Starting phenix.real_space_refine on Mon Jun 23 17:52:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9e_37366/06_2025/8w9e_37366_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9e_37366/06_2025/8w9e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9e_37366/06_2025/8w9e_37366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9e_37366/06_2025/8w9e_37366.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9e_37366/06_2025/8w9e_37366_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9e_37366/06_2025/8w9e_37366_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.87, per 1000 atoms: 0.57 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: 6.70 Conformation dependent library (CDL) restraints added in 2.8 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: 11.64 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: 14.81 Time building geometry restraints manager: 7.99 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 78.070 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5522 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= 0.611 Angle : 1.023 25.019 40480 Z= 0.607 Chirality : 0.063 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 : 14.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.050 0.005 TRP G 31 HIS 0.009 0.002 HIS G 18 PHE 0.033 0.002 PHE A1301 TYR 0.053 0.002 TYR G 100 ARG 0.010 0.001 ARG h 33 Details of bonding type rmsd hydrogen bonds : bond 0.13547 ( 1489) hydrogen bonds : angle 5.86889 ( 4083) metal coordination : bond 0.10081 ( 20) metal coordination : angle 18.59200 ( 12) covalent geometry : bond 0.01270 (29050) covalent geometry : angle 0.97160 (40468) *********************** 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 : 2.606 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: 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: 0.3973 (t-170) REVERT: A 1009 ARG cc_start: 0.3927 (mtp180) cc_final: 0.3449 (tpt90) REVERT: A 1164 MET cc_start: 0.0791 (mtm) cc_final: 0.0040 (tpp) REVERT: A 1209 ARG cc_start: 0.2884 (ttp-170) cc_final: 0.0811 (tmm-80) REVERT: A 1286 TYR cc_start: 0.1359 (t80) cc_final: 0.1009 (m-80) REVERT: A 1290 VAL cc_start: 0.1613 (t) cc_final: 0.0823 (p) REVERT: E 105 ASP cc_start: 0.1790 (OUTLIER) cc_final: 0.1551 (t0) REVERT: E 316 MET cc_start: 0.0241 (mmp) cc_final: -0.0341 (mtm) REVERT: E 350 GLN cc_start: 0.2243 (pt0) cc_final: 0.1325 (mm-40) REVERT: E 523 ILE cc_start: 0.3386 (pt) cc_final: 0.3148 (tp) REVERT: E 557 LYS cc_start: 0.1253 (pptt) cc_final: 0.0910 (tppt) REVERT: B 163 LEU cc_start: 0.0472 (tp) cc_final: -0.0159 (tp) REVERT: D 227 LYS cc_start: -0.0452 (tttt) cc_final: -0.0683 (tttp) REVERT: D 296 MET cc_start: 0.2181 (ttp) cc_final: 0.1595 (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: 0.7170 (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: 0.7920 (t) outliers start: 86 outliers final: 25 residues processed: 455 average time/residue: 0.4943 time to fit residues: 328.7636 Evaluate side-chains 224 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 2.661 ------------------------------------------------------------------------------- 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 244 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 87 optimal weight: 0.0020 chunk 138 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 263 optimal weight: 5.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN A 798 HIS A 857 HIS A 884 HIS A 974 GLN A1127 GLN A1252 HIS A1293 HIS A1345 HIS E 355 ASN ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 ASN B 31 ASN B 177 HIS C 389 ASN F 302 HIS F 329 GLN F 331 ASN a 39 HIS b 93 GLN c 31 HIS d 84 ASN d 109 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.194575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.173364 restraints weight = 70410.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.171857 restraints weight = 113429.