Starting phenix.real_space_refine on Fri Aug 7 23:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2026/7yp9_33996.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 100 5.16 5 C 15232 2.51 5 N 4337 2.21 5 O 4814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24547 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1649 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1583 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 199} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 9548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9548 Classifications: {'peptide': 1230} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1180} Chain breaks: 8 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 121 Chain: "D" Number of atoms: 9937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 9937 Classifications: {'peptide': 1285} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1231} Chain breaks: 8 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 517 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna3p': 10} Chain: "D" 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} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13220 SG CYS D 70 102.849 43.200 55.763 1.00 57.05 S ATOM 13366 SG CYS D 88 105.019 45.869 54.094 1.00 61.37 S ATOM 18828 SG CYS D 814 80.360 62.455 113.857 1.00 50.20 S ATOM 19354 SG CYS D 888 79.640 63.643 109.166 1.00 30.92 S ATOM 19426 SG CYS D 898 77.002 63.070 111.952 1.00 31.94 S Time building chain proxies: 5.17, per 1000 atoms: 0.21 Number of scatterers: 24547 At special positions: 0 Unit cell: (127, 151, 146, 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 2 29.99 S 100 16.00 P 61 15.00 Mg 1 11.99 O 4814 8.00 N 4337 7.00 C 15232 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: 1.63 Conformation dependent library (CDL) restraints added in 847.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 39 sheets defined 34.4% alpha, 12.6% beta 20 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.567A pdb=" N LEU A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.650A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'B' and resid 34 through 50 removed outlier: 4.220A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.535A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.745A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.668A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 40 removed outlier: 3.776A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.628A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.901A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 217 through 225 removed outlier: 4.221A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 removed outlier: 4.116A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 4.302A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.520A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.571A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 359 through 369 removed outlier: 3.538A pdb=" N LEU C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.729A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.883A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 471 Processing helix chain 'C' and resid 471 through 482 removed outlier: 3.658A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 507 removed outlier: 4.493A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.624A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.057A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.723A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.607A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET C 685 " --> pdb=" O MET C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 4.212A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 3.761A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 969 removed outlier: 4.202A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 953 " --> pdb=" O GLU C 949 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 968 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1038 removed outlier: 4.037A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1149 Processing helix chain 'C' and resid 1165 through 1176 removed outlier: 3.677A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.681A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C1196 " --> pdb=" O GLU C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1279 removed outlier: 3.575A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.628A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C1292 " --> pdb=" O GLN C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.797A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.647A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.837A pdb=" N ARG D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 99' Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.572A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 