Starting phenix.real_space_refine on Sun Jul 5 09:50:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd3_37123/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd3_37123/07_2026/8kd3_37123.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.45, 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: 2.33 Conformation dependent library (CDL) restraints added in 875.7 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: 3.83 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: 7.65 Time building geometry restraints manager: 3.10 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: 15.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.610 Find NCS groups from input model: 0.290 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:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.720 ------------------------------------------------------------------------------- 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 : 0.847 17.397 40291 Z= 0.591 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 0.84674 / 0.59 (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 : 1.001 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: 0.5781 time to fit residues: 224.9828 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 : 0.913 ------------------------------------------------------------------------------- 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 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 85 GLN S 93 GLN T 25 ASN U 38 ASN V 60 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.141859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109459 restraints weight = 57609.768| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.16 r_work: 0.3485 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 28814 Z= 0.268 Angle : 0.741 12.889 40291 Z= 0.396 Chirality : 0.046 0.268 4442 Planarity : 0.006 0.079 3978 Dihedral : 26.804 171.489 6379 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.44 % Allowed : 24.19 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.83 (0.16), residues: 2507 helix: 0.20 (0.13), residues: 1382 sheet: 0.56 (0.58), residues: 96 loop : -1.67 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG U 71 TYR 0.041 0.002 TYR F 238 PHE 0.022 0.002 PHE B1224 TRP 0.020 0.002 TRP F 365 HIS 0.012 0.002 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (28809) covalent geometry : angle 0.74053 / 0.40 (40285) SS BOND : bond 0.00793 / 0.40 ( 3) SS BOND : angle 2.91131 / 1.51 ( 6) hydrogen bonds : bond 0.05039 / 3.35 ( 1350) hydrogen bonds : angle 3.92268 / 2.72 ( 3635) metal coordination : bond 0.00810 / 0.43 ( 1) Misc. bond : bond 0.01121 / 0.59 ( 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 464 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 340 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8960 (t0) cc_final: 0.8516 (t0) REVERT: A 204 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7734 (ttp) REVERT: A 306 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.7915 (tpp) REVERT: A 373 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.6947 (mpp) REVERT: B 982 LYS cc_start: 0.6316 (mttt) cc_final: 0.6109 (tttt) REVERT: B 1137 ASN cc_start: 0.7304 (m-40) cc_final: 0.7035 (m-40) REVERT: D 107 MET cc_start: 0.6978 (ttt) cc_final: 0.6713 (pp-130) REVERT: D 368 MET cc_start: 0.6900 (mmm) cc_final: 0.6568 (mmp) REVERT: E 369 ARG cc_start: 0.7287 (pmm-80) cc_final: 0.6999 (pmm-80) REVERT: E 387 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6179 (t80) REVERT: E 435 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7899 (mmt90) REVERT: F 94 TYR cc_start: 0.2554 (OUTLIER) cc_final: 0.2007 (p90) REVERT: F 96 ARG cc_start: 0.0359 (OUTLIER) cc_final: -0.0977 (mmt180) REVERT: F 237 GLU cc_start: 0.4569 (tp30) cc_final: 0.3525 (pm20) REVERT: F 373 TYR cc_start: 0.2520 (p90) cc_final: 0.2299 (p90) REVERT: P 40 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8028 (ttp-170) REVERT: P 44 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8485 (tttt) REVERT: P 84 MET cc_start: 0.8990 (tpp) cc_final: 0.8789 (mmt) REVERT: Q 90 ASP cc_start: 0.8332 (t0) cc_final: 0.8061 (t70) outliers start: 124 outliers final: 37 residues processed: 423 average time/residue: 0.6674 time to fit residues: 328.8671 Evaluate side-chains 344 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 320 LEU 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 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: 0.3980 chunk 203 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 210 optimal weight: 0.5980 chunk 229 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 270 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 189 HIS B 886 HIS B1230 GLN D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN O 39 HIS Q 73 ASN T 25 ASN V 