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.170599 restraints weight = 96088.966| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.196 29070 Z= 0.456 Angle : 0.672 23.298 40480 Z= 0.378 Chirality : 0.040 0.357 4468 Planarity : 0.005 0.124 4131 Dihedral : 25.758 87.599 6278 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 2.04 % Allowed : 11.93 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2647 helix: 0.95 (0.13), residues: 1520 sheet: -0.89 (0.49), residues: 109 loop : -2.16 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 236 HIS 0.014 0.001 HIS B 188 PHE 0.024 0.002 PHE D 362 TYR 0.027 0.002 TYR E 514 ARG 0.007 0.000 ARG A 674 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 1489) hydrogen bonds : angle 3.91244 ( 4083) metal coordination : bond 0.01144 ( 20) metal coordination : angle 4.95983 ( 12) covalent geometry : bond 0.01045 (29050) covalent geometry : angle 0.66625 (40468) *********************** 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 280 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 HIS cc_start: 0.3711 (t-170) cc_final: 0.3466 (t-170) REVERT: A 1129 ILE cc_start: 0.2826 (OUTLIER) cc_final: 0.2020 (tt) REVERT: A 1150 HIS cc_start: 0.0505 (m90) cc_final: 0.0301 (m90) REVERT: A 1164 MET cc_start: 0.0647 (mtm) cc_final: -0.0417 (tpp) REVERT: A 1209 ARG cc_start: 0.3469 (ttp-170) cc_final: 0.1216 (tmm-80) REVERT: A 1286 TYR cc_start: 0.1735 (t80) cc_final: 0.1086 (t80) REVERT: E 350 GLN cc_start: 0.2574 (pt0) cc_final: 0.1465 (mm-40) REVERT: B 163 LEU cc_start: 0.0533 (tp) cc_final: 0.0320 (tp) REVERT: D 310 LEU cc_start: 0.1628 (OUTLIER) cc_final: 0.0543 (tt) REVERT: D 401 MET cc_start: 0.2547 (mpp) cc_final: 0.1423 (ppp) REVERT: F 331 ASN cc_start: 0.4131 (t0) cc_final: 0.3674 (p0) REVERT: F 565 LYS cc_start: 0.0895 (tptt) cc_final: 0.0672 (mtmt) REVERT: c 41 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6381 (tp30) outliers start: 49 outliers final: 19 residues processed: 270 average time/residue: 0.4166 time to fit residues: 176.0761 Evaluate side-chains 178 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain C residue 336 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 D residue 382 SER Chi-restraints excluded: chain c residue 40 SER 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 f residue 21 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain g residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 61 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 chunk 143 optimal weight: 30.0000 chunk 238 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 302 HIS E 469 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 164 ASN C 305 GLN a 76 GLN e 68 GLN h 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.192787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.166228 restraints weight = 69587.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.163643 restraints weight = 104486.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.161552 restraints weight = 89156.088| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.3406 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= 0.452 Angle : 0.620 23.274 40480 Z= 0.350 Chirality : 0.038 0.265 4468 Planarity : 0.005 0.110 4131 Dihedral : 25.443 85.175 6246 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 2.04 % Allowed : 13.55 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2647 helix: 1.38 (0.13), residues: 1549 sheet: -0.65 (0.51), residues: 105 loop : -1.82 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.005 0.001 HIS A 815 PHE 0.023 0.001 PHE A1017 TYR 0.022 0.001 TYR A1316 ARG 0.005 0.000 ARG a 42 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 1489) hydrogen bonds : angle 3.63314 ( 4083) metal coordination : bond 0.00746 ( 20) metal coordination : angle 2.91110 ( 12) covalent geometry : bond 0.01038 (29050) covalent geometry : angle 0.61840 (40468) *********************** 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 