removed outlier: 3.521A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 136' Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.522A pdb=" N LEU D 169 " --> pdb=" O TYR D 165 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.830A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.681A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.684A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 265 through 284 removed outlier: 3.591A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.718A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.550A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 394 through 404 removed outlier: 3.672A pdb=" N LYS D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.079A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.870A pdb=" N GLU D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.671A pdb=" N MET D 513 " --> pdb=" O GLY D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.693A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.807A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 removed outlier: 3.633A pdb=" N MET D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 4.553A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 671 removed outlier: 4.033A pdb=" N HIS D 651 " --> pdb=" O PRO D 647 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.729A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.785A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.511A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.613A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.600A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 925 removed outlier: 3.625A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1223 removed outlier: 3.915A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.800A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 4.190A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.720A pdb=" N ILE D1287 " --> pdb=" O SER D1283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D1288 " --> pdb=" O ARG D1284 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.602A pdb=" N SER D1324 " --> pdb=" O ILE D1320 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 3.535A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.754A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.731A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.541A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.611A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.519A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 6.364A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 7.472A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.552A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 17 removed outlier: 7.115A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.647A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.795A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.143A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.862A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 151 removed outlier: 3.764A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 231 removed outlier: 4.049A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.904A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 529 through 531 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.887A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.546A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.785A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 722 through 727 removed outlier: 3.663A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 798 through 804 removed outlier: 8.168A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C1074 " --> pdb=" O MET C1066 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 839 removed outlier: 3.529A pdb=" N VAL C1052 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C1050 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 934 " --> pdb=" O ILE C1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.591A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.996A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AD3, first strand: chain 'D' and resid 352 through 354 Processing sheet with id=AD4, first strand: chain 'D' and resid 367 through 369 removed outlier: 6.335A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.707A pdb=" N VAL D 548 " --> pdb=" O THR D 572 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 552 through 554 removed outlier: 4.239A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.515A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 982 through 985 Processing sheet with id=AD9, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE1, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 4.193A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.519A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.640A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7787 