Starting phenix.real_space_refine on Sat Aug 8 09:55:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9e_37366/08_2026/8w9e_37366_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9e_37366/08_2026/8w9e_37366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9e_37366/08_2026/8w9e_37366_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9e_37366/08_2026/8w9e_37366_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9e_37366/08_2026/8w9e_37366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9e_37366/08_2026/8w9e_37366.map" } resolution = 3.6 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= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16810 2.51 5 N 4896 2.21 5 O 5776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 242 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27886 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "g" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "j" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "G" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 570 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 2 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 101.457 103.747 85.536 1.00117.79 S ATOM 5555 SG CYS E 266 98.472 102.325 86.955 1.00105.03 S ATOM 5708 SG CYS E 286 102.814 101.271 87.448 1.00 96.46 S ATOM 5619 SG CYS E 275 110.324 110.355 78.330 1.00161.47 S ATOM 5640 SG CYS E 278 107.953 108.771 76.416 1.00166.22 S ATOM 5843 SG CYS E 303 110.280 106.376 76.659 1.00145.68 S ATOM 5866 SG CYS E 306 111.101 108.678 74.290 1.00146.36 S ATOM 6956 SG CYS E 440 68.269 86.757 97.346 1.00 80.51 S ATOM 6982 SG CYS E 443 65.850 83.503 97.220 1.00 83.12 S ATOM 7170 SG CYS E 466 66.498 84.995 100.330 1.00 85.78 S ATOM 6768 SG CYS E 417 59.602 86.865 107.059 1.00 90.08 S ATOM 6795 SG CYS E 420 57.427 86.765 109.770 1.00 89.58 S ATOM 7051 SG CYS E 451 61.549 86.260 110.056 1.00 70.30 S ATOM 14065 SG CYS F 263 74.355 33.528 55.854 1.00226.83 S ATOM 14235 SG CYS F 286 72.269 32.825 58.472 1.00233.15 S ATOM 14370 SG CYS F 303 71.289 45.077 55.093 1.00224.38 S Time building chain proxies: 5.56, per 1000 atoms: 0.20 Number of scatterers: 27886 At special positions: 0 Unit cell: (133.701, 185.877, 158.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 K 1 19.00 S 104 16.00 P 292 15.00 O 5776 8.00 N 4896 7.00 C 16810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 417 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 263 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " Number of angles added : 12 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5114 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 21 sheets defined 59.0% alpha, 5.2% beta 147 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.581A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 Processing helix chain 'A' and resid 772 through 778 removed outlier: 3.739A pdb=" N LEU A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.618A pdb=" N GLU A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 922 Proline residue: A 892 - end of helix removed outlier: 4.462A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.933A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 964 " --> pdb=" O THR A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 4.155A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.517A pdb=" N PHE A1022 " --> pdb=" O ILE A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.557A pdb=" N ASN A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1070 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.765A pdb=" N ASN A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1141 through 1174 removed outlier: 3.548A pdb=" N TYR A1145 " --> pdb=" O ASN A1141 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 4.017A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.619A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1240 Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.743A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 3.543A pdb=" N GLN A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1343 removed outlier: 3.688A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 331 through 334 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.510A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 Processing helix chain 'E' and resid 544 through 580 removed outlier: 3.509A pdb=" N ASN E 580 " --> pdb=" O LYS E 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 removed outlier: 3.914A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.719A pdb=" N LYS B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.879A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.589A pdb=" N LYS B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 288 through 301 removed outlier: 4.807A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.633A pdb=" N VAL C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.562A pdb=" N GLN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.686A pdb=" N ARG C 324 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 Proline residue: C 339 - end of helix Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.632A pdb=" N HIS C 369 " --> pdb=" O TRP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.083A pdb=" N TYR C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.917A pdb=" N LYS D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.587A pdb=" N VAL D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 271 through 293 removed outlier: 3.516A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 317 