_final: 0.6117 (tttt) REVERT: B 1299 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.6036 (m-40) REVERT: D 107 MET cc_start: 0.6968 (ttt) cc_final: 0.6724 (pp-130) REVERT: D 317 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7247 (mm110) REVERT: D 357 LYS cc_start: 0.8195 (tptt) cc_final: 0.7886 (ttmt) REVERT: D 368 MET cc_start: 0.6863 (mmm) cc_final: 0.6570 (mmp) REVERT: E 387 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.6097 (t80) REVERT: E 548 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (ptpp) REVERT: F 96 ARG cc_start: 0.0508 (OUTLIER) cc_final: -0.0991 (mmt180) REVERT: F 107 MET cc_start: -0.0052 (OUTLIER) cc_final: -0.0636 (ptt) REVERT: F 288 TYR cc_start: 0.4776 (OUTLIER) cc_final: 0.4512 (t80) REVERT: P 44 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8193 (tmtt) REVERT: P 50 ILE cc_start: 0.8853 (tt) cc_final: 0.8600 (tt) REVERT: Q 51 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8893 (tp) REVERT: Q 90 ASP cc_start: 0.8318 (t0) cc_final: 0.8014 (t70) REVERT: R 53 SER cc_start: 0.9248 (p) cc_final: 0.8828 (m) REVERT: U 73 ASN cc_start: 0.8222 (t0) cc_final: 0.7969 (m110) outliers start: 85 outliers final: 32 residues processed: 365 average time/residue: 0.5628 time to fit residues: 240.8676 Evaluate side-chains 339 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain B residue 1299 ASN Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 175 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS Q 38 ASN U 38 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.130970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098196 restraints weight = 55886.827| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.84 r_work: 0.3230 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 28814 Z= 0.280 Angle : 0.739 15.320 40291 Z= 0.391 Chirality : 0.048 0.312 4442 Planarity : 0.006 0.057 3978 Dihedral : 26.957 174.549 6379 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.49 % Allowed : 24.01 % Favored : 70.50 % 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: -0.49 (0.16), residues: 2507 helix: 0.49 (0.14), residues: 1394 sheet: -0.37 (0.53), residues: 93 loop : -1.44 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 89 TYR 0.051 0.003 TYR P 88 PHE 0.052 0.003 PHE G 308 TRP 0.020 0.002 TRP B 775 HIS 0.011 0.002 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 (28809) covalent geometry : angle 0.73848 / 0.39 (40285) SS BOND : bond 0.00763 / 0.39 ( 3) SS BOND : angle 2.66580 / 1.33 ( 6) hydrogen bonds : bond 0.05757 / 3.82 ( 1350) hydrogen bonds : angle 3.94042 / 2.76 ( 3635) metal coordination : bond 0.00388 / 0.20 ( 1) Misc. bond : bond 0.00086 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 322 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.6931 (p-80) REVERT: A 211 TYR cc_start: 0.8158 (t80) cc_final: 0.7764 (t80) REVERT: A 248 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8092 (mmm-85) REVERT: A 313 TYR cc_start: 0.7411 (m-80) cc_final: 0.6731 (m-80) REVERT: A 373 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7321 (mpp) REVERT: B 695 ASP cc_start: 0.7943 (m-30) cc_final: 0.7711 (m-30) REVERT: B 701 ASP cc_start: 0.7341 (m-30) cc_final: 0.7092 (m-30) REVERT: B 821 ILE cc_start: 0.8671 (mt) cc_final: 0.8418 (mp) REVERT: B 825 LEU cc_start: 0.8855 (mt) cc_final: 0.8644 (mm) REVERT: B 1299 ASN cc_start: 0.6395 (OUTLIER) cc_final: 0.6188 (m-40) REVERT: D 82 GLN cc_start: 0.7200 (pm20) cc_final: 0.6926 (mm110) REVERT: D 107 MET cc_start: 0.6950 (ttt) cc_final: 0.6639 (pp-130) REVERT: D 353 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7678 (mm-40) REVERT: D 368 MET cc_start: 0.7309 (mmm) cc_final: 0.7101 (mmp) REVERT: E 333 VAL cc_start: 0.5937 (m) cc_final: 0.5620 (p) REVERT: E 350 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.9065 (tt0) REVERT: E 371 GLN cc_start: 0.8652 (pm20) cc_final: 0.8250 (pm20) REVERT: F 107 MET cc_start: 0.0096 (OUTLIER) cc_final: -0.0456 (ptt) REVERT: F 288 TYR cc_start: 0.4732 (OUTLIER) cc_final: 0.4417 (t80) REVERT: F 368 MET cc_start: 0.4153 (OUTLIER) cc_final: 0.3234 (ppp) REVERT: G 338 LYS cc_start: 0.3342 (OUTLIER) cc_final: 0.3097 (mtmt) REVERT: P 44 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8910 (tttt) REVERT: Q 56 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: Q 73 ASN cc_start: 0.8847 (t0) cc_final: 0.8516 (t0) REVERT: Q 90 ASP cc_start: 0.8322 (t0) cc_final: 0.8033 (t70) REVERT: R 53 SER cc_start: 0.9309 (p) cc_final: 0.8875 (m) REVERT: R 73 GLU cc_start: 0.8512 (tp30) cc_final: 0.8239 (tp30) REVERT: S 109 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8924 (mp) REVERT: T 91 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8650 (tttt) REVERT: U 73 ASN cc_start: 0.8687 (t0) cc_final: 0.8432 (m110) outliers start: 125 outliers final: 49 residues processed: 406 average time/residue: 0.5850 time to fit residues: 276.7560 Evaluate side-chains 361 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 300 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 717 PHE Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1299 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 31 optimal weight: 0.0470 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 393 GLN E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN S 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.133332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.100470 restraints weight = 55959.511| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.92 r_work: 0.3285 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28814 Z= 0.134 Angle : 0.598 11.053 40291 Z= 0.321 Chirality : 0.041 0.239 4442 Planarity : 0.004 0.052 3978 Dihedral : 27.015 169.507 6379 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.73 % Allowed : 25.86 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2507 helix: 0.79 (0.14), residues: 1386 sheet: -0.68 (0.52), residues: 93 loop : -1.35 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 96 TYR 0.036 0.001 TYR P 88 PHE 0.013 0.001 PHE A 214 TRP 0.012 0.001 TRP B 775 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (28809) covalent geometry : angle 0.59727 / 0.32 (40285) SS BOND : bond 0.00603 / 0.31 ( 3) SS BOND : angle 2.00263 / 1.05 ( 6) hydrogen bonds : bond 0.03677 / 2.43 ( 1350) hydrogen bonds : angle 3.69434 / 2.59 ( 3635) metal coordination : bond 0.00877 / 0.46 ( 1) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 316 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6508 (p-80) REVERT: A 248 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8059 (mmm-85) REVERT: A 313 TYR cc_start: 0.7292 (m-80) cc_final: 0.6820 (m-80) REVERT: B 695 ASP cc_start: 0.7925 (m-30) cc_final: 0.7713 (m-30) REVERT: B 701 ASP cc_start: 0.7437 (m-30) cc_final: 0.7169 (m-30) REVERT: B 986 TYR cc_start: 0.7947 (m-10) cc_final: 0.7700 (m-10) REVERT: D 85 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6981 (mtmm) REVERT: D 107 MET cc_start: 0.6861 (ttt) cc_final: 0.6578 (pp-130) REVERT: D 353 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7636 (mm-40) REVERT: D 368 MET cc_start: 0.7303 (mmm) cc_final: 0.7052 (mmp) REVERT: E 350 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8938 (tt0) REVERT: E 371 GLN cc_start: 0.8671 (pm20) cc_final: 0.8281 (pm20) REVERT: E 387 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: E 557 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7529 (pptt) REVERT: F 107 MET cc_start: 0.0196 (OUTLIER) cc_final: -0.0329 (ptt) REVERT: F 237 GLU cc_start: 0.4565 (tp30) cc_final: 0.3439 (pm20) REVERT: F 288 TYR cc_start: 0.4781 (OUTLIER) cc_final: 0.4453 (t80) REVERT: G 556 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.4936 (m-80) REVERT: P 50 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8513 (tt) REVERT: Q 56 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: Q 73 ASN cc_start: 0.8855 (t0) cc_final: 0.8539 (t0) REVERT: Q 90 ASP cc_start: 0.8310 (t0) cc_final: 0.8006 (t70) REVERT: R 53 SER cc_start: 0.9232 (p) cc_final: 0.8863 (m) REVERT: V 81 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7904 (m110) outliers start: 85 outliers final: 27 residues processed: 372 average time/residue: 0.5798 time