1.34 - 1.46: 3336 1.46 - 1.57: 13614 1.57 - 1.69: 119 1.69 - 1.81: 173 Bond restraints: 25029 Sorted by residual: bond pdb=" C3' DG G 9 " pdb=" C2' DG G 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC G -5 " pdb=" C2' DC G -5 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.10e+00 bond pdb=" C3' DG G 8 " pdb=" C2' DG G 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.56e+00 bond pdb=" C3' DG G 10 " pdb=" O3' DG G 10 " ideal model delta sigma weight residual 1.435 1.471 -0.036 1.30e-02 5.92e+03 7.75e+00 bond pdb=" C3' DG F -9 " pdb=" C2' DG F -9 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.62e+00 ... (remaining 25024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 33081 1.76 - 3.52: 869 3.52 - 5.28: 91 5.28 - 7.04: 35 7.04 - 8.80: 15 Bond angle restraints: 34091 Sorted by residual: angle pdb=" C VAL B 192 " pdb=" N GLU B 193 " pdb=" CA GLU B 193 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C LEU D 128 " pdb=" N ASP D 129 " pdb=" CA ASP D 129 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" N3 DT F 10 " pdb=" C4 DT F 10 " pdb=" O4 DT F 10 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT G -11 " pdb=" C4 DT G -11 " pdb=" O4 DT G -11 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT F -2 " pdb=" C4 DT F -2 " pdb=" O4 DT F -2 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 34086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 14459 27.87 - 55.75: 684 55.75 - 83.62: 64 83.62 - 111.50: 9 111.50 - 139.37: 1 Dihedral angle restraints: 15217 sinusoidal: 6570 harmonic: 8647 Sorted by residual: dihedral pdb=" C4' U H 0 " pdb=" C3' U H 0 " pdb=" C2' U H 0 " pdb=" C1' U H 0 " ideal model delta sinusoidal sigma weight residual 36.34 -34.28 70.62 1 3.10e+00 1.04e-01 6.68e+02 dihedral pdb=" O4' U H 0 " pdb=" C4' U H 0 " pdb=" C3' U H 0 " pdb=" C2' U H 0 " ideal model delta sinusoidal sigma weight residual -35.15 21.09 -56.24 1 4.00e+00 6.25e-02 2.67e+02 dihedral pdb=" O4' U H 0 " pdb=" C2' U H 0 " pdb=" C1' U H 0 " pdb=" C3' U H 0 " ideal model delta sinusoidal sigma weight residual -94.41 -36.72 -57.69 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 15214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2994 0.049 - 0.098: 710 0.098 - 0.147: 213 0.147 - 0.196: 25 0.196 - 0.245: 16 Chirality restraints: 3958 Sorted by residual: chirality pdb=" P U H -6 " pdb=" OP1 U H -6 " pdb=" OP2 U H -6 " pdb=" O5' U H -6 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" P C H -8 " pdb=" OP1 C H -8 " pdb=" OP2 C H -8 " pdb=" O5' C H -8 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" P C H -9 " pdb=" OP1 C H -9 " pdb=" OP2 C H -9 " pdb=" O5' C H -9 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3955 not shown) Planarity restraints: 4218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C1103 " -0.047 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO C1104 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C1104 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1104 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO D1139 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO C 552 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " -0.033 5.00e-02 4.00e+02 ... (remaining 4215 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 580 2.69 - 3.24: 21555 3.24 - 3.80: 39302 3.80 - 4.35: 52610 4.35 - 4.90: 84078 Nonbonded interactions: 198125 Sorted by model distance: nonbonded pdb=" NH2 ARG D 425 " pdb=" O3' U H 0 " model vdw 2.140 3.120 nonbonded pdb=" O VAL C 296 " pdb=" OG1 THR C 335 " model vdw 2.258 3.040 nonbonded pdb=" NH1 ARG D 425 " pdb=" O3' U H 0 " model vdw 2.259 3.120 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.286 3.040 nonbonded pdb=" O GLN C1288 " pdb=" OG1 THR C1292 " model vdw 2.320 3.040 ... (remaining 198120 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 'A' and (resid 8 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 75 or (resid 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 130 or re \ sid 140 through 144 or (resid 145 and (name N or name CA or name C or name O or \ name CB )) or resid 146 through 157 or resid 168 or resid 172 through 190 or (re \ sid 191 through 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 232)) selection = (chain 'B' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 31 or (resid 32 through 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 149 or (resid 150 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name NE )) or resi \ d 151 through 157 or resid 159 through 191 or (resid 192 and (name N or name CA \ or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or name \ CA or name C or name O or name CB )) or resid 195 through 232)) } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.470 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.299 25034 Z= 0.239 Angle : 0.677 8.803 34091 Z= 0.392 Chirality : 0.049 