234 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1129 ILE cc_start: 0.3158 (OUTLIER) cc_final: 0.2380 (tt) REVERT: A 1164 MET cc_start: 0.0606 (mtm) cc_final: 0.0153 (ttp) REVERT: A 1209 ARG cc_start: 0.3019 (ttp-170) cc_final: 0.1161 (tmm-80) REVERT: A 1266 MET cc_start: 0.3011 (ttp) cc_final: 0.2776 (ttp) REVERT: A 1286 TYR cc_start: 0.2051 (t80) cc_final: 0.1476 (t80) REVERT: E 350 GLN cc_start: 0.2273 (pt0) cc_final: 0.1164 (mm-40) REVERT: B 280 ARG cc_start: 0.3997 (OUTLIER) cc_final: 0.3727 (mtm180) REVERT: B 284 PHE cc_start: -0.0939 (m-10) cc_final: -0.1228 (m-10) REVERT: C 381 ARG cc_start: 0.1090 (OUTLIER) cc_final: 0.0771 (ttp80) REVERT: D 310 LEU cc_start: 0.1440 (OUTLIER) cc_final: 0.0451 (tt) REVERT: c 41 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6649 (tm-30) outliers start: 49 outliers final: 21 residues processed: 226 average time/residue: 0.4452 time to fit residues: 160.0445 Evaluate side-chains 169 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 430 HIS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 336 SER 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 D residue 310 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain c residue 40 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 25 optimal weight: 0.0370 chunk 48 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 206 optimal weight: 4.9990 chunk 208 optimal weight: 0.0980 chunk 126 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 240 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 HIS A1254 HIS E 515 GLN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.193715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.175960 restraints weight = 71873.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.174448 restraints weight = 114660.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.172958 restraints weight = 104424.091| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.3873 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= 0.446 Angle : 0.574 23.199 40480 Z= 0.328 Chirality : 0.037 0.255 4468 Planarity : 0.004 0.096 4131 Dihedral : 25.166 87.657 6244 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 1.67 % Allowed : 14.89 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2647 helix: 1.74 (0.13), residues: 1540 sheet: -0.46 (0.56), residues: 92 loop : -1.62 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 236 HIS 0.008 0.001 HIS A 815 PHE 0.026 0.001 PHE A1305 TYR 0.021 0.001 TYR F 372 ARG 0.005 0.000 ARG A1009 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1489) hydrogen bonds : angle 3.41822 ( 4083) metal coordination : bond 0.00337 ( 20) metal coordination : angle 2.13116 ( 12) covalent geometry : bond 0.01025 (29050) covalent geometry : angle 0.57322 (40468) *********************** 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 210 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 TYR cc_start: 0.2035 (p90) cc_final: 0.1144 (m-10) REVERT: A 881 ASP cc_start: 0.3187 (OUTLIER) cc_final: 0.1763 (m-30) REVERT: A 1129 ILE cc_start: 0.2920 (OUTLIER) cc_final: 0.2216 (tt) REVERT: A 1164 MET cc_start: 0.0655 (mtm) cc_final: 0.0358 (ttp) REVERT: A 1209 ARG cc_start: 0.2854 (ttp-170) cc_final: 0.1452 (tmm-80) REVERT: A 1221 HIS cc_start: 0.1269 (OUTLIER) cc_final: 0.0962 (t-170) REVERT: A 1247 GLN cc_start: 0.6129 (tt0) cc_final: 0.5849 (tm-30) REVERT: A 1286 TYR cc_start: 0.2590 (t80) cc_final: 0.2084 (t80) REVERT: E 523 ILE cc_start: 0.2995 (pt) cc_final: 0.2599 (tp) REVERT: E 562 GLN cc_start: 0.1329 (tm-30) cc_final: 0.0780 (pp30) REVERT: B 280 ARG cc_start: 0.3904 (OUTLIER) cc_final: 0.3692 (mtm180) REVERT: B 284 PHE cc_start: -0.1163 (m-10) cc_final: -0.1453 (m-10) REVERT: B 373 MET cc_start: 0.0542 (mmm) cc_final: 0.0317 (ttm) REVERT: D 310 LEU cc_start: 0.0937 (OUTLIER) cc_final: 0.0176 (tt) REVERT: F 331 ASN cc_start: 0.4014 (t0) cc_final: 0.3321 (p0) REVERT: c 41 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6625 (tm-30) outliers start: 40 outliers final: 13 residues processed: 201 average time/residue: 0.4010 time to fit residues: 128.5117 Evaluate side-chains 164 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1301 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 216 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 229 optimal weight: 0.0970 chunk 223 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 132 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 35 optimal weight: 0.0370 overall best weight: 1.