to fit residues: 252.2424 Evaluate side-chains 332 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 357 LYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 157 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 89 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 317 GLN D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN V 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.133173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101047 restraints weight = 55946.885| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.80 r_work: 0.3292 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28814 Z= 0.136 Angle : 0.585 14.734 40291 Z= 0.313 Chirality : 0.041 0.239 4442 Planarity : 0.004 0.051 3978 Dihedral : 26.918 170.725 6379 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.42 % Allowed : 26.16 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2507 helix: 0.91 (0.14), residues: 1394 sheet: -0.74 (0.53), residues: 93 loop : -1.30 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 96 TYR 0.035 0.001 TYR P 88 PHE 0.012 0.001 PHE B 669 TRP 0.013 0.001 TRP B 775 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (28809) covalent geometry : angle 0.58472 / 0.31 (40285) SS BOND : bond 0.00654 / 0.33 ( 3) SS BOND : angle 2.10626 / 1.09 ( 6) hydrogen bonds : bond 0.03646 / 2.40 ( 1350) hydrogen bonds : angle 3.60837 / 2.52 ( 3635) metal coordination : bond 0.00311 / 0.16 ( 1) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 302 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6615 (p-80) REVERT: A 248 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8023 (mmm-85) REVERT: A 313 TYR cc_start: 0.7382 (m-80) cc_final: 0.6951 (m-80) REVERT: A 380 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 695 ASP cc_start: 0.7900 (m-30) cc_final: 0.7674 (m-30) REVERT: B 701 ASP cc_start: 0.7423 (m-30) cc_final: 0.7129 (m-30) REVERT: B 986 TYR cc_start: 0.7830 (m-10) cc_final: 0.7612 (m-10) REVERT: D 107 MET cc_start: 0.6831 (ttt) cc_final: 0.6535 (pp-130) REVERT: D 353 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7646 (mm-40) REVERT: E 350 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8928 (tt0) REVERT: E 371 GLN cc_start: 0.8617 (pm20) cc_final: 0.8234 (pm20) REVERT: F 96 ARG cc_start: 0.0647 (OUTLIER) cc_final: -0.0723 (mmt-90) REVERT: F 107 MET cc_start: 0.0209 (OUTLIER) cc_final: -0.0312 (ptt) REVERT: F 237 GLU cc_start: 0.4487 (tp30) cc_final: 0.3352 (pm20) REVERT: F 288 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.4439 (t80) REVERT: G 556 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5161 (m-80) REVERT: P 50 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8511 (tt) REVERT: Q 56 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: Q 73 ASN cc_start: 0.8803 (t0) cc_final: 0.8504 (t0) REVERT: Q 90 ASP cc_start: 0.8291 (t0) cc_final: 0.7995 (t70) REVERT: R 53 SER cc_start: 0.9202 (p) cc_final: 0.8876 (m) outliers start: 78 outliers final: 34 residues processed: 355 average time/residue: 0.5883 time to fit residues: 244.1665 Evaluate side-chains 333 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 241 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 237 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 130 optimal weight: 0.0770 chunk 164 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.132751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.099681 restraints weight = 55803.961| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.96 r_work: 0.3284 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28814 Z= 0.143 Angle : 0.598 13.722 40291 Z= 0.318 Chirality : 0.041 0.238 4442 Planarity : 0.004 0.057 3978 Dihedral : 26.898 171.089 6379 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.99 % Allowed : 26.47 % Favored : 70.54 % 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: 2507 helix: 0.97 (0.14), residues: 1387 sheet: -0.70 (0.54), residues: 93 loop : -1.24 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.037 0.001 TYR P 88 PHE 0.012 0.001 PHE A 215 TRP 0.014 0.001 TRP B 775 