0.245 3958 Planarity : 0.005 0.070 4218 Dihedral : 14.857 139.371 9641 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.11), residues: 2965 helix: -4.78 (0.05), residues: 950 sheet: -1.90 (0.30), residues: 256 loop : -2.52 (0.11), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 250 TYR 0.010 0.001 TYR C 47 PHE 0.013 0.001 PHE D 892 TRP 0.006 0.001 TRP D 580 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.20 (25029) covalent geometry : angle 0.67676 / 0.39 (34091) hydrogen bonds : bond 0.30932 / 20.65 ( 726) hydrogen bonds : angle 10.39846 / 7.18 ( 2024) metal coordination : bond 0.27997 / 15.49 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 672 time to evaluate : 0.862 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: C 476 LYS cc_start: 0.6107 (mttt) cc_final: 0.5485 (tptp) REVERT: C 530 ILE cc_start: 0.9189 (mm) cc_final: 0.8741 (mm) REVERT: C 808 ASN cc_start: 0.6979 (t0) cc_final: 0.6670 (t0) REVERT: C 810 TYR cc_start: 0.8319 (m-80) cc_final: 0.7681 (m-80) REVERT: C 1064 ASP cc_start: 0.6786 (m-30) cc_final: 0.6518 (m-30) REVERT: C 1278 LEU cc_start: 0.8575 (tp) cc_final: 0.8318 (tp) REVERT: D 96 LYS cc_start: 0.7266 (ptmt) cc_final: 0.7058 (ptmt) REVERT: D 133 ARG cc_start: 0.6786 (mpt-90) cc_final: 0.6180 (tpt170) REVERT: D 889 ASP cc_start: 0.4795 (p0) cc_final: 0.4580 (p0) outliers start: 2 outliers final: 1 residues processed: 674 average time/residue: 0.2051 time to fit residues: 206.0793 Evaluate side-chains 439 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 438 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 706 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 343 HIS C 568 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 688 GLN C 761 GLN C 762 ASN C 766 ASN C 799 ASN C 808 ASN C 811 ASN C1061 GLN C1135 GLN C1236 ASN D 157 GLN D 164 GLN D 341 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 665 GLN D 667 GLN D 736 GLN D 865 HIS D1252 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.203586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181204 restraints weight = 34422.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180827 restraints weight = 30606.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.181617 restraints weight = 29212.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183065 restraints weight = 22921.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183032 restraints weight = 18643.873| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25034 Z= 0.170 Angle : 0.641 14.111 34091 Z= 0.328 Chirality : 0.044 0.355 3958 Planarity : 0.006 0.084 4218 Dihedral : 13.050 140.692 3977 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.72 % Allowed : 14.42 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.12), residues: 2965 helix: -2.81 (0.12), residues: 972 sheet: -1.81 (0.29), residues: 268 loop : -2.09 (0.12), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 143 TYR 0.022 0.001 TYR B 68 PHE 0.017 0.002 PHE D 437 TRP 0.026 0.002 TRP C 807 HIS 0.014 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (25029) covalent geometry : angle 0.64112 / 0.33 (34091) hydrogen bonds : bond 0.05469 / 3.61 ( 726) hydrogen bonds : angle 6.09219 / 4.24 ( 2024) metal coordination : bond 0.01389 / 0.71 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 486 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 211 ILE cc_start: 0.7935 (pt) cc_final: 0.7491 (pt) REVERT: C 807 TRP cc_start: 0.5883 (t60) cc_final: 0.5145 (t60) REVERT: C 808 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6993 (t0) REVERT: C 1084 ASP cc_start: 0.8126 (m-30) cc_final: 0.7718 (m-30) REVERT: C 1278 LEU cc_start: 0.8715 (tp) cc_final: 0.8454 (tp) REVERT: D 133 ARG cc_start: 0.7015 (mpt-90) cc_final: 0.6330 (tpt170) REVERT: D 475 GLU cc_start: 0.7463 (pt0) cc_final: 0.7183 (mt-10) REVERT: D 760 THR cc_start: 0.7872 (p) cc_final: 0.7657 (p) REVERT: E 69 ARG cc_start: 0.7388 (ptp-110) cc_final: 0.6858 (mtt-85) outliers start: 68 outliers final: 43 residues processed: 521 average time/residue: 0.1684 time to fit residues: 137.2085 Evaluate side-chains 450 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 405 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 131 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 37 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C1061 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1220 GLN D 300 GLN D 430 HIS D 435 GLN D1019 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.195868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172318 restraints weight = 34401.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171623 restraints weight = 29640.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.172623 restraints weight = 27977.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173344 restraints weight = 24200.