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.191440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.166581 restraints weight = 69913.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.164281 restraints weight = 107757.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.163406 restraints weight = 95092.631| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.4327 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= 0.453 Angle : 0.591 23.302 40480 Z= 0.335 Chirality : 0.037 0.190 4468 Planarity : 0.004 0.082 4131 Dihedral : 25.261 89.791 6243 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 1.92 % Allowed : 15.60 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2647 helix: 1.79 (0.13), residues: 1548 sheet: -0.28 (0.57), residues: 92 loop : -1.43 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.038 0.001 HIS A1221 PHE 0.019 0.001 PHE B 24 TYR 0.023 0.001 TYR F 372 ARG 0.004 0.000 ARG A1009 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 1489) hydrogen bonds : angle 3.42751 ( 4083) metal coordination : bond 0.00352 ( 20) metal coordination : angle 1.97428 ( 12) covalent geometry : bond 0.01042 (29050) covalent geometry : angle 0.58964 (40468) *********************** 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 191 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 TYR cc_start: 0.1922 (p90) cc_final: 0.1009 (m-10) REVERT: A 881 ASP cc_start: 0.3428 (OUTLIER) cc_final: 0.1906 (m-30) REVERT: A 1129 ILE cc_start: 0.3085 (OUTLIER) cc_final: 0.2428 (tt) REVERT: A 1164 MET cc_start: 0.0339 (mtm) cc_final: 0.0067 (ttp) REVERT: A 1209 ARG cc_start: 0.2998 (ttp-170) cc_final: 0.1509 (tmm-80) REVERT: A 1286 TYR cc_start: 0.2374 (t80) cc_final: 0.1831 (t80) REVERT: E 523 ILE cc_start: 0.3015 (pt) cc_final: 0.2584 (tp) REVERT: E 562 GLN cc_start: 0.1443 (tm-30) cc_final: 0.0932 (pp30) REVERT: B 305 MET cc_start: 0.1435 (mmm) cc_final: 0.0597 (mmm) REVERT: B 351 TYR cc_start: 0.3924 (m-80) cc_final: 0.3612 (m-80) REVERT: D 310 LEU cc_start: 0.1053 (OUTLIER) cc_final: 0.0275 (tt) REVERT: D 401 MET cc_start: 0.3029 (mpp) cc_final: 0.1794 (ppp) REVERT: c 41 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6701 (tm-30) outliers start: 46 outliers final: 25 residues processed: 187 average time/residue: 0.4025 time to fit residues: 120.3095 Evaluate side-chains 160 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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 1013 LEU Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1215 ILE 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 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU 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 c residue 40 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain d residue 106 LEU 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 113 GLU Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 72 optimal weight: 30.0000 chunk 212 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN E 516 ASN B 38 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.192433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.171016 restraints weight = 70663.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.168695 restraints weight = 111276.