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.141777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.110540 restraints weight = 57780.306| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.04 r_work: 0.3485 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2708 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= 0.136 Angle : 0.576 14.293 40291 Z= 0.313 Chirality : 0.040 0.233 4442 Planarity : 0.004 0.060 3978 Dihedral : 26.846 168.064 6379 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.91 % Allowed : 26.03 % 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: -0.29 (0.16), residues: 2507 helix: 0.72 (0.14), residues: 1384 sheet: 0.16 (0.56), residues: 96 loop : -1.49 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG V 89 TYR 0.020 0.001 TYR U 39 PHE 0.015 0.001 PHE E 551 TRP 0.015 0.001 TRP B 775 HIS 0.007 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (28809) covalent geometry : angle 0.57577 / 0.31 (40285) SS BOND : bond 0.00574 / 0.29 ( 3) SS BOND : angle 2.13597 / 1.12 ( 6) hydrogen bonds : bond 0.03841 / 2.56 ( 1350) hydrogen bonds : angle 3.68723 / 2.59 ( 3635) metal coordination : bond 0.00197 / 0.10 ( 1) Misc. bond : bond 0.00698 / 0.37 ( 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 404 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 315 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7209 (t) REVERT: A 105 ASN cc_start: 0.8973 (t0) cc_final: 0.8500 (t0) REVERT: A 248 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7795 (mmm-85) REVERT: A 373 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6843 (mpp) REVERT: B 701 ASP cc_start: 0.7042 (m-30) cc_final: 0.6842 (m-30) REVERT: B 982 LYS cc_start: 0.6345 (mttt) cc_final: 0.6139 (tttt) REVERT: B 1299 ASN cc_start: 0.6338 (OUTLIER) cc_final: 0.6069 (m-40) REVERT: D 22 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6967 (mtt) REVERT: D 107 MET cc_start: 0.7004 (ttt) cc_final: 0.6756 (pp-130) REVERT: D 357 LYS cc_start: 0.8187 (tptt) cc_final: 0.7874 (ttmt) REVERT: D 368 MET cc_start: 0.6883 (mmm) cc_final: 0.6576 (mmp) REVERT: E 387 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: E 548 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7398 (ptpt) REVERT: F 96 ARG cc_start: 0.0467 (OUTLIER) cc_final: -0.1003 (mmt180) REVERT: F 107 MET cc_start: 0.0043 (OUTLIER) cc_final: -0.0549 (ptt) REVERT: F 235 ASP cc_start: 0.5793 (OUTLIER) cc_final: 0.5509 (t0) REVERT: F 288 TYR cc_start: 0.4831 (OUTLIER) cc_final: 0.4587 (t80) REVERT: G 556 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.5031 (m-80) REVERT: P 44 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8202 (tmtt) REVERT: P 50 ILE cc_start: 0.8863 (tt) cc_final: 0.8618 (tt) REVERT: P 80 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.9013 (p) REVERT: Q 51 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8875 (tp) REVERT: Q 90 ASP cc_start: 0.8321 (t0) cc_final: 0.8019 (t70) REVERT: R 53 SER cc_start: 0.9247 (p) cc_final: 0.8733 (m) REVERT: T 91 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8552 (tttt) REVERT: U 73 ASN cc_start: 0.8221 (t0) cc_final: 0.7960 (m110) outliers start: 89 outliers final: 32 residues processed: 369 average time/residue: 0.6076 time to fit residues: 261.9302 Evaluate side-chains 341 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 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 1025 SER 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 22 MET 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 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 235 ASP 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 G residue 308 PHE Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain O residue 73 GLU 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 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: 20.0000 chunk 255 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 277 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 264 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS B1230 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.140495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.109158 restraints weight = 57512.900| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.91 r_work: 0.3466 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2997 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= 0.131 Angle : 0.550 10.769 40291 Z= 0.301 Chirality : 0.040 0.227 4442 Planarity : 0.004 0.053 3978 Dihedral : 26.816 168.941 6379 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.78 % Allowed : 26.38 % Favored : 69.84 % 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 (0.16), residues: 2507 helix: 0.96 (0.14), residues: 1383 sheet: 0.10 (0.56), residues: 96 loop : -1.40 (0.18), residues: 1028 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 0.025 0.001 PHE B 708 TRP 0.014 0.001 TRP