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173538 restraints weight = 20144.122| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25034 Z= 0.150 Angle : 0.574 8.540 34091 Z= 0.294 Chirality : 0.043 0.259 3958 Planarity : 0.005 0.058 4218 Dihedral : 13.017 138.949 3976 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.48 % Allowed : 16.74 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.13), residues: 2965 helix: -1.75 (0.15), residues: 987 sheet: -1.54 (0.29), residues: 275 loop : -1.78 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 827 TYR 0.021 0.002 TYR B 177 PHE 0.017 0.001 PHE C 157 TRP 0.020 0.003 TRP D 236 HIS 0.011 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (25029) covalent geometry : angle 0.57434 / 0.29 (34091) hydrogen bonds : bond 0.04398 / 2.88 ( 726) hydrogen bonds : angle 5.47714 / 3.81 ( 2024) metal coordination : bond 0.00449 / 0.22 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 463 time to evaluate : 0.826 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: A 75 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 39 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8489 (mm) REVERT: C 653 MET cc_start: 0.7294 (tmm) cc_final: 0.6763 (ttt) REVERT: C 699 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8113 (mt) REVERT: C 734 ILE cc_start: 0.8709 (mm) cc_final: 0.8389 (mm) REVERT: C 807 TRP cc_start: 0.6830 (t60) cc_final: 0.5924 (t60) REVERT: C 810 TYR cc_start: 0.8494 (m-80) cc_final: 0.8263 (m-80) REVERT: C 1084 ASP cc_start: 0.8085 (m-30) cc_final: 0.7877 (m-30) REVERT: C 1090 ASN cc_start: 0.7906 (p0) cc_final: 0.7680 (p0) REVERT: C 1216 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.7062 (mtp180) REVERT: C 1278 LEU cc_start: 0.8825 (tp) cc_final: 0.8402 (tp) REVERT: C 1290 MET cc_start: 0.7732 (tpp) cc_final: 0.7504 (mmp) REVERT: D 38 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6927 (p) REVERT: D 133 ARG cc_start: 0.7203 (mpt-90) cc_final: 0.6389 (tpt170) REVERT: D 619 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7742 (mp) REVERT: D 897 HIS cc_start: 0.7632 (m-70) cc_final: 0.7407 (m-70) REVERT: E 69 ARG cc_start: 0.7449 (ptp-110) cc_final: 0.6845 (mtt-85) outliers start: 87 outliers final: 55 residues processed: 513 average time/residue: 0.1658 time to fit residues: 136.4592 Evaluate side-chains 472 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 413 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 chunk 299 optimal weight: 50.0000 chunk 133 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 302 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 766 ASN C 808 ASN C1061 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 300 GLN D 594 GLN D 962 ASN D1098 GLN D1326 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155351 restraints weight = 33839.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154251 restraints weight = 28587.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156050 restraints weight = 27015.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156438 restraints weight = 20989.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.156828 restraints weight = 18173.000| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25034 Z= 0.243 Angle : 0.671 13.227 34091 Z= 0.344 Chirality : 0.045 0.245 3958 Planarity : 0.005 0.063 4218 Dihedral : 13.179 137.503 3976 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.39 % Allowed : 18.02 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.14), residues: 2965 helix: -1.32 (0.15), residues: 1000 sheet: -1.36 (0.29), residues: 285 loop : -1.49 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 101 TYR 0.024 0.002 TYR D 512 PHE 0.021 0.002 PHE C 828 TRP 0.034 0.003 TRP D 236 HIS 0.011 0.001 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (25029) covalent geometry : angle 0.67125 / 0.34 (34091) hydrogen bonds : bond 0.03978 / 2.62 ( 726) hydrogen bonds : angle 5.28441 / 3.67 ( 2024) metal coordination : bond 0.00151 / 0.11 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 458 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 39 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 71 LYS cc_start: 0.6250 (mmmt) cc_final: 0.6018 (mmtt) REVERT: C 72 SER cc_start: 0.6573 (t) cc_final: 0.6070 (m) REVERT: C 349 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6264 (tt0) REVERT: C 407 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6941 (mmm-85) REVERT: C 653 MET cc_start: 0.7612 (tmm) cc_final: 0.7128 (ttt) REVERT: C 711 ASP cc_start: 0.5811 (m-30) cc_final: 0.5482 (m-30) REVERT: C 734 ILE cc_start: 0.8781 (mm) cc_final: 0.8430 (mm) REVERT: C 760 ASN cc_start: 0.7867 (m-40) cc_final: 0.7594 (m-40) REVERT: C 807 TRP cc_start: 0.7579 (t60) cc_final: 0.7154 (t60) REVERT: C 808 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7288 (t0) REVERT: C 865 LEU cc_start: 0.6983 (mt) cc_final: 0.6732 (mt) REVERT: C 1090 ASN cc_start: 0.8113 (p0) cc_final: 0.7886 (p0) REVERT: C 1278 LEU