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.167377 restraints weight = 112123.053| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.4741 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= 0.446 Angle : 0.555 23.306 40480 Z= 0.317 Chirality : 0.036 0.180 4468 Planarity : 0.004 0.064 4131 Dihedral : 25.079 87.114 6243 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 1.58 % Allowed : 16.26 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2647 helix: 2.00 (0.13), residues: 1540 sheet: -0.19 (0.56), residues: 93 loop : -1.26 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.004 0.001 HIS A1221 PHE 0.028 0.001 PHE A1305 TYR 0.022 0.001 TYR F 372 ARG 0.005 0.000 ARG c 71 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1489) hydrogen bonds : angle 3.28472 ( 4083) metal coordination : bond 0.00317 ( 20) metal coordination : angle 1.86338 ( 12) covalent geometry : bond 0.01025 (29050) covalent geometry : angle 0.55396 (40468) *********************** 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 190 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 TYR cc_start: 0.1964 (p90) cc_final: 0.1117 (m-10) REVERT: A 881 ASP cc_start: 0.3471 (OUTLIER) cc_final: 0.1887 (m-30) REVERT: A 1063 MET cc_start: 0.0801 (tpt) cc_final: -0.0543 (pmm) REVERT: A 1129 ILE cc_start: 0.2809 (OUTLIER) cc_final: 0.2248 (tt) REVERT: A 1164 MET cc_start: 0.0379 (mtm) cc_final: 0.0108 (ttp) REVERT: A 1166 GLU cc_start: 0.1528 (OUTLIER) cc_final: 0.0954 (mm-30) REVERT: A 1209 ARG cc_start: 0.3091 (ttp-170) cc_final: 0.1604 (tmm-80) REVERT: A 1294 MET cc_start: -0.0198 (pmm) cc_final: -0.0701 (pmm) REVERT: A 1317 ILE cc_start: 0.1557 (mm) cc_final: 0.1237 (mt) REVERT: E 470 SER cc_start: -0.0692 (OUTLIER) cc_final: -0.0930 (p) REVERT: E 523 ILE cc_start: 0.3111 (pt) cc_final: 0.2673 (tp) REVERT: E 562 GLN cc_start: 0.1195 (tm-30) cc_final: 0.0874 (pp30) REVERT: B 44 ARG cc_start: 0.2946 (OUTLIER) cc_final: 0.1163 (ppt90) REVERT: B 72 GLN cc_start: 0.2905 (OUTLIER) cc_final: 0.1752 (mp10) REVERT: B 188 HIS cc_start: 0.2679 (m-70) cc_final: 0.2472 (m-70) REVERT: B 284 PHE cc_start: -0.0704 (m-10) cc_final: -0.1136 (m-10) REVERT: B 331 ASN cc_start: 0.5048 (m-40) cc_final: 0.4768 (t0) REVERT: B 373 MET cc_start: 0.0930 (ttm) cc_final: 0.0538 (mmm) REVERT: D 262 GLU cc_start: 0.0706 (OUTLIER) cc_final: 0.0024 (mp0) REVERT: D 310 LEU cc_start: 0.0540 (OUTLIER) cc_final: 0.0126 (tt) REVERT: h 105 GLU cc_start: 0.6296 (mp0) cc_final: 0.6047 (mp0) REVERT: G 107 MET cc_start: 0.3119 (ptp) cc_final: 0.2246 (ptt) outliers start: 38 outliers final: 20 residues processed: 184 average time/residue: 0.4261 time to fit residues: 128.7710 Evaluate side-chains 165 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 90 THR 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 368 MET Chi-restraints excluded: chain C residue 401 MET 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 c residue 40 SER Chi-restraints excluded: chain d residue 69 ILE Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 6.9990 chunk 284 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 185 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS c 24 GLN d 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.190218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.172633 restraints weight = 70547.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.171647 restraints weight = 120235.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.170607 restraints weight = 110043.802| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 0.5113 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= 0.454 Angle : 0.586 23.436 40480 Z= 0.332 Chirality : 0.037 0.177 4468 Planarity : 0.004 0.052 4131 Dihedral : 25.268 84.916 6241 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 1.88 % Allowed : 16.06 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2647 helix: 1.88 (0.13), residues: 1543 sheet: -0.63 (0.55), residues: 94 loop : -1.25 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.005 0.001 