B 775 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (28809) covalent geometry : angle 0.54952 / 0.30 (40285) SS BOND : bond 0.00637 / 0.32 ( 3) SS BOND : angle 2.18776 / 1.12 ( 6) hydrogen bonds : bond 0.03658 / 2.43 ( 1350) hydrogen bonds : angle 3.56231 / 2.49 ( 3635) metal coordination : bond 0.00184 / 0.10 ( 1) Misc. bond : bond 0.00185 / 0.10 ( 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 398 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 312 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 89 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7229 (t) REVERT: A 105 ASN cc_start: 0.8985 (t0) cc_final: 0.8534 (t0) REVERT: A 128 MET cc_start: 0.9002 (mtm) cc_final: 0.8769 (mtp) REVERT: A 248 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7878 (mmm-85) REVERT: A 306 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: A 422 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.4175 (mtt-85) REVERT: B 701 ASP cc_start: 0.7132 (m-30) cc_final: 0.6897 (m-30) REVERT: B 982 LYS cc_start: 0.6448 (mttt) cc_final: 0.6231 (tttt) REVERT: B 1299 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.5985 (m-40) REVERT: D 107 MET cc_start: 0.6969 (ttt) cc_final: 0.6655 (pp-130) REVERT: D 317 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7239 (mm110) REVERT: D 357 LYS cc_start: 0.8224 (tptt) cc_final: 0.7913 (ttmt) REVERT: D 368 MET cc_start: 0.7024 (mmm) cc_final: 0.6739 (mmp) REVERT: E 387 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6077 (t80) REVERT: E 494 LYS cc_start: 0.5174 (OUTLIER) cc_final: 0.4835 (tptm) REVERT: F 96 ARG cc_start: 0.0526 (OUTLIER) cc_final: -0.0992 (mmt180) REVERT: F 107 MET cc_start: 0.0160 (OUTLIER) cc_final: -0.0365 (ptt) REVERT: F 235 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5524 (t0) REVERT: F 288 TYR cc_start: 0.4833 (OUTLIER) cc_final: 0.4587 (t80) REVERT: F 368 MET cc_start: 0.4027 (OUTLIER) cc_final: 0.3009 (ppp) REVERT: P 44 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8275 (tmtt) REVERT: Q 73 ASN cc_start: 0.8585 (t0) cc_final: 0.8345 (t0) REVERT: Q 90 ASP cc_start: 0.8277 (t0) cc_final: 0.7988 (t70) REVERT: R 53 SER cc_start: 0.9234 (p) cc_final: 0.8834 (m) REVERT: U 73 ASN cc_start: 0.8325 (t0) cc_final: 0.8122 (m110) outliers start: 86 outliers final: 34 residues processed: 366 average time/residue: 0.6012 time to fit residues: 259.2401 Evaluate side-chains 337 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 422 ARG 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 934 THR Chi-restraints excluded: chain B residue 1159 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 367 LEU Chi-restraints excluded: chain E residue 47 ASP 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 494 LYS 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 235 ASP Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 101 THR Chi-restraints excluded: chain R residue 33 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS Q 104 GLN R 60 ASN V 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.137372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.106545 restraints weight = 56810.373| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.76 r_work: 0.3389 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28814 Z= 0.156 Angle : 0.585 14.537 40291 Z= 0.316 Chirality : 0.041 0.225 4442 Planarity : 0.004 0.060 3978 Dihedral : 26.856 169.429 6379 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.04 % Allowed : 25.55 % 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: 0.02 (0.17), residues: 2507 helix: 0.98 (0.14), residues: 1385 sheet: -0.10 (0.55), residues: 94 loop : -1.32 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 35 TYR 0.043 0.001 TYR P 88 PHE 0.039 0.001 PHE G 308 TRP 0.025 0.001 TRP E 301 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (28809) covalent geometry : angle 0.58517 / 0.32 (40285) SS BOND : bond 0.00507 / 0.26 ( 3) SS BOND : angle 1.42304 / 0.85 ( 6) hydrogen bonds : bond 0.03843 / 2.53 ( 1350) hydrogen bonds : angle 3.57989 / 2.50 ( 3635) metal coordination : bond 0.00237 / 0.12 ( 1) Misc. bond : bond 0.00066 / 0.03 ( 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 403 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 311 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7244 (t) REVERT: A 189 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6160 (p-80) REVERT: A 248 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7940 (mmm-85) REVERT: A 306 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8380 (ttp) REVERT: B 695 ASP cc_start: 0.7875 (m-30) cc_final: 0.7626 (m-30) REVERT: B 701 ASP cc_start: 0.7247 (m-30) cc_final: 0.6972 (m-30) REVERT: B 982 LYS cc_start: 0.6602 (mttt) cc_final: 0.6365 (tttt) REVERT: D 82 GLN cc_start: 0.7210 (pm20) cc_final: 0.6893 (mm110) REVERT: D 107 MET cc_start: 0.6911 (ttt) cc_final: 0.6599 (pp-130) REVERT: D 317 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7310 (mm110) REVERT: D 357 LYS cc_start: 0.8280 (tptt) cc_final: 0.8039 (ttmt) REVERT: D 368 MET cc_start: 0.7178 (mmm) cc_final: 0.6919 (mmp) REVERT: E 350 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8842 (tt0) REVERT: E 435 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7971 (mmt90) REVERT: F 107 MET cc_start: 0.0182 (OUTLIER) cc_final: -0.0318 (ptt) REVERT: G 338 LYS cc_start: 0.3380 (OUTLIER) cc_final: 0.3113 (mtmt) REVERT: P 44 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8341 (tmtt) REVERT: P 50 ILE cc_start: 0.8835 (tt) cc_final: 0.8437 (tt) REVERT: Q 73 ASN cc_start: 0.8699 (t0) cc_final: 0.8396 (t0) REVERT: Q 90 ASP cc_start: 0.8265 (t0) cc_final: 0.7986 (t70) REVERT: R 53 SER cc_start: 0.9229 (p) cc_final: 0.8875 (m) REVERT: V 102 GLU cc_start: 0.7407 (mp0) cc_final: 0.7106 (mp0) outliers start: 92 outliers final: 44 residues processed: 373 average time/residue: 0.5809 time to fit residues: 253.9841 Evaluate side-chains 355 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 214 PHE 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 306 MET Chi-restraints excluded: chain A residue 414 THR 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 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 1290 VAL 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 359 THR 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 435 ARG 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 356 ILE 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 49 LEU 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 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 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: 7.9990 chunk 244 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 241 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 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** D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099756 restraints weight = 55943.428| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.98 r_work: 0.3264 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28814 Z= 0.197 Angle : 0.626 12.612 40291 Z= 0.334 Chirality : 0.042 0.231 4442 Planarity : 0.004 0.057 3978 Dihedral : 26.984 169.639 6379 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.43 % Allowed : 25.20 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2507 helix: 0.86 (0.14), residues: 1388 sheet: -0.49 (0.54), residues: 93 loop : -1.29 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 324 TYR 0.045 0.002 TYR P 88 PHE 0.022 0.002 PHE A 160 TRP 0.031 0.001 TRP E 301 HIS 0.007 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (28809) covalent geometry : angle 0.62514 / 0.33 (40285) SS BOND : bond 0.00937 / 0.47 ( 3) SS BOND : angle 2.28335 / 1.15 ( 6) hydrogen bonds : bond 0.04102 / 2.69 ( 1350) hydrogen bonds : angle 3.67134 / 2.58 ( 3635) metal coordination : bond 0.00127 / 0.07 ( 1) Misc. bond : bond 0.00053 / 0.03 ( 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 423 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 322 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.6793 (p-80) REVERT: A 211 TYR cc_start: 0.8119 (t80) cc_final: 0.7728 (t80) REVERT: A 248 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8081 (mmm-85) REVERT: A 306 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8402 (ttp) REVERT: A 313 TYR cc_start: 0.7122 (m-80) cc_final: 0.6898 (m-80) REVERT: B 695 ASP cc_start: 0.7952 (m-30) cc_final: 0.7736 (m-30) REVERT: B 822 GLU cc_start: 0.6762 (pt0) cc_final: 0.6165 (pt0) REVERT: B 878 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: B 986 TYR cc_start: 0.7984 (m-10) cc_final: 0.7773 (m-10) REVERT: D 82 GLN cc_start: 0.7250 (pm20) cc_final: 0.7026 (mm110) REVERT: D 107 MET cc_start: 0.6877 (ttt) cc_final: 0.6565 (pp-130) REVERT: D 357 LYS cc_start: 0.8386 (tptt) cc_final: 0.8168 (ttmt) REVERT: D 368 MET cc_start: 0.7331 (mmm) cc_final: 0.7113 (mmp) REVERT: E 333 VAL cc_start: 0.5845 (m) cc_final: 0.5582 (p) REVERT: E 350 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8990 (tt0) REVERT: E 371 GLN cc_start: 0.8647 (pm20) cc_final: 0.8259 (pm20) REVERT: E 387 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: E 435 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7999 (mmt90) REVERT: E 548 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7415 (ptpt) REVERT: F 96 ARG cc_start: 0.0683 (OUTLIER) cc_final: -0.0776 (mmt180) REVERT: F 107 MET cc_start: 0.0248 (OUTLIER) cc_final: -0.0271 (ptt) REVERT: F 235 ASP cc_start: 0.5974 (OUTLIER) cc_final: 0.5722 (t0) REVERT: F 288 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.4468 (t80) REVERT: G 556 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: P 44 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8466 (tmtt) REVERT: Q 73 ASN cc_start: 0.8843 (t0) cc_final: 0.8542 (t0) REVERT: Q 90 ASP cc_start: 0.8324 (t0) cc_final: 0.8040 (t70) REVERT: R 53 SER cc_start: 0.9238 (p) cc_final: 0.8893 (m) REVERT: V 46 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (m170) outliers start: 101 outliers final: 45 residues processed: 388 average time/residue: 0.6728 time to fit residues: 304.0062 Evaluate side-chains 363 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 414 THR Chi-restraints excluded: chain B residue 689 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 976 ASP Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU 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 359 THR 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 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 435 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 548 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 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 335 ILE Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR 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 T residue 50 ILE 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 Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 241 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN D 317 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.132596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100170 restraints weight = 55716.659| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.90 r_work: 0.3283 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28814 Z= 0.158 Angle : 0.600 13.575 40291 Z= 0.321 Chirality : 0.041 0.227 4442 Planarity : 0.004 0.071 3978 Dihedral : 26.988 169.058 6379 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.34 % Allowed : 26.34 % 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: -0.09 (0.16), residues: 2507 helix: 0.87 (0.14), residues: 1393 sheet: -0.61 (0.55), residues: 93 loop : -1.29 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 324 TYR 0.044 0.002 TYR P 88 PHE 0.022 0.001 PHE G 308 TRP 0.030 0.001 TRP E 301 HIS 0.005 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (28809) covalent geometry : angle 0.59957 / 0.32 (40285) SS BOND : bond 0.00580 / 0.29 ( 3) SS BOND : angle 2.12832 / 1.08 ( 6) hydrogen bonds : bond 0.03730 / 2.45 ( 1350) hydrogen bonds : angle 3.63339 / 2.55 ( 3635) metal coordination : bond 0.00188 / 0.10 ( 1) Misc. bond : bond 0.00060 / 0.03 ( 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 382 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6722 (p-80) REVERT: A 211 TYR cc_start: 0.8007 (t80) cc_final: 0.7740 (t80) REVERT: A 248 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8049 (mmm-85) REVERT: A 306 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: A 313 TYR cc_start: 0.7155 (m-80) cc_final: 0.6816 (m-80) REVERT: A 380 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8925 (mp) REVERT: B 695 ASP cc_start: 0.7914 (m-30) cc_final: 0.7684 (m-30) REVERT: B 986 TYR cc_start: 0.7871 (m-10) cc_final: 0.7653 (m-10) REVERT: D 107 MET cc_start: 0.6841 (ttt) cc_final: 0.6567 (pp-130) REVERT: D 368 MET cc_start: 0.7386 (mmm) cc_final: 0.7160 (mmp) REVERT: E 333 VAL cc_start: 0.5837 (m) cc_final: 0.5486 (p) REVERT: E 350 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8979 (tt0) REVERT: E 371 GLN cc_start: 0.8633 (pm20) cc_final: 0.8213 (pm20) REVERT: E 435 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8009 (mmt90) REVERT: E 548 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7331 (ptpt) REVERT: F 96 ARG cc_start: 0.0697 (OUTLIER) cc_final: -0.0795 (mmt180) REVERT: F 107 MET cc_start: 0.0232 (OUTLIER) cc_final: -0.0280 (ptt) REVERT: F 237 GLU cc_start: 0.4527 (tp30) cc_final: 0.3321 (pm20) REVERT: F 241 LYS cc_start: 0.2128 (OUTLIER) cc_final: 0.1805 (mmmt) REVERT: F 288 TYR cc_start: 0.4763 (OUTLIER) cc_final: 0.4445 (t80) REVERT: G 338 LYS cc_start: 0.3403 (OUTLIER) cc_final: 0.3164 (mtmt) REVERT: P 50 ILE cc_start: 0.8828 (tt) cc_final: 0.8498 (tt) REVERT: Q 73 ASN cc_start: 0.8861 (t0) cc_final: 0.8540 (t0) REVERT: Q 90 ASP cc_start: 0.8326 (t0) cc_final: 0.8027 (t70) REVERT: R 53 SER cc_start: 0.9196 (p) cc_final: 0.8862 (m) outliers start: 76 outliers final: 35 residues processed: 357 average time/residue: 0.6431 time to fit residues: 267.1895 Evaluate side-chains 339 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 PHE 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 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR 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 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 282 CYS 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 435 ARG 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 E residue 548 