cc_start: 0.9018 (tp) cc_final: 0.8535 (tp) REVERT: C 1291 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7874 (pp) REVERT: D 78 LEU cc_start: 0.3268 (OUTLIER) cc_final: 0.2643 (mp) REVERT: D 133 ARG cc_start: 0.7558 (mpt-90) cc_final: 0.6601 (tpt170) REVERT: D 1356 LEU cc_start: 0.8606 (mt) cc_final: 0.8348 (mp) REVERT: E 44 ASP cc_start: 0.5809 (p0) cc_final: 0.5557 (p0) outliers start: 110 outliers final: 71 residues processed: 521 average time/residue: 0.1629 time to fit residues: 136.1284 Evaluate side-chains 488 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 413 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 872 TYR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 299 optimal weight: 40.0000 chunk 162 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.196635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167907 restraints weight = 33272.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.168223 restraints weight = 24971.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169995 restraints weight = 22314.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.170446 restraints weight = 16013.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170622 restraints weight = 14154.856| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25034 Z= 0.191 Angle : 0.619 13.355 34091 Z= 0.310 Chirality : 0.043 0.191 3958 Planarity : 0.004 0.052 4218 Dihedral : 13.169 135.391 3976 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.12 % Allowed : 20.02 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 2965 helix: -1.02 (0.16), residues: 1003 sheet: -1.32 (0.30), residues: 285 loop : -1.36 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1231 TYR 0.017 0.002 TYR C1229 PHE 0.015 0.002 PHE C 157 TRP 0.031 0.002 TRP D 236 HIS 0.006 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (25029) covalent geometry : angle 0.61945 / 0.31 (34091) hydrogen bonds : bond 0.03680 / 2.42 ( 726) hydrogen bonds : angle 5.19649 / 3.61 ( 2024) metal coordination : bond 0.00232 / 0.17 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 432 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8595 (mm) REVERT: C 44 GLU cc_start: 0.6487 (pm20) cc_final: 0.6103 (tm-30) REVERT: C 72 SER cc_start: 0.6825 (t) cc_final: 0.6227 (m) REVERT: C 133 ASN cc_start: 0.7405 (t0) cc_final: 0.6986 (t0) REVERT: C 138 ILE cc_start: 0.7515 (mm) cc_final: 0.7300 (mm) REVERT: C 349 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6385 (tt0) REVERT: C 653 MET cc_start: 0.7670 (tmm) cc_final: 0.7392 (ttt) REVERT: C 734 ILE cc_start: 0.8787 (mm) cc_final: 0.8477 (mm) REVERT: C 760 ASN cc_start: 0.8019 (m-40) cc_final: 0.7730 (m-40) REVERT: C 807 TRP cc_start: 0.7562 (t60) cc_final: 0.7202 (t60) REVERT: C 865 LEU cc_start: 0.7076 (mt) cc_final: 0.6840 (mt) REVERT: C 1119 MET cc_start: 0.8180 (tpt) cc_final: 0.7122 (ttm) REVERT: C 1278 LEU cc_start: 0.9043 (tp) cc_final: 0.8619 (tp) REVERT: C 1291 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7959 (pp) REVERT: D 78 LEU cc_start: 0.3558 (OUTLIER) cc_final: 0.2976 (mp) REVERT: D 133 ARG cc_start: 0.7667 (mpt-90) cc_final: 0.6515 (tpt170) REVERT: D 347 VAL cc_start: 0.9335 (t) cc_final: 0.9050 (m) REVERT: D 996 LYS cc_start: 0.7321 (tmtt) cc_final: 0.6989 (tttt) outliers start: 103 outliers final: 77 residues processed: 496 average time/residue: 0.1629 time to fit residues: 131.0838 Evaluate side-chains 486 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 406 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 TYR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 16 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 186 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 243 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C1061 GLN C1072 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165190 restraints weight = 33460.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165517 restraints weight = 26619.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166923 restraints weight = 23646.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.167374 restraints weight = 17570.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.167668 restraints weight = 15472.026| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25034 Z= 0.160 Angle : 0.600 12.591 34091 Z= 0.298 Chirality : 0.043 0.249 3958 Planarity : 0.004 0.049 4218 Dihedral : 13.123 133.385 3976 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.23 % Allowed : 21.37 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 2965 helix: -0.79 (0.16), residues: 1008 sheet: -1.14 (0.31), residues: 281 loop : -1.28 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 647 TYR 0.020 0.001 TYR C 555 PHE 0.013 0.001 PHE C 157 TRP 0.024 0.002 TRP D 236 HIS 0.006 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (25029) covalent geometry : angle 0.60034 / 0.30 (34091) hydrogen bonds : bond 0.03496 / 2.29 ( 726) hydrogen bonds : angle 5.07906 / 3.53 ( 2024) metal coordination : bond 0.00218 / 0.