HIS E 406 PHE 0.023 0.001 PHE A1305 TYR 0.024 0.001 TYR F 372 ARG 0.004 0.000 ARG E 564 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1489) hydrogen bonds : angle 3.38744 ( 4083) metal coordination : bond 0.00372 ( 20) metal coordination : angle 1.89792 ( 12) covalent geometry : bond 0.01046 (29050) covalent geometry : angle 0.58484 (40468) *********************** 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 188 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 2.689 Fit side-chains revert: symmetry clash REVERT: A 881 ASP cc_start: 0.3554 (OUTLIER) cc_final: 0.1964 (m-30) REVERT: A 1063 MET cc_start: 0.0731 (tpt) cc_final: -0.0810 (pmm) REVERT: A 1129 ILE cc_start: 0.3046 (OUTLIER) cc_final: 0.2456 (tt) REVERT: A 1166 GLU cc_start: 0.1681 (OUTLIER) cc_final: 0.1102 (mm-30) REVERT: A 1209 ARG cc_start: 0.3146 (ttp-170) cc_final: 0.1586 (tmm-80) REVERT: A 1294 MET cc_start: -0.0168 (pmm) cc_final: -0.0436 (pmm) REVERT: E 310 ILE cc_start: 0.2090 (mm) cc_final: 0.1569 (mt) REVERT: E 470 SER cc_start: -0.0670 (OUTLIER) cc_final: -0.0947 (p) REVERT: E 516 ASN cc_start: 0.0091 (t0) cc_final: -0.0158 (t0) REVERT: B 44 ARG cc_start: 0.3061 (OUTLIER) cc_final: 0.1239 (ppt90) REVERT: B 305 MET cc_start: 0.0694 (tpt) cc_final: 0.0371 (tpp) REVERT: D 262 GLU cc_start: 0.0895 (OUTLIER) cc_final: 0.0225 (mt-10) REVERT: h 105 GLU cc_start: 0.6522 (mp0) cc_final: 0.6305 (mp0) outliers start: 45 outliers final: 28 residues processed: 183 average time/residue: 0.4161 time to fit residues: 122.4905 Evaluate side-chains 167 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 2.670 ------------------------------------------------------------------------------- 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 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 106 LEU 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 112 SER Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.0060 chunk 242 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 209 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.191809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.175449 restraints weight = 71216.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.174291 restraints weight = 119988.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.172963 restraints weight = 104613.323| |-----------------------------------------------------------------------------| r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5219 moved from start: 0.5347 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 : 0.552 23.369 40480 Z= 0.315 Chirality : 0.036 0.163 4468 Planarity : 0.004 0.052 4131 Dihedral : 25.026 85.103 6241 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 1.42 % Allowed : 17.22 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2647 helix: 2.11 (0.13), residues: 1542 sheet: -0.50 (0.59), residues: 82 loop : -1.06 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 236 HIS 0.005 0.001 HIS B 189 PHE 0.064 0.001 PHE E 567 TYR 0.022 0.001 TYR F 372 ARG 0.003 0.000 ARG a 42 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1489) hydrogen bonds : angle 3.23023 ( 4083) metal coordination : bond 0.00418 ( 20) metal coordination : angle 1.90058 ( 12) covalent geometry : bond 0.01022 (29050) covalent geometry : angle 0.55085 (40468) *********************** 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 184 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 881 ASP cc_start: 0.3472 (OUTLIER) cc_final: 0.1880 (m-30) REVERT: A 1063 MET cc_start: 0.0785 (tpt) cc_final: -0.0788 (pmm) REVERT: A 1129 ILE cc_start: 0.2981 (OUTLIER) cc_final: 0.2442 (tt) REVERT: A 1166 GLU cc_start: 0.1759 (OUTLIER) cc_final: 0.1120 (mm-30) REVERT: A 1209 ARG cc_start: 0.3554 (ttp-170) cc_final: 0.1873 (tmm-80) REVERT: E 470 SER cc_start: -0.1898 (OUTLIER) cc_final: -0.2242 (p) REVERT: E 523 ILE cc_start: 0.3042 (pt) cc_final: 0.2582 (tp) REVERT: B 284 PHE