removed outlier: 3.555A pdb=" N GLN D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 344 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 375 removed outlier: 4.237A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.625A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.558A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 544 through 577 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.520A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.636A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.643A pdb=" N VAL a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.570A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.940A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.660A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.482A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.624A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 removed outlier: 3.529A pdb=" N ALA d 107 " --> pdb=" O PRO d 103 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 56 Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.649A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.748A pdb=" N VAL e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.622A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.699A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.549A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 22 Processing helix chain 'g' and resid 26 through 37 removed outlier: 3.659A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.481A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 removed outlier: 3.624A pdb=" N ASP g 90 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.529A pdb=" N ALA h 107 " --> pdb=" O PRO h 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.115A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.115A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AA4, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA6, first strand: chain 'E' and resid 505 through 506 removed outlier: 3.675A pdb=" N GLN E 521 " --> pdb=" O THR E 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.575A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB2, first strand: chain 'F' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.791A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.353A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 'c' and resid 100 through 102 removed outlier: 6.514A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC1, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.090A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AC3, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.854A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE G 78 " --> pdb=" O LEU G 28 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 8.28 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.44: 13197 1.44 - 1.76: 15693 1.76 - 2.08: 158 2.08 - 2.39: 1 2.39 - 2.71: 1 Bond restraints: 29050 Sorted by residual: bond pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 1.512 2.710 -1.198 2.20e-02 2.07e+03 2.97e+03 bond pdb=" CE3 TRP D 236 " pdb=" CZ3 TRP D 236 " ideal model delta sigma weight residual 1.382 2.260 -0.878 3.00e-02 1.11e+03 8.57e+02 bond pdb=" CE2 TRP D 236 " pdb=" CZ2 TRP D 236 " ideal model delta sigma weight residual 1.394 1.829 -0.435 2.10e-02 2.27e+03 4.30e+02 bond pdb=" CZ3 TRP D 236 " pdb=" CH2 TRP D 236 " ideal model delta sigma weight residual 1.400 1.859 -0.459 2.50e-02 1.60e+03 3.37e+02 bond pdb=" N PRO E 380 " pdb=" CA PRO E 380 " ideal model delta sigma weight residual 1.469 1.694 -0.225 1.28e-02 6.10e+03 3.10e+02 ... (remaining 29045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 40242 4.69 - 9.38: 202 9.38 - 14.08: 18 14.08 - 18.77: 3 18.77 - 23.46: 3 Bond angle restraints: 40468 Sorted by residual: angle pdb=" C ILE E 379 " pdb=" N PRO E 380 " pdb=" CA PRO E 380 " ideal model delta sigma weight residual 119.84 138.49 -18.65 1.25e+00 6.40e-01 2.23e+02 angle pdb=" CA TYR F 372 " pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 113.90 137.36 -23.46 1.80e+00 3.09e-01 1.70e+02 angle pdb=" C LYS B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.84 135.70 -15.86 1.25e+00 6.40e-01 1.61e+02 angle pdb=" C THR c 16 " pdb=" CA THR c 16 " pdb=" CB THR c 16 " ideal model delta sigma weight residual 111.71 92.67 19.04 2.23e+00 2.01e-01 7.29e+01 angle pdb=" N ILE E 181 " pdb=" CA ILE E 181 " pdb=" C ILE E 181 " ideal model delta sigma weight residual 113.43 104.13 9.30 1.09e+00 8.42e-01 7.28e+01 ... (remaining 40463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12944 17.89 - 35.78: 2063 35.78 - 53.66: 1408 53.66 - 71.55: 406 71.55 - 89.44: 31 Dihedral angle restraints: 16852 sinusoidal: 8939 harmonic: 7913 Sorted by residual: dihedral pdb=" C THR E 169 " pdb=" N THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual -122.00 -152.25 30.25 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual 123.40 150.97 -27.57 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C THR E 172 " pdb=" N THR E 172 " pdb=" CA THR E 172 " pdb=" CB THR E 172 " ideal model delta harmonic sigma weight residual -122.00 -145.09 23.09 0 2.50e+00 1.60e-01 8.53e+01 ... (remaining 16849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4430 0.239 - 0.477: 29 0.477 - 0.716: 6 0.716 - 0.954: 2 0.954 - 1.193: 1 Chirality restraints: 4468 Sorted by residual: chirality pdb=" CA THR E 169 " pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CB THR E 169 " both_signs ideal model delta sigma weight residual False 2.53 1.33 