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 241 LYS 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 49 LEU Chi-restraints excluded: chain P residue 96 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 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 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 119 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 266 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 231 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN V 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.133162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101089 restraints weight = 56245.440| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.79 r_work: 0.3299 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 0.040 28814 Z= 0.133 Angle : 0.589 14.042 40291 Z= 0.316 Chirality : 0.041 0.234 4442 Planarity : 0.004 0.068 3978 Dihedral : 26.951 169.355 6379 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.12 % Allowed : 27.09 % Favored : 69.80 % 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: 0.99 (0.14), residues: 1387 sheet: -0.65 (0.54), residues: 93 loop : -1.26 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 324 TYR 0.040 0.001 TYR P 88 PHE 0.018 0.001 PHE A 160 TRP 0.034 0.001 TRP E 301 HIS 0.005 0.001 HIS B 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (28809) covalent geometry : angle 0.58822 / 0.32 (40285) SS BOND : bond 0.00688 / 0.35 ( 3) SS BOND : angle 2.20006 / 1.09 ( 6) hydrogen bonds : bond 0.03507 / 2.31 ( 1350) hydrogen bonds : angle 3.58551 / 2.51 ( 3635) metal coordination : bond 0.00118 / 0.06 ( 1) Misc. bond : bond 0.00056 / 0.03 ( 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 370 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 299 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6596 (p-80) REVERT: A 248 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8124 (mmm-85) REVERT: A 306 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8349 (ttp) REVERT: A 313 TYR cc_start: 0.7131 (m-80) cc_final: 0.6869 (m-80) REVERT: A 380 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 695 ASP cc_start: 0.7909 (m-30) cc_final: 0.7689 (m-30) REVERT: B 821 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 878 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: B 986 TYR cc_start: 0.7902 (m-10) cc_final: 0.7665 (m-10) REVERT: D 107 MET cc_start: 0.6844 (ttt) cc_final: 0.6568 (pp-130) REVERT: E 350 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8937 (tt0) REVERT: E 359 GLU cc_start: 0.7468 (pt0) cc_final: 0.7196 (tm-30) REVERT: E 371 GLN cc_start: 0.8632 (pm20) cc_final: 0.8221 (pm20) REVERT: E 387 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: E 435 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8034 (mmt90) REVERT: E 548 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7359 (ptpt) REVERT: F 96 ARG cc_start: 0.0593 (OUTLIER) cc_final: -0.0746 (mmt180) REVERT: F 107 MET cc_start: 0.0200 (OUTLIER) cc_final: -0.0297 (ptt) REVERT: F 237 GLU cc_start: 0.4498 (tp30) cc_final: 0.3309 (pm20) REVERT: F 241 LYS cc_start: 0.2102 (OUTLIER) cc_final: 0.1809 (mmmt) REVERT: F 288 TYR cc_start: 0.4725 (OUTLIER) cc_final: 0.4444 (t80) REVERT: G 338 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.3177 (mtmt) REVERT: G 556 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.5123 (m-80) REVERT: P 50 ILE cc_start: 0.8761 (tt) cc_final: 0.8439 (tt) REVERT: Q 73 ASN cc_start: 0.8834 (t0) cc_final: 0.8537 (t0) REVERT: Q 90 ASP cc_start: 0.8278 (t0) cc_final: 0.7979 (t70) REVERT: R 53 SER cc_start: 0.9160 (p) cc_final: 0.8867 (m) REVERT: S 120 MET cc_start: 0.8997 (mmm) cc_final: 0.8214 (mtm) outliers start: 71 outliers final: 38 residues processed: 349 average time/residue: 0.6634 time to fit residues: 269.9664 Evaluate side-chains 340 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 821 ILE 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 989 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG 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 E residue 44 VAL 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 435 ARG 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 523 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 548 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 241 LYS 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 49 LEU Chi-restraints excluded: chain P residue 96 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 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 109 SER 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: 2.9990 chunk 145 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.132151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099947 restraints weight = 56200.970| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.84 r_work: 0.3279 