cc_start: -0.0430 (m-10) cc_final: -0.1023 (m-80) REVERT: D 256 MET cc_start: -0.0352 (ptm) cc_final: -0.0597 (ptm) REVERT: D 262 GLU cc_start: 0.0860 (OUTLIER) cc_final: 0.0107 (mt-10) REVERT: G 107 MET cc_start: 0.2481 (ptp) cc_final: 0.1375 (ptt) outliers start: 34 outliers final: 21 residues processed: 179 average time/residue: 0.3960 time to fit residues: 114.3149 Evaluate side-chains 161 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 220 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.189181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.172253 restraints weight = 69762.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.171356 restraints weight = 128327.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.170349 restraints weight = 110699.478| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5323 moved from start: 0.5760 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= 0.461 Angle : 0.612 23.645 40480 Z= 0.345 Chirality : 0.038 0.166 4468 Planarity : 0.004 0.048 4131 Dihedral : 25.446 89.432 6241 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 1.33 % Allowed : 17.81 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2647 helix: 1.87 (0.13), residues: 1529 sheet: -0.83 (0.50), residues: 109 loop : -1.17 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.006 0.001 HIS E 406 PHE 0.056 0.002 PHE E 567 TYR 0.025 0.001 TYR F 372 ARG 0.006 0.001 ARG g 35 Details of bonding type rmsd hydrogen bonds : bond 0.05045 ( 1489) hydrogen bonds : angle 3.46119 ( 4083) metal coordination : bond 0.00494 ( 20) metal coordination : angle 2.29265 ( 12) covalent geometry : bond 0.01063 (29050) covalent geometry : angle 0.61083 (40468) *********************** 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 172 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: -0.0583 (mmm) cc_final: -0.1192 (mtt) REVERT: A 881 ASP cc_start: 0.3804 (OUTLIER) cc_final: 0.3479 (p0) REVERT: A 884 HIS cc_start: 0.2011 (m90) cc_final: 0.0560 (p-80) REVERT: A 1063 MET cc_start: 0.0535 (tpt) cc_final: -0.1160 (pmm) REVERT: A 1129 ILE cc_start: 0.2798 (OUTLIER) cc_final: 0.2223 (tt) REVERT: A 1166 GLU cc_start: 0.1768 (OUTLIER) cc_final: 0.1156 (mm-30) REVERT: A 1209 ARG cc_start: 0.3474 (ttp-170) cc_final: 0.1897 (tmt170) REVERT: E 175 MET cc_start: 0.1418 (mpp) cc_final: 0.0090 (mpp) REVERT: E 310 ILE cc_start: 0.1808 (mm) cc_final: 0.1349 (mt) REVERT: B 315 MET cc_start: 0.2557 (mmp) cc_final: 0.2257 (mmp) REVERT: D 256 MET cc_start: -0.0021 (ptm) cc_final: -0.0256 (ptm) REVERT: D 262 GLU cc_start: 0.0856 (OUTLIER) cc_final: 0.0330 (mt-10) REVERT: D 296 MET cc_start: 0.4631 (ttp) cc_final: 0.4236 (tmm) REVERT: G 107 MET cc_start: 0.2709 (ptp) cc_final: 0.1918 (ptt) outliers start: 32 outliers final: 20 residues processed: 168 average time/residue: 0.4045 time to fit residues: 111.4643 Evaluate side-chains 155 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 2.672 ------------------------------------------------------------------------------- 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 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 147 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.189949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.173892 restraints weight = 70471.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.172711 restraints weight = 121955.