1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CA THR E 172 " pdb=" N THR E 172 " pdb=" C THR E 172 " pdb=" CB THR E 172 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA TYR B 32 " pdb=" N TYR B 32 " pdb=" C TYR B 32 " pdb=" CB TYR B 32 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.50e+01 ... (remaining 4465 not shown) Planarity restraints: 4131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 20 " 0.033 2.00e-02 2.50e+03 7.02e-02 4.93e+01 pdb=" C ARG B 20 " -0.121 2.00e-02 2.50e+03 pdb=" O ARG B 20 " 0.047 2.00e-02 2.50e+03 pdb=" N VAL B 21 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR g 16 " 0.027 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C THR g 16 " -0.096 2.00e-02 2.50e+03 pdb=" O THR g 16 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG g 17 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 379 " -0.029 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C ILE E 379 " 0.090 2.00e-02 2.50e+03 pdb=" O ILE E 379 " -0.032 2.00e-02 2.50e+03 pdb=" N PRO E 380 " -0.029 2.00e-02 2.50e+03 ... (remaining 4128 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.84: 12 1.84 - 2.66: 852 2.66 - 3.49: 42895 3.49 - 4.31: 86742 4.31 - 5.14: 143286 Nonbonded interactions: 273787 Sorted by model distance: nonbonded pdb=" CD1 TRP E 187 " pdb=" OE1 GLN B 72 " model vdw 1.013 3.260 nonbonded pdb=" CB SER E 179 " pdb=" OE2 GLU B 129 " model vdw 1.135 3.440 nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.327 3.860 nonbonded pdb=" OE2 GLU A 918 " pdb=" CA LEU E 128 " model vdw 1.410 3.470 nonbonded pdb=" OE2 GLU A 918 " pdb=" CB LEU E 128 " model vdw 1.555 3.440 ... (remaining 273782 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 'C' selection = (chain 'D' and resid 219 through 401) } ncs_group { reference = (chain 'a' and resid 38 through 134) selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = (chain 'b' and resid 23 through 101) selection = (chain 'f' and resid 23 through 101) } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 12 through 118) } ncs_group { reference = chain 'd' selection = chain 'h' } ncs_group { reference = (chain 'i' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'j' and (resid -73 through -1 or resid 1 through 73)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.900 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.440 Find NCS groups from input model: 0.460 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 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 : 0.013 1.198 29070 Z= 0.728 Angle : 1.079 25.019 40480 Z= 0.739 Chirality : 0.066 1.193 4468 Planarity : 0.007 0.108 4131 Dihedral : 23.116 89.440 11738 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.82 % Favored : 93.54 % Rotamer: Outliers : 3.59 % Allowed : 7.76 % Favored : 88.66 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % 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: -2.40 (0.14), residues: 2647 helix: -0.73 (0.12), residues: 1508 sheet: -1.72 (0.45), residues: 106 loop : -2.86 (0.16), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG h 33 TYR 0.053 0.002 TYR G 100 PHE 0.033 0.002 PHE A1301 TRP 0.050 0.005 TRP G 31 HIS 0.009 0.002 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01301 / 0.72 (29050) covalent geometry : angle 1.03096 / 0.74 (40468) hydrogen bonds : bond 0.13547 / 8.79 ( 1489) hydrogen bonds : angle 5.86889 / 4.08 ( 4083) metal coordination : bond 0.10081 / 5.92 ( 20) metal coordination : angle 18.59200 / 11.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 387 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 LYS cc_start: 0.0373 (mmpt) cc_final: -0.0153 (ttmt) REVERT: A 998 HIS cc_start: 0.4273 (t-170) cc_final: 0.3982 (t-170) REVERT: A 1009 ARG cc_start: 0.3927 (mtp180) cc_final: 0.3444 (tpt90) REVERT: A 1164 MET cc_start: 0.0791 (mtm) cc_final: 0.0042 (tpp) REVERT: A 1209 ARG cc_start: 0.2885 (ttp-170) cc_final: 0.0812 (tmm-80) REVERT: A 1286 TYR cc_start: 0.1359 (t80) cc_final: 0.1010 (m-80) REVERT: A 1290 VAL cc_start: 0.1613 (t) cc_final: 0.0822 (p) REVERT: E 105 ASP cc_start: 0.1790 (OUTLIER) cc_final: 0.1548 (t0) REVERT: E 316 MET cc_start: 0.0241 (mmp) cc_final: -0.0344 (mtm) REVERT: E 350 GLN cc_start: 0.2242 (pt0) cc_final: 0.1328 (mm-40) REVERT: E 523 ILE cc_start: 0.3386 (pt) cc_final: 0.3149 (tp) REVERT: E 557 LYS cc_start: 0.1253 (pptt) cc_final: 0.0911 (tppt) REVERT: D 227 LYS cc_start: -0.0452 (tttt) cc_final: -0.0681 (tttp) REVERT: D 296 MET cc_start: 0.2181 (ttp) cc_final: 0.1597 (tmm) REVERT: F 331 ASN cc_start: 0.3576 (t0) cc_final: 0.3004 (p0) REVERT: F 559 LYS cc_start: 0.1437 (mtpt) cc_final: 0.0871 (tptp) REVERT: F 560 MET cc_start: 0.1275 (mmp) cc_final: 0.1064 (tmm) REVERT: a 76 GLN cc_start: 0.7918 (tp40) cc_final: 0.7165 (mt0) REVERT: c 110 ASN cc_start: 0.8091 (t0) cc_final: 0.7545 (p0) REVERT: d 91 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7919 (t) outliers start: 86 outliers final: 25 residues processed: 455 average time/residue: 0.2230 time to fit residues: 150.1066 Evaluate side-chains 225 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 187 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 115 THR Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 663 ASN A 690 ASN A 798 HIS A 857 HIS A 884 HIS A 974 GLN A1127 GLN A1293 HIS A1345 HIS E 355 ASN ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 ASN ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 177 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN C 389 ASN F 302 HIS F 329 GLN F 331 ASN a 39 HIS b 93 GLN c 31 HIS d 109 HIS e 39 HIS e 125 GLN f 75 HIS f 93 GLN g 31 HIS ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.194682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.168610 restraints weight = 70004.