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28814 Z= 0.152 Angle : 0.603 14.451 40291 Z= 0.322 Chirality : 0.041 0.237 4442 Planarity : 0.004 0.069 3978 Dihedral : 26.934 169.978 6379 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.07 % Allowed : 27.26 % Favored : 69.67 % 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: 0.05 (0.17), residues: 2507 helix: 1.00 (0.14), residues: 1389 sheet: -0.70 (0.55), residues: 93 loop : -1.24 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 324 TYR 0.047 0.002 TYR P 88 PHE 0.018 0.001 PHE A 160 TRP 0.038 0.001 TRP E 301 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (28809) covalent geometry : angle 0.60255 / 0.32 (40285) SS BOND : bond 0.00654 / 0.33 ( 3) SS BOND : angle 2.22306 / 1.11 ( 6) hydrogen bonds : bond 0.03665 / 2.41 ( 1350) hydrogen bonds : angle 3.59110 / 2.52 ( 3635) metal coordination : bond 0.00226 / 0.12 ( 1) Misc. bond : bond 0.00056 / 0.03 ( 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 360 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 290 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.6776 (p-80) REVERT: A 248 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8088 (mmm-85) REVERT: A 306 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8341 (ttp) REVERT: A 313 TYR cc_start: 0.7236 (m-80) cc_final: 0.6938 (m-80) REVERT: A 314 THR cc_start: 0.8527 (t) cc_final: 0.8323 (t) REVERT: A 380 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8924 (mp) REVERT: B 695 ASP cc_start: 0.7941 (m-30) cc_final: 0.7705 (m-30) REVERT: B 878 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: B 986 TYR cc_start: 0.7889 (m-10) cc_final: 0.7650 (m-10) REVERT: D 107 MET cc_start: 0.6850 (ttt) cc_final: 0.6570 (pp-130) REVERT: E 350 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8976 (tt0) REVERT: E 359 GLU cc_start: 0.7491 (pt0) cc_final: 0.7244 (tm-30) REVERT: E 371 GLN cc_start: 0.8673 (pm20) cc_final: 0.8219 (pm20) REVERT: E 387 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: E 435 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8048 (mmt90) REVERT: E 548 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7359 (ptpt) REVERT: F 96 ARG cc_start: 0.0754 (OUTLIER) cc_final: -0.0756 (mmt180) REVERT: F 107 MET cc_start: 0.0193 (OUTLIER) cc_final: -0.0304 (ptt) REVERT: F 237 GLU cc_start: 0.4447 (tp30) cc_final: 0.3215 (pm20) REVERT: F 241 LYS cc_start: 0.2082 (OUTLIER) cc_final: 0.1795 (mmmt) REVERT: F 288 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.4478 (t80) REVERT: G 338 LYS cc_start: 0.3531 (OUTLIER) cc_final: 0.3287 (mtmt) REVERT: P 50 ILE cc_start: 0.8788 (tt) cc_final: 0.8468 (tt) REVERT: Q 73 ASN cc_start: 0.8851 (t0) cc_final: 0.8536 (t0) REVERT: Q 90 ASP cc_start: 0.8281 (t0) cc_final: 0.7976 (t70) REVERT: R 53 SER cc_start: 0.9161 (p) cc_final: 0.8867 (m) REVERT: R 90 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: T 27 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8742 (mm-40) outliers start: 70 outliers final: 37 residues processed: 339 average time/residue: 0.6729 time to fit residues: 265.8822 Evaluate side-chains 341 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 306 MET Chi-restraints excluded: chain A residue 373 MET 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 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 989 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG 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 E residue 44 VAL 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 435 ARG 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 523 ILE Chi-restraints excluded: chain E residue 548 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 241 LYS Chi-restraints excluded: chain F residue 247 ARG 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 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 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 V residue 46 HIS Chi-restraints excluded: chain V residue 109 SER 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: 3.9990 chunk 110 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 276 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 210 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN V 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.131679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.099282 restraints weight = 55984.056| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.87 r_work: 0.3266 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4660 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= 0.152 Angle : 0.614 14.202 40291 Z= 0.326 Chirality : 0.042 0.296 4442 Planarity : 0.004 0.070 3978 Dihedral : 26.952 169.678 6379 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.50 % Allowed : 27.83 % Favored : 69.67 % 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: 