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (28809) covalent geometry : angle 0.59721 / 0.32 (40285) SS BOND : bond 0.00676 / 0.34 ( 3) SS BOND : angle 2.14784 / 1.10 ( 6) hydrogen bonds : bond 0.03618 / 2.39 ( 1350) hydrogen bonds : angle 3.58711 / 2.51 ( 3635) metal coordination : bond 0.00123 / 0.06 ( 1) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.6587 (p-80) REVERT: A 248 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8037 (mmm-85) REVERT: A 313 TYR cc_start: 0.7425 (m-80) cc_final: 0.6977 (m-80) REVERT: A 380 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8909 (mp) REVERT: B 695 ASP cc_start: 0.7906 (m-30) cc_final: 0.7677 (m-30) REVERT: B 821 ILE cc_start: 0.8624 (mt) cc_final: 0.8412 (mp) REVERT: D 107 MET cc_start: 0.6867 (ttt) cc_final: 0.6577 (pp-130) REVERT: E 333 VAL cc_start: 0.5787 (m) cc_final: 0.5420 (p) REVERT: E 350 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8953 (tt0) REVERT: E 371 GLN cc_start: 0.8673 (pm20) cc_final: 0.8225 (pm20) REVERT: F 96 ARG cc_start: 0.0640 (OUTLIER) cc_final: -0.0790 (mmt180) REVERT: F 107 MET cc_start: 0.0104 (OUTLIER) cc_final: -0.0394 (ptt) REVERT: F 235 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.5668 (t0) REVERT: F 237 GLU cc_start: 0.4536 (tp30) cc_final: 0.3348 (pm20) REVERT: F 288 TYR cc_start: 0.4775 (OUTLIER) cc_final: 0.4455 (t80) REVERT: G 338 LYS cc_start: 0.3444 (OUTLIER) cc_final: 0.3178 (mtmt) REVERT: G 556 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.4952 (m-80) REVERT: P 50 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8498 (tt) REVERT: Q 56 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: Q 73 ASN cc_start: 0.8834 (t0) cc_final: 0.8522 (t0) REVERT: Q 90 ASP cc_start: 0.8305 (t0) cc_final: 0.8015 (t70) REVERT: R 53 SER cc_start: 0.9189 (p) cc_final: 0.8881 (m) outliers start: 68 outliers final: 37 residues processed: 342 average time/residue: 0.5859 time to fit residues: 234.7431 Evaluate side-chains 335 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 46 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 119 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 121 optimal weight: 0.0470 chunk 120 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 266 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 317 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.132361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100225 restraints weight = 56049.920| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.79 r_work: 0.3282 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28814 Z= 0.144 Angle : 0.600 14.116 40291 Z= 0.319 Chirality : 0.041 0.237 4442 Planarity : 0.004 0.050 3978 Dihedral : 26.880 170.965 6379 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.81 % Allowed : 26.87 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2507 helix: 1.04 (0.14), residues: 1388 sheet: -0.73 (0.55), residues: 93 loop : -1.26 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.039 0.001 TYR P 88 PHE 0.034 0.001 PHE G 308 TRP 0.018 0.001 TRP B 775 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (28809) covalent geometry : angle 0.60012 / 0.32 (40285) SS BOND : bond 0.00387 / 0.20 ( 3) SS BOND : angle 1.56287 / 0.89 ( 6) hydrogen bonds : bond 0.03578 / 2.36 ( 1350) hydrogen bonds : angle 3.59082 / 2.51 ( 3635) metal coordination : bond 0.00177 / 0.09 ( 1) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6510 (p-80) REVERT: A 248 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8110 (mmm-85) REVERT: A 313 TYR cc_start: 0.7523 (m-80) cc_final: 0.7005 (m-80) REVERT: A 380 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 422 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.4396 (ttt-90) REVERT: B 695 ASP cc_start: 0.7948 (m-30) cc_final: 0.7730 (m-30) REVERT: B 821 ILE cc_start: 0.8633 (mt) cc_final: 0.8422 (mp) REVERT: B 878 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: D 107 MET cc_start: 0.6865 (ttt) cc_final: 0.6577 (pp-130) REVERT: E 350 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8965 (tt0) REVERT: E 359 GLU cc_start: 0.7516 (pt0) cc_final: 0.7220 (tm-30) REVERT: E 371 GLN cc_start: 0.8680 (pm20) cc_final: 0.8236 (pm20) REVERT: F 96 ARG cc_start: 0.0640 (OUTLIER) cc_final: -0.0781 (mmt180) REVERT: F 107 MET cc_start: 0.0062 (OUTLIER) cc_final: -0.0430 (ptt) REVERT: F 237 GLU cc_start: 0.4440 (tp30) cc_final: 0.3281 (pm20) REVERT: F 256 MET cc_start: 0.4397 (mpp) cc_final: 0.4133 (mpm) REVERT: F 288 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.4450 (t80) REVERT: G 556 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5188 (m-80) REVERT: P 50 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8491 (tt) REVERT: Q 56 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: Q 73 ASN cc_start: 0.8847 (t0) cc_final: 0.8550 (t0) REVERT: Q 90 ASP cc_start: 0.8291 (t0) cc_final: 0.8000 (t70) REVERT: R 53 SER cc_start: 0.9173 (p) cc_final: 0.8883 (m) REVERT: T 27 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8753 (mm-40) outliers start: 64 outliers final: 37 residues processed: 338 average time/residue: 0.5547 time to fit residues: 219.3046 Evaluate side-chains 332 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 46 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 235 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.131140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098232 restraints weight = 55945.459| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.98 r_work: 0.3243 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28814 Z= 0.158 Angle : 0.619 15.044 40291 Z= 0.327 Chirality : 0.041 0.241 4442 Planarity : 0.004 0.049 3978 Dihedral : 26.895 170.958 6379 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.77 % Allowed : 26.95 % Favored : 70.28 % 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: 2507 helix: 1.01 (0.14), residues: 1388 sheet: -0.81 (0.54), residues: 93 loop : -1.25 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 83 TYR 0.045 0.002 TYR P 88 PHE 0.017 0.001 PHE G 308 TRP 0.034 0.001 TRP B 719 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (28809) covalent geometry : angle 0.61816 / 0.33 (40285) SS BOND : bond 0.00714 / 0.36 ( 3) SS BOND : angle 2.13746 / 1.10 ( 6) hydrogen bonds : bond 0.03697 / 2.43 ( 1350) hydrogen bonds : angle 3.61395 / 2.54 ( 3635) metal coordination : bond 0.00189 / 0.10 ( 1) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 294 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.6697 (p-80) REVERT: A 248 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8193 (mtp-110) REVERT: A 313 TYR cc_start: 0.7622 (m-80) cc_final: 0.7277 (m-80) REVERT: A 380 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8971 (mp) REVERT: B 695 ASP cc_start: 0.7973 (m-30) cc_final: 0.7753 (m-30) REVERT: B 821 ILE cc_start: 0.8643 (mt) cc_final: 0.8435 (mp) REVERT: D 107 MET cc_start: 0.6842 (ttt) cc_final: 0.6562 (pp-130) REVERT: E 350 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.9027 (tt0) REVERT: E 359 GLU cc_start: 0.7572 (pt0) cc_final: 0.7323 (tm-30) REVERT: E 371 GLN cc_start: 0.8707 (pm20) cc_final: 0.8233 (pm20) REVERT: F 96 ARG cc_start: 0.0828 (OUTLIER) cc_final: -0.0773 (mmt180) REVERT: F 107 MET cc_start: 0.0066 (OUTLIER) cc_final: -0.0426 (ptt) REVERT: F 237 GLU cc_start: 0.4413 (tp30) cc_final: 0.3241 (pm20) REVERT: F 256 MET cc_start: 0.4524 (mpp) cc_final: 0.4232 (mpm) REVERT: F 288 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4425 (t80) REVERT: G 338 LYS cc_start: 0.3442 (OUTLIER) cc_final: 0.3223 (mtmt) REVERT: P 50 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8510 (tt) REVERT: Q 56 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: Q 73 ASN cc_start: 0.8858 (t0) cc_final: 0.8549 (t0) REVERT: Q 90 ASP cc_start: 0.8303 (t0) cc_final: 0.8014 (t70) REVERT: R 53 SER cc_start: 0.9177 (p) cc_final: 0.8892 (m) outliers start: 63 outliers final: 38 residues processed: 338 average time/residue: 0.5771 time to fit residues: 227.1723 Evaluate side-chains 337 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 289 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 46 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 249 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 