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.167018 restraints weight = 106802.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.165776 restraints weight = 93914.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.164905 restraints weight = 86542.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.164547 restraints weight = 77892.894| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.192 29070 Z= 0.461 Angle : 0.761 23.460 40480 Z= 0.415 Chirality : 0.047 0.496 4468 Planarity : 0.006 0.124 4131 Dihedral : 26.161 86.393 6278 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.98 % Rotamer: Outliers : 2.34 % Allowed : 11.47 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.19 % 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: -0.76 (0.16), residues: 2647 helix: 0.63 (0.13), residues: 1527 sheet: -0.91 (0.49), residues: 109 loop : -2.27 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG g 11 TYR 0.027 0.002 TYR E 549 PHE 0.027 0.002 PHE B 301 TRP 0.041 0.002 TRP D 236 HIS 0.065 0.002 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01046 / 0.46 (29050) covalent geometry : angle 0.75071 / 0.41 (40468) hydrogen bonds : bond 0.05823 / 3.85 ( 1489) hydrogen bonds : angle 4.21647 / 2.92 ( 4083) metal coordination : bond 0.02938 / 1.74 ( 20) metal coordination : angle 7.36987 / 4.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1009 ARG cc_start: 0.3950 (mtp180) cc_final: 0.3513 (tpt90) REVERT: A 1150 HIS cc_start: 0.0524 (m90) cc_final: 0.0280 (m90) REVERT: A 1164 MET cc_start: 0.0941 (mtm) cc_final: -0.0312 (tpp) REVERT: A 1209 ARG cc_start: 0.3324 (ttp-170) cc_final: 0.1251 (tmm-80) REVERT: A 1286 TYR cc_start: 0.1740 (t80) cc_final: 0.1272 (m-80) REVERT: E 105 ASP cc_start: 0.1910 (OUTLIER) cc_final: 0.1519 (m-30) REVERT: E 350 GLN cc_start: 0.2150 (pt0) cc_final: 0.1252 (mm-40) REVERT: D 310 LEU cc_start: 0.2079 (OUTLIER) cc_final: 0.1108 (tt) REVERT: F 331 ASN cc_start: 0.4036 (t0) cc_final: 0.3623 (p0) REVERT: c 110 ASN cc_start: 0.7768 (t0) cc_final: 0.7474 (p0) outliers start: 56 outliers final: 22 residues processed: 267 average time/residue: 0.1797 time to fit residues: 75.0268 Evaluate side-chains 180 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain e residue 39 HIS Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 56 optimal weight: 30.0000 chunk 231 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 275 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 192 optimal weight: 0.3980 chunk 9 optimal weight: 20.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 302 HIS E 314 ASN ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN B 31 ASN B 76 GLN a 76 GLN e 68 GLN ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.190595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.163122 restraints weight = 69714.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.160369 restraints weight = 105246.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.158788 restraints weight = 94799.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.158340 restraints weight = 85237.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.157587 restraints weight = 81775.828| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.200 29070 Z= 0.478 Angle : 0.775 23.347 40480 Z= 0.422 Chirality : 0.049 0.339 4468 Planarity : 0.006 0.128 4131 Dihedral : 26.186 82.645 6248 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.06 % Favored : 94.71 % Rotamer: Outliers : 2.59 % Allowed : 14.64 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: -0.47 (0.16), residues: 2647 helix: 0.79 (0.13), residues: 1522 sheet: -0.68 (0.47), residues: 110 loop : -2.02 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1071 TYR 0.026 0.002 TYR c 57 PHE 0.037 0.002 PHE e 78 TRP 0.043 0.003 TRP D 236 HIS 0.030 0.002 HIS e 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01088 / 0.48 (29050) covalent geometry : angle 0.77232 / 0.42 (40468) hydrogen bonds : bond 0.06614 / 4.38 ( 1489) hydrogen bonds : angle 4.06921 / 2.81 ( 4083) metal coordination : bond 0.01005 / 0.60 ( 20) metal coordination : angle 3.99370 / 2.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1071 ARG cc_start: 0.3205 (tmm160) cc_final: 0.1885 (tpp-160) REVERT: A 1164 MET cc_start: 0.0190 (mtm) cc_final: -0.0886 (tpp) REVERT: A 1209 ARG cc_start: 0.3336 (ttp-170) cc_final: 0.1072 (tmm-80) REVERT: A 1257 MET cc_start: 0.3015 (tmm) cc_final: 0.2601 (tmm) REVERT: A 1286 TYR cc_start: 0.1838 (t80) cc_final: 0.1237 (t80) REVERT: A 1300 MET cc_start: 0.1150 (tpp) cc_final: 0.0780 (tpt) REVERT: E 350 GLN cc_start: 0.2636 (pt0) cc_final: 0.1359 (mm-40) REVERT: E 368 SER cc_start: 0.2462 (p) cc_final: 0.2044 (t) REVERT: B 301 PHE cc_start: 0.3773 (m-80) cc_final: 0.3553 (t80) REVERT: B 351 TYR cc_start: 0.4086 (m-80) cc_final: 0.3599 (m-80) REVERT: C 310 LEU cc_start: 0.2655 (OUTLIER) cc_final: 0.1883 (pp) REVERT: D 310 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.0715 (tt) REVERT: D 401 MET cc_start: 0.3105 (mpp) cc_final: 0.1559 (ppp) REVERT: F 560 MET cc_start: 0.2803 (tmm) cc_final: 0.0478 (ptp) REVERT: c 110 ASN cc_start: 0.7803 (t0) cc_final: 0.7510 (p0) outliers start: 62 outliers final: 29 residues processed: 236 average time/residue: 0.1762 time to fit residues: 67.1017 Evaluate side-chains 171 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1301 PHE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 113 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 161 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 260 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 264 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.191024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.166289 restraints weight = 70319.