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.171402 restraints weight = 117402.574| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5291 moved from start: 0.5947 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= 0.450 Angle : 0.585 23.605 40480 Z= 0.329 Chirality : 0.037 0.159 4468 Planarity : 0.004 0.045 4131 Dihedral : 25.288 89.222 6241 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 1.29 % Allowed : 18.02 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2647 helix: 1.96 (0.13), residues: 1535 sheet: -0.59 (0.55), residues: 94 loop : -1.14 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.006 0.001 HIS B 38 PHE 0.057 0.002 PHE E 567 TYR 0.024 0.001 TYR F 372 ARG 0.005 0.000 ARG g 35 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1489) hydrogen bonds : angle 3.34727 ( 4083) metal coordination : bond 0.00479 ( 20) metal coordination : angle 2.20226 ( 12) covalent geometry : bond 0.01036 (29050) covalent geometry : angle 0.58355 (40468) ********************** 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 173 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 2.475 Fit side-chains revert: symmetry clash REVERT: A 765 MET cc_start: -0.0517 (mmm) cc_final: -0.1065 (mtt) REVERT: A 881 ASP cc_start: 0.3639 (OUTLIER) cc_final: 0.3227 (p0) REVERT: A 884 HIS cc_start: 0.2034 (m90) cc_final: 0.0600 (p-80) REVERT: A 1016 TYR cc_start: 0.3529 (m-80) cc_final: 0.3193 (m-80) REVERT: A 1129 ILE cc_start: 0.2785 (OUTLIER) cc_final: 0.2225 (tt) REVERT: A 1166 GLU cc_start: 0.1932 (OUTLIER) cc_final: 0.1274 (mm-30) REVERT: A 1209 ARG cc_start: 0.3514 (ttp-170) cc_final: 0.1765 (tmm-80) REVERT: A 1328 LYS cc_start: 0.1481 (mmtp) cc_final: 0.1148 (mmtm) REVERT: E 310 ILE cc_start: 0.2147 (mm) cc_final: 0.1697 (mt) REVERT: E 516 ASN cc_start: 0.0596 (t0) cc_final: 0.0321 (t0) REVERT: B 44 ARG cc_start: 0.3211 (OUTLIER) cc_final: 0.1264 (ppt90) REVERT: B 315 MET cc_start: 0.2523 (mmp) cc_final: 0.2251 (mmp) REVERT: D 256 MET cc_start: -0.0135 (ptm) cc_final: -0.0348 (ptm) REVERT: D 262 GLU cc_start: 0.0822 (OUTLIER) cc_final: 0.0201 (mt-10) REVERT: D 263 HIS cc_start: 0.2324 (OUTLIER) cc_final: 0.1521 (m-70) REVERT: D 296 MET cc_start: 0.4605 (ttp) cc_final: 0.4161 (tmm) REVERT: D 310 LEU cc_start: 0.0146 (OUTLIER) cc_final: -0.0310 (tp) REVERT: G 107 MET cc_start: 0.2770 (ptp) cc_final: 0.1966 (ptt) outliers start: 31 outliers final: 20 residues processed: 171 average time/residue: 0.3989 time to fit residues: 109.5853 Evaluate side-chains 164 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 90 THR 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 D residue 262 GLU Chi-restraints excluded: chain D residue 263 HIS 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 F residue 547 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain d residue 69 ILE Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 112 SER Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 287 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 140 optimal weight: 0.2980 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN A1311 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 364 ASN C 330 HIS F 267 ASN f 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.186669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.162954 restraints weight = 69728.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.161261 restraints weight = 117476.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.160094 restraints weight = 111465.402| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.204 29070 Z= 0.516 Angle : 0.794 24.204 40480 Z= 0.438 Chirality : 0.046 0.192 4468 Planarity : 0.006 0.054 4131 Dihedral : 26.301 89.566 6241 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 1.54 % Allowed : 18.22 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2647 helix: 0.87 (0.13), residues: 1539 sheet: -1.24 (0.46), residues: 123 loop : -1.66 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D 236 HIS 0.010 0.002 HIS E 406 PHE 0.060 0.003 PHE E 567 TYR 0.031 0.003 TYR F 372 ARG 0.008 0.001 ARG b 36 Details of bonding type rmsd hydrogen bonds : bond 0.07451 ( 1489) hydrogen bonds : angle 4.08241 ( 4083) metal coordination : bond 0.00941 ( 20) metal coordination : angle 4.58697 ( 12) covalent geometry : bond 0.01192 (29050) covalent geometry : angle 0.79061 (40468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7596.40 seconds wall clock time: 133 minutes 48.90 seconds (8028.90 seconds total)