127 optimal weight: 0.0020 chunk 276 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.131621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099622 restraints weight = 55833.882| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.79 r_work: 0.3272 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28814 Z= 0.138 Angle : 0.614 12.690 40291 Z= 0.326 Chirality : 0.041 0.244 4442 Planarity : 0.004 0.050 3978 Dihedral : 26.895 170.664 6379 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.46 % Allowed : 27.52 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2507 helix: 1.01 (0.14), residues: 1389 sheet: -0.80 (0.54), residues: 93 loop : -1.24 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 83 TYR 0.048 0.002 TYR P 88 PHE 0.020 0.001 PHE G 308 TRP 0.035 0.001 TRP B 719 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (28809) covalent geometry : angle 0.61324 / 0.33 (40285) SS BOND : bond 0.00702 / 0.36 ( 3) SS BOND : angle 2.19309 / 1.12 ( 6) hydrogen bonds : bond 0.03574 / 2.34 ( 1350) hydrogen bonds : angle 3.67500 / 2.58 ( 3635) metal coordination : bond 0.00185 / 0.10 ( 1) Misc. bond : bond 0.00431 / 0.23 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.6621 (p-80) REVERT: A 248 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8163 (mmm-85) REVERT: A 313 TYR cc_start: 0.7690 (m-80) cc_final: 0.7070 (m-80) REVERT: A 380 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8993 (mp) REVERT: B 695 ASP cc_start: 0.8099 (m-30) cc_final: 0.7886 (m-30) REVERT: B 821 ILE cc_start: 0.8721 (mt) cc_final: 0.8505 (mp) REVERT: D 107 MET cc_start: 0.6779 (ttt) cc_final: 0.6502 (pp-130) REVERT: E 350 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9024 (tt0) REVERT: E 359 GLU cc_start: 0.7786 (pt0) cc_final: 0.7465 (tm-30) REVERT: E 371 GLN cc_start: 0.8844 (pm20) cc_final: 0.8336 (pm20) REVERT: F 96 ARG cc_start: 0.1299 (OUTLIER) cc_final: -0.0776 (mmt180) REVERT: F 107 MET cc_start: 0.0085 (OUTLIER) cc_final: -0.0417 (ptt) REVERT: F 237 GLU cc_start: 0.4383 (tp30) cc_final: 0.3214 (pm20) REVERT: F 256 MET cc_start: 0.4487 (mpp) cc_final: 0.4198 (mpm) REVERT: F 288 TYR cc_start: 0.4769 (OUTLIER) cc_final: 0.4466 (t80) REVERT: G 338 LYS cc_start: 0.3477 (OUTLIER) cc_final: 0.3234 (mtmt) REVERT: P 50 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8546 (tt) REVERT: Q 73 ASN cc_start: 0.8994 (t0) cc_final: 0.8647 (t0) REVERT: Q 90 ASP cc_start: 0.8572 (t0) cc_final: 0.8285 (t70) REVERT: R 53 SER cc_start: 0.9267 (p) cc_final: 0.8996 (m) outliers start: 56 outliers final: 34 residues processed: 334 average time/residue: 0.5734 time to fit residues: 223.5343 Evaluate side-chains 326 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 46 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 102 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.129720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097246 restraints weight = 55552.737| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.78 r_work: 0.3222 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28814 Z= 0.176 Angle : 0.646 16.186 40291 Z= 0.338 Chirality : 0.042 0.247 4442 Planarity : 0.004 0.052 3978 Dihedral : 26.944 171.241 6379 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.41 % Allowed : 27.48 % Favored : 70.11 % 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: -0.03 (0.17), residues: 2507 helix: 0.92 (0.14), residues: 1390 sheet: -1.21 (0.51), residues: 101 loop : -1.20 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 83 TYR 0.049 0.002 TYR P 88 PHE 0.021 0.001 PHE G 308 TRP 0.034 0.001 TRP B 719 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (28809) covalent geometry : angle 0.64501 / 0.34 (40285) SS BOND : bond 0.00677 / 0.34 ( 3) SS BOND : angle 2.22557 / 1.14 ( 6) hydrogen bonds : bond 0.03971 / 2.62 ( 1350) hydrogen bonds : angle 3.65291 / 2.57 ( 3635) metal coordination : bond 0.00248 / 0.13 ( 1) Misc. bond : bond 0.00115 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9200.86 seconds wall clock time: 157 minutes 23.34 seconds (9443.34 seconds total)