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.163862 restraints weight = 102777.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.163026 restraints weight = 90353.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.162526 restraints weight = 73086.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.161839 restraints weight = 71472.853| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5702 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.197 29070 Z= 0.451 Angle : 0.667 23.359 40480 Z= 0.370 Chirality : 0.044 0.259 4468 Planarity : 0.005 0.118 4131 Dihedral : 25.969 84.242 6245 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 1.92 % Allowed : 16.31 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2647 helix: 1.19 (0.13), residues: 1534 sheet: -0.48 (0.49), residues: 109 loop : -1.86 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 324 TYR 0.023 0.001 TYR F 372 PHE 0.020 0.001 PHE B 301 TRP 0.042 0.002 TRP D 236 HIS 0.012 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.01028 / 0.45 (29050) covalent geometry : angle 0.66580 / 0.37 (40468) hydrogen bonds : bond 0.05021 / 3.34 ( 1489) hydrogen bonds : angle 3.76400 / 2.59 ( 4083) metal coordination : bond 0.00415 / 0.25 ( 20) metal coordination : angle 2.72486 / 1.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 881 ASP cc_start: 0.3082 (OUTLIER) cc_final: 0.1575 (m-30) REVERT: A 1129 ILE cc_start: 0.2821 (OUTLIER) cc_final: 0.2187 (tt) REVERT: A 1164 MET cc_start: 0.0616 (mtm) cc_final: -0.0417 (tpp) REVERT: A 1209 ARG cc_start: 0.3129 (ttp-170) cc_final: 0.1009 (tmm-80) REVERT: A 1286 TYR cc_start: 0.2148 (t80) cc_final: 0.1385 (t80) REVERT: A 1300 MET cc_start: 0.1288 (tpp) cc_final: 0.1070 (tpt) REVERT: E 350 GLN cc_start: 0.2561 (pt0) cc_final: 0.1338 (mm-40) REVERT: E 507 GLU cc_start: 0.2727 (mt-10) cc_final: 0.2516 (pp20) REVERT: B 25 TYR cc_start: 0.0789 (t80) cc_final: 0.0403 (p90) REVERT: B 108 ASP cc_start: 0.2243 (m-30) cc_final: 0.2028 (p0) REVERT: B 204 MET cc_start: 0.1068 (mtp) cc_final: 0.0780 (ttt) REVERT: B 351 TYR cc_start: 0.4080 (m-80) cc_final: 0.3552 (m-80) REVERT: C 310 LEU cc_start: 0.2478 (OUTLIER) cc_final: 0.1628 (pp) REVERT: D 310 LEU cc_start: 0.1385 (OUTLIER) cc_final: 0.0358 (tt) REVERT: F 339 LEU cc_start: 0.1978 (OUTLIER) cc_final: 0.1019 (tp) REVERT: F 560 MET cc_start: 0.2725 (tmm) cc_final: 0.0559 (ptp) REVERT: c 110 ASN cc_start: 0.7843 (t0) cc_final: 0.7536 (p0) outliers start: 46 outliers final: 29 residues processed: 196 average time/residue: 0.1870 time to fit residues: 58.9717 Evaluate side-chains 173 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1301 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 113 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 187 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 104 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 ASN A1311 HIS ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.190913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.168539 restraints weight = 69997.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.167028 restraints weight = 108221.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.166051 restraints weight = 103859.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.165103 restraints weight = 98891.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.164597 restraints weight = 95767.370| |-----------------------------------------------------------------------------| r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.199 29070 Z= 0.448 Angle : 0.640 23.315 40480 Z= 0.355 Chirality : 0.042 0.225 4468 Planarity : 0.005 0.128 4131 Dihedral : 25.813 85.827 6244 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 2.29 % Allowed : 16.22 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: 0.36 (0.16), residues: 2647 helix: 1.44 (0.13), residues: 1536 sheet: -0.19 (0.51), residues: 108 loop : -1.67 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 564 TYR 0.023 0.001 TYR F 372 PHE 0.025 0.001 PHE A1305 TRP 0.042 0.002 TRP D 236 HIS 0.019 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01023 / 0.45 (29050) covalent geometry : angle 0.63915 / 0.35 (40468) hydrogen bonds : bond 0.04611 / 3.05 ( 1489) hydrogen bonds : angle 3.60729 / 2.47 ( 4083) metal coordination : bond 0.00321 / 0.20 ( 20) metal coordination : angle 2.04124 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 881 ASP cc_start: 0.3294 (OUTLIER) cc_final: 0.1801 (m-30) REVERT: A 1129 ILE cc_start: 0.2957 (OUTLIER) cc_final: 0.2295 (tt) REVERT: A 1164 MET cc_start: 0.0263 (mtm) cc_final: -0.0105 (ttp) REVERT: A 1209 ARG cc_start: 0.3317 (ttp-170) cc_final: 0.1222 (tmm-80) REVERT: A 1286 TYR cc_start: 0.2409 (t80) cc_final: 0.1603 (t80) REVERT: E 350 GLN cc_start: 0.2351 (pt0) cc_final: 0.1191 (mm-40) REVERT: B 38 HIS cc_start: 0.2220 (m-70) cc_final: 0.1948 (m-70) REVERT: B 204 MET cc_start: 0.0895 (mtp) cc_final: 0.0671 (ttt) REVERT: B 351 TYR cc_start: 0.3898 (m-80) cc_final: 0.3446 (m-80) REVERT: B 373 MET cc_start: 0.0334 (mmm) cc_final: 0.0055 (ttm) REVERT: C 310 LEU cc_start: 0.2493 (OUTLIER) cc_final: 