0.98 (0.14), residues: 1390 sheet: -0.74 (0.55), residues: 93 loop : -1.25 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 324 TYR 0.048 0.002 TYR P 88 PHE 0.021 0.001 PHE A 160 TRP 0.042 0.002 TRP E 301 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (28809) covalent geometry : angle 0.61369 / 0.33 (40285) SS BOND : bond 0.00651 / 0.33 ( 3) SS BOND : angle 2.21056 / 1.11 ( 6) hydrogen bonds : bond 0.03615 / 2.38 ( 1350) hydrogen bonds : angle 3.61649 / 2.53 ( 3635) metal coordination : bond 0.00193 / 0.10 ( 1) Misc. bond : bond 0.00053 / 0.03 ( 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 354 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6827 (p-80) REVERT: A 248 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8338 (mtp-110) REVERT: A 306 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8600 (ttp) REVERT: A 313 TYR cc_start: 0.7388 (m-80) cc_final: 0.7015 (m-80) REVERT: A 314 THR cc_start: 0.8479 (t) cc_final: 0.8225 (t) REVERT: A 380 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8968 (mp) REVERT: B 695 ASP cc_start: 0.8099 (m-30) cc_final: 0.7893 (m-30) REVERT: B 878 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: B 986 TYR cc_start: 0.8050 (m-10) cc_final: 0.7795 (m-10) REVERT: D 107 MET cc_start: 0.6806 (ttt) cc_final: 0.6522 (pp-130) REVERT: E 333 VAL cc_start: 0.5962 (m) cc_final: 0.5607 (p) REVERT: E 350 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.9022 (tt0) REVERT: E 359 GLU cc_start: 0.7792 (pt0) cc_final: 0.7415 (pp20) REVERT: E 371 GLN cc_start: 0.8861 (pm20) cc_final: 0.8321 (pm20) REVERT: E 387 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: E 435 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8123 (mmt90) REVERT: E 548 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7491 (ptpt) REVERT: F 96 ARG cc_start: 0.1061 (OUTLIER) cc_final: -0.0769 (mmt180) REVERT: F 107 MET cc_start: 0.0208 (OUTLIER) cc_final: -0.0297 (ptt) REVERT: F 237 GLU cc_start: 0.4469 (tp30) cc_final: 0.3230 (pm20) REVERT: F 241 LYS cc_start: 0.2020 (OUTLIER) cc_final: 0.1762 (mmmt) REVERT: F 256 MET cc_start: 0.4550 (mpp) cc_final: 0.4288 (mpm) REVERT: F 288 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.4484 (t80) REVERT: G 338 LYS cc_start: 0.3466 (OUTLIER) cc_final: 0.3228 (mtmt) REVERT: P 50 ILE cc_start: 0.8880 (tt) cc_final: 0.8518 (tt) REVERT: Q 73 ASN cc_start: 0.8938 (t0) cc_final: 0.8645 (t0) REVERT: Q 90 ASP cc_start: 0.8593 (t0) cc_final: 0.8293 (t70) REVERT: R 53 SER cc_start: 0.9275 (p) cc_final: 0.8993 (m) REVERT: R 90 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: S 94 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8433 (mm-30) outliers start: 57 outliers final: 37 residues processed: 337 average time/residue: 0.6600 time to fit residues: 259.5926 Evaluate side-chains 340 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 306 MET 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 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 1025 SER Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1308 ARG 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 E residue 44 VAL 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 435 ARG Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 548 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 241 LYS 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 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU 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 Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 102 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.130753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098158 restraints weight = 55748.705| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.89 r_work: 0.3247 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28814 Z= 0.174 Angle : 0.624 14.035 40291 Z= 0.332 Chirality : 0.042 0.245 4442 Planarity : 0.004 0.067 3978 Dihedral : 26.972 169.765 6379 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.59 % Allowed : 27.66 % Favored : 69.75 % 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: 0.94 (0.14), residues: 1391 sheet: -1.10 (0.53), residues: 101 loop : -1.22 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 324 TYR 0.051 0.002 TYR P 88 PHE 0.023 0.001 PHE A 160 TRP 0.047 0.002 TRP E 301 HIS 0.008 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (28809) covalent geometry : angle 0.62382 / 0.33 (40285) SS BOND : bond 0.00647 / 0.33 ( 3) SS BOND : angle 2.21511 / 1.11 ( 6) hydrogen bonds : bond 0.03780 / 2.49 ( 1350) hydrogen bonds : angle 3.69747 / 2.59 ( 3635) metal coordination : bond 0.00233 / 0.12 ( 1) Misc. bond : bond 0.00028 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10330.26 seconds wall clock time: 176 minutes 43.56 seconds (10603.56 seconds total)