0.1624 (pp) REVERT: C 381 ARG cc_start: 0.1490 (OUTLIER) cc_final: 0.1090 (ttp80) REVERT: D 310 LEU cc_start: 0.1351 (OUTLIER) cc_final: 0.0519 (tt) REVERT: D 401 MET cc_start: 0.3457 (mpp) cc_final: 0.1865 (ppp) REVERT: F 339 LEU cc_start: 0.1953 (OUTLIER) cc_final: 0.0906 (tp) REVERT: F 560 MET cc_start: 0.2821 (tmm) cc_final: 0.0673 (ptp) outliers start: 55 outliers final: 30 residues processed: 199 average time/residue: 0.1629 time to fit residues: 52.7586 Evaluate side-chains 168 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 140 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 50.0000 chunk 213 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 247 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 HIS A1311 HIS ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.188868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.164312 restraints weight = 69949.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.162837 restraints weight = 108363.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.161262 restraints weight = 99227.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.160441 restraints weight = 98465.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.159044 restraints weight = 98315.546| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.201 29070 Z= 0.466 Angle : 0.701 23.451 40480 Z= 0.383 Chirality : 0.045 0.236 4468 Planarity : 0.005 0.123 4131 Dihedral : 25.993 85.601 6243 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 2.63 % Allowed : 16.97 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 2647 helix: 1.14 (0.13), residues: 1549 sheet: -0.33 (0.51), residues: 109 loop : -1.68 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 36 TYR 0.026 0.002 TYR F 372 PHE 0.027 0.002 PHE e 78 TRP 0.043 0.002 TRP D 236 HIS 0.014 0.002 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01066 / 0.47 (29050) covalent geometry : angle 0.70091 / 0.38 (40468) hydrogen bonds : bond 0.05892 / 3.90 ( 1489) hydrogen bonds : angle 3.77073 / 2.60 ( 4083) metal coordination : bond 0.00431 / 0.29 ( 20) metal coordination : angle 1.71845 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 138 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 765 MET cc_start: -0.0424 (mmm) cc_final: -0.1151 (mtp) REVERT: A 881 ASP cc_start: 0.3382 (OUTLIER) cc_final: 0.1855 (m-30) REVERT: A 1129 ILE cc_start: 0.2862 (OUTLIER) cc_final: 0.2265 (tt) REVERT: A 1164 MET cc_start: 0.0129 (mtm) cc_final: -0.0271 (ttp) REVERT: A 1209 ARG cc_start: 0.3533 (ttp-110) cc_final: 0.1271 (tmm-80) REVERT: A 1317 ILE cc_start: 0.1568 (OUTLIER) cc_final: 0.1068 (mt) REVERT: E 350 GLN cc_start: 0.2320 (pt0) cc_final: 0.1167 (mm-40) REVERT: E 516 ASN cc_start: 0.0204 (t0) cc_final: -0.0024 (t0) REVERT: B 204 MET cc_start: 0.0896 (mtp) cc_final: 0.0692 (ttt) REVERT: B 351 TYR cc_start: 0.3569 (m-80) cc_final: 0.3174 (m-80) REVERT: C 287 LEU cc_start: 0.4373 (mp) cc_final: 0.3405 (tp) REVERT: C 381 ARG cc_start: 0.1619 (OUTLIER) cc_final: 0.1076 (ttp80) REVERT: D 310 LEU cc_start: 0.1296 (OUTLIER) cc_final: 0.0440 (tt) REVERT: D 368 MET cc_start: 0.0789 (tpp) cc_final: 0.0577 (tpp) REVERT: D 401 MET cc_start: 0.3767 (mpp) cc_final: 0.2074 (ppp) REVERT: F 560 MET cc_start: 0.2857 (tmm) cc_final: 0.0712 (ptp) REVERT: h 105 GLU cc_start: 0.6184 (mp0) cc_final: 0.5940 (mp0) outliers start: 63 outliers final: 44 residues processed: 194 average time/residue: 0.1702 time to fit residues: 54.1037 Evaluate side-chains 173 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 63 ASN Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 62 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 256 optimal weight: 50.0000 chunk 171 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 GLN A1311 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.188711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.168481 restraints weight = 69725.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.166873 restraints weight = 122004.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.165300 restraints weight = 115477.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.164675 restraints weight = 109518.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.164468 restraints weight = 103977.184| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.201 29070 Z= 0.460 Angle : 0.669 23.567 40480 Z= 0.369 Chirality : 0.044 0.227 4468 Planarity : 0.005 0.132 4131 Dihedral : 25.953 88.474 6243 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.50 % Allowed : 17.39 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % 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: 0.18 (0.16), residues: 2647 helix: 1.24 (0.13), residues: 1531 sheet: -0.43 (0.51), residues: 115 loop : -1.61 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 564 TYR 0.030 0.002 TYR D 288 PHE 0.022 0.002 PHE E 567 TRP 0.043 0.002 TRP D 236 HIS 0.009 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.46 (29050) covalent geometry : angle 0.66845 / 0.37 (40468) hydrogen bonds : bond 0.05323 / 3.53 ( 1489) hydrogen bonds : angle 3.68604 / 2.54 ( 4083) metal coordination : bond 0.00407 / 0.28 ( 20) metal coordination : angle 1.85036 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 715 GLU cc_start: 0.2649 (OUTLIER) cc_final: 0.2385 (tm-30) REVERT: A 765 MET cc_start: -0.0346 (mmm) cc_final: -0.1168 (mtp) REVERT: A 874 GLU cc_start: -0.0201 (OUTLIER) cc_final: -0.0608 (tp30) REVERT: A 1129 ILE cc_start: 0.2884 (OUTLIER) cc_final: 0.2335 (tt) REVERT: A 1164 MET cc_start: 0.0084 (mtm) cc_final: -0.0259 (ttp) REVERT: A 1209 ARG cc_start: 0.3366 (ttp-110) cc_final: 0.1355 (tmm-80) REVERT: A 1294 MET cc_start: -0.0096 (pmm) cc_final: -0.0523 (pmm) REVERT: A 1317 ILE cc_start: 0.1599 (mm) cc_final: 0.1125 (mt) REVERT: E 350 GLN cc_start: 0.2471 (pt0) cc_final: 0.1240 (mm-40) REVERT: E 438 MET cc_start: 0.2419 (mmm) cc_final: 0.2064 (mmm) REVERT: E 516 ASN cc_start: 0.0110 (t0) cc_final: -0.0164 (t0) REVERT: B 53 MET cc_start: -0.0607 (ptp) cc_final: -0.0859 (mmt) REVERT: B 204 MET cc_start: 0.0857 (mtp) cc_final: 0.0654 (ttt) REVERT: B 351 TYR cc_start: 0.3475 (m-80) cc_final: 0.3187 (m-80) REVERT: C 381 ARG cc_start: 0.1520 (OUTLIER) cc_final: 0.1097 (ttp80) REVERT: D 310 LEU cc_start: 0.1052 (OUTLIER) cc_final: 0.0169 (tt) REVERT: D 368 MET cc_start: 0.0593 (tpp) cc_final: 0.0386 (tpp) REVERT: D 401 MET cc_start: 0.3879 (mpp) cc_final: 0.2296 (ppp) REVERT: F 560 MET cc_start: 0.3059 (tmm) cc_final: 0.0837 (ptp) REVERT: h 105 GLU cc_start: 0.6400 (mp0) cc_final: 0.6179 (mp0) outliers start: 60 outliers final: 39 residues processed: 189 average time/residue: 0.1676 time to fit residues: 51.8442 Evaluate side-chains 168 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 63 ASN Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 166 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS E 469 HIS ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS B 364 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.188830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.166706 restraints weight = 69990.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.166029 restraints weight = 115751.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.164359 restraints weight = 104414.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.163225 restraints weight = 100948.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.161608 restraints weight = 107420.469| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.200 29070 Z= 0.452 Angle : 0.646 23.564 40480 Z= 0.357 Chirality : 0.043 0.228 4468 Planarity : 0.005 0.129 4131 Dihedral : 25.884 88.988 6243 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 2.29 % Allowed : 17.81 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % 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: 0.34 (0.16), residues: 2647 helix: 1.38 (0.13), residues: 1534 sheet: -0.57 (0.53), residues: 103 loop : -1.54 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 381 TYR 0.025 0.001 TYR F 372 PHE 0.043 0.002 PHE E 567 TRP 0.043 0.002 TRP D 236 HIS 0.009 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.45 (29050) covalent geometry : angle 0.64537 / 0.36 (40468) hydrogen bonds : bond 0.04951 / 3.28 ( 1489) hydrogen bonds : angle 3.63147 / 2.50 ( 4083) metal coordination : bond 0.00377 / 0.25 ( 20) metal coordination : angle 1.85769 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.895 Fit side-chains REVERT: A 765 MET cc_start: -0.0141 (mmm) cc_final: -0.1126 (mtp) REVERT: A 874 GLU cc_start: -0.0070 (OUTLIER) cc_final: -0.0564 (tp30) REVERT: A 1129 ILE cc_start: 0.2662 (OUTLIER) cc_final: 0.2127 (tt) REVERT: A 1164 MET cc_start: 0.0159 (mtm) cc_final: -0.0181 (ttp) REVERT: A 1209 ARG cc_start: 0.3076 (ttp-110) cc_final: 0.1486 (tmm-80) REVERT: E 350 GLN cc_start: 0.2436 (pt0) cc_final: 0.1146 (mm-40) REVERT: E 562 GLN cc_start: 0.1250 (tm-30) cc_final: -0.1462 (mp10) REVERT: C 381 ARG cc_start: 0.1524 (OUTLIER) cc_final: 0.0945 (ttp80) REVERT: D 310 LEU cc_start: 0.0872 (OUTLIER) cc_final: 0.0049 (tt) REVERT: D 401 MET cc_start: 0.3827 (mpp) cc_final: 0.2271 (ppp) REVERT: F 560 MET cc_start: 0.3014 (tmm) cc_final: 0.0809 (ptp) outliers start: 55 outliers final: 38 residues processed: 188 average time/residue: 0.1821 time to fit residues: 55.7859 Evaluate side-chains 171 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 189 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 202 optimal weight: 0.0870 chunk 98 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 57 optimal weight: 30.0000 chunk 161 optimal weight: 0.0050 chunk 126 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS B 43 HIS B 364 ASN d 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.190002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.171153 restraints weight = 70706.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.169488 restraints weight = 116591.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.168324 restraints weight = 107384.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.168114 restraints weight = 103910.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.167707 restraints weight = 98467.869| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.198 29070 Z= 0.445 Angle : 0.613 23.481 40480 Z= 0.344 Chirality : 0.041 0.225 4468 Planarity : 0.004 0.123 4131 Dihedral : 25.705 89.928 6243 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 1.50 % Allowed : 18.77 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.66 (0.17), residues: 2647 helix: 1.62 (0.13), residues: 1532 sheet: -0.63 (0.57), residues: 85 loop : -1.33 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 35 TYR 0.023 0.001 TYR F 372 PHE 0.037 0.001 PHE E 567 TRP 0.042 0.002 TRP D 236 HIS 0.009 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.01015 / 0.44 (29050) covalent geometry : angle 0.61201 / 0.34 (40468) hydrogen bonds : bond 0.04237 / 2.80 ( 1489) hydrogen bonds : angle 3.49689 / 2.41 ( 4083) metal coordination : bond 0.00278 / 0.18 ( 20) metal coordination : angle 1.88634 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 765 MET cc_start: -0.0070 (mmm) cc_final: -0.1103 (mtp) REVERT: A 874 GLU cc_start: -0.0111 (OUTLIER) cc_final: -0.0530 (tp30) REVERT: A 1129 ILE cc_start: 0.2834 (OUTLIER) cc_final: 0.2301 (tt) REVERT: A 1164 MET cc_start: 0.0305 (mtm) cc_final: 0.0035 (ttp) REVERT: A 1209 ARG cc_start: 0.2982 (ttp-110) cc_final: 0.1489 (tmm-80) REVERT: A 1286 TYR cc_start: 0.2173 (t80) cc_final: 0.1105 (t80) REVERT: E 310 ILE cc_start: 0.1831 (mm) cc_final: 0.1173 (mt) REVERT: B 97 PHE cc_start: 0.1416 (m-80) cc_final: 0.1119 (m-80) REVERT: B 369 LEU cc_start: 0.0853 (OUTLIER) cc_final: 0.0083 (mp) REVERT: C 381 ARG cc_start: 0.1259 (OUTLIER) cc_final: 0.0965 (ttp80) REVERT: D 310 LEU cc_start: 0.0957 (OUTLIER) cc_final: 0.0458 (tt) REVERT: D 401 MET cc_start: 0.3779 (mpp) cc_final: 0.2087 (ppp) REVERT: F 560 MET cc_start: 0.2989 (tmm) cc_final: 0.0838 (ptp) outliers start: 36 outliers final: 27 residues processed: 181 average time/residue: 0.1886 time to fit residues: 55.1590 Evaluate side-chains 166 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 29 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 240 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.189724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.170739 restraints weight = 70255.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.169080 restraints weight = 114304.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.168234 restraints weight = 116849.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.167920 restraints weight = 112624.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.167039 restraints weight = 105615.663| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5521 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.199 29070 Z= 0.445 Angle : 0.612 23.483 40480 Z= 0.342 Chirality : 0.041 0.223 4468 Planarity : 0.004 0.138 4131 Dihedral : 25.668 89.997 6242 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 1.21 % Allowed : 19.35 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.78 (0.17), residues: 2647 helix: 1.70 (0.13), residues: 1541 sheet: -0.58 (0.57), residues: 85 loop : -1.28 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 35 TYR 0.026 0.001 TYR A1074 PHE 0.064 0.001 PHE E 567 TRP 0.042 0.002 TRP D 236 HIS 0.010 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.01016 / 0.44 (29050) covalent geometry : angle 0.61140 / 0.34 (40468) hydrogen bonds : bond 0.04256 / 2.81 ( 1489) hydrogen bonds : angle 3.47602 / 2.39 ( 4083) metal coordination : bond 0.00283 / 0.19 ( 20) metal coordination : angle 1.82877 / 1.03 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: -0.0252 (mmm) cc_final: -0.1172 (mtp) REVERT: A 874 GLU cc_start: 0.0007 (OUTLIER) cc_final: -0.0469 (tp30) REVERT: A 1129 ILE cc_start: 0.3124 (OUTLIER) cc_final: 0.2564 (tt) REVERT: A 1164 MET cc_start: 0.0307 (mtm) cc_final: 0.0043 (ttp) REVERT: A 1209 ARG cc_start: 0.3290 (ttp-110) cc_final: 0.1345 (tmm-80) REVERT: A 1286 TYR cc_start: 0.2196 (t80) cc_final: 0.1096 (t80) REVERT: E 107 LYS cc_start: 0.0956 (mttp) cc_final: 0.0525 (mtmt) REVERT: E 310 ILE cc_start: 0.1770 (mm) cc_final: 0.1172 (mt) REVERT: E 438 MET cc_start: 0.1483 (mmm) cc_final: 0.1232 (mmm) REVERT: B 373 MET cc_start: 0.0674 (ttp) cc_final: 0.0328 (mmm) REVERT: C 381 ARG cc_start: 0.1203 (OUTLIER) cc_final: 0.0995 (ttp80) REVERT: D 310 LEU cc_start: 0.0682 (OUTLIER) cc_final: 0.0240 (tt) REVERT: D 401 MET cc_start: 0.3695 (mpp) cc_final: 0.2020 (ppp) REVERT: F 560 MET cc_start: 0.3000 (tmm) cc_final: 0.0958 (ptp) outliers start: 29 outliers final: 24 residues processed: 165 average time/residue: 0.1790 time to fit residues: 47.5270 Evaluate side-chains 163 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1017 PHE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 84 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 270 optimal weight: 50.0000 chunk 52 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 234 optimal weight: 0.2980 chunk 289 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.187938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.164263 restraints weight = 70222.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.163850 restraints weight = 119122.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.162919 restraints weight = 100446.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.162121 restraints weight = 89287.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.161582 restraints weight = 84043.765| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.201 29070 Z= 0.461 Angle : 0.673 23.663 40480 Z= 0.370 Chirality : 0.044 0.242 4468 Planarity : 0.005 0.140 4131 Dihedral : 25.874 88.699 6242 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 1.71 % Allowed : 18.85 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.44 (0.16), residues: 2647 helix: 1.45 (0.13), residues: 1538 sheet: -0.82 (0.53), residues: 96 loop : -1.45 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 35 TYR 0.026 0.002 TYR F 372 PHE 0.060 0.002 PHE E 567 TRP 0.043 0.002 TRP D 236 HIS 0.009 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.01056 / 0.46 (29050) covalent geometry : angle 0.67263 / 0.37 (40468) hydrogen bonds : bond 0.05567 / 3.67 ( 1489) hydrogen bonds : angle 3.65810 / 2.52 ( 4083) metal coordination : bond 0.00495 / 0.34 ( 20) metal coordination : angle 2.07595 / 1.33 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3886.69 seconds wall clock time: 68 minutes 18.68 seconds (4098.68 seconds total)