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 437 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8621 (mm) REVERT: C 44 GLU cc_start: 0.6471 (pm20) cc_final: 0.6096 (tm-30) REVERT: C 72 SER cc_start: 0.6571 (t) cc_final: 0.6035 (m) REVERT: C 129 LEU cc_start: 0.8855 (mm) cc_final: 0.8617 (mm) REVERT: C 133 ASN cc_start: 0.7372 (t0) cc_final: 0.6934 (t0) REVERT: C 430 LYS cc_start: 0.7613 (mttp) cc_final: 0.7327 (mttp) REVERT: C 611 GLU cc_start: 0.7669 (tt0) cc_final: 0.7330 (tt0) REVERT: C 653 MET cc_start: 0.7733 (tmm) cc_final: 0.7405 (ttt) REVERT: C 734 ILE cc_start: 0.8780 (mm) cc_final: 0.8510 (mm) REVERT: C 760 ASN cc_start: 0.8055 (m-40) cc_final: 0.7763 (m-40) REVERT: C 865 LEU cc_start: 0.7098 (mt) cc_final: 0.6752 (mt) REVERT: C 1085 MET cc_start: 0.8717 (mmt) cc_final: 0.8316 (mmm) REVERT: C 1119 MET cc_start: 0.8183 (tpt) cc_final: 0.7140 (ttm) REVERT: C 1291 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7987 (pp) REVERT: D 133 ARG cc_start: 0.7699 (mpt-90) cc_final: 0.6577 (tpt170) REVERT: D 172 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5719 (t80) REVERT: D 347 VAL cc_start: 0.9328 (t) cc_final: 0.9039 (m) REVERT: D 362 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7335 (mtp85) REVERT: D 707 ILE cc_start: 0.5020 (OUTLIER) cc_final: 0.4795 (tt) REVERT: D 719 PHE cc_start: 0.7324 (m-80) cc_final: 0.7054 (m-80) REVERT: D 996 LYS cc_start: 0.7242 (tmtt) cc_final: 0.6958 (tttt) outliers start: 106 outliers final: 77 residues processed: 501 average time/residue: 0.1572 time to fit residues: 127.7876 Evaluate side-chains 490 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 409 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 291 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 278 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS A 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C1061 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.193796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164598 restraints weight = 33458.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.165864 restraints weight = 24812.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167132 restraints weight = 19868.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.167733 restraints weight = 14831.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.167803 restraints weight = 13694.973| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25034 Z= 0.134 Angle : 0.589 12.473 34091 Z= 0.291 Chirality : 0.043 0.222 3958 Planarity : 0.004 0.052 4218 Dihedral : 13.069 131.712 3976 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.19 % Allowed : 21.97 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.15), residues: 2965 helix: -0.61 (0.16), residues: 1007 sheet: -1.09 (0.31), residues: 287 loop : -1.19 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1223 TYR 0.018 0.001 TYR C 751 PHE 0.011 0.001 PHE D 437 TRP 0.022 0.002 TRP D 236 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (25029) covalent geometry : angle 0.58868 / 0.29 (34091) hydrogen bonds : bond 0.03351 / 2.20 ( 726) hydrogen bonds : angle 4.97865 / 3.46 ( 2024) metal coordination : bond 0.00206 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 441 time to evaluate : 0.896 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: B 39 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8579 (mm) REVERT: C 44 GLU cc_start: 0.6447 (pm20) cc_final: 0.6096 (tm-30) REVERT: C 72 SER cc_start: 0.6471 (t) cc_final: 0.5987 (m) REVERT: C 129 LEU cc_start: 0.8730 (mm) cc_final: 0.8464 (mp) REVERT: C 133 ASN cc_start: 0.7373 (t0) cc_final: 0.6921 (t0) REVERT: C 179 TYR cc_start: 0.7438 (t80) cc_final: 0.7213 (t80) REVERT: C 611 GLU cc_start: 0.7548 (tt0) cc_final: 0.7287 (tt0) REVERT: C 653 MET cc_start: 0.7618 (tmm) cc_final: 0.7298 (ttt) REVERT: C 657 THR cc_start: 0.8477 (t) cc_final: 0.8183 (p) REVERT: C 760 ASN cc_start: 0.7932 (m-40) cc_final: 0.7668 (m-40) REVERT: C 761 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: C 810 TYR cc_start: 0.8827 (m-80) cc_final: 0.8203 (m-80) REVERT: C 865 LEU cc_start: 0.7023 (mt) cc_final: 0.6672 (mt) REVERT: C 1107 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6674 (mmp) REVERT: C 1119 MET cc_start: 0.8146 (tpt) cc_final: 0.7266 (ttm) REVERT: C 1291 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7938 (pp) REVERT: D 133 ARG cc_start: 0.7633 (mpt-90) cc_final: 0.6611 (tpt170) REVERT: D 172 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5728 (t80) REVERT: D 347 VAL cc_start: 0.9337 (t) cc_final: 0.9086 (m) REVERT: D 362 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7393 (mtp85) REVERT: D 581 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6859 (ptp) REVERT: D 719 PHE cc_start: 0.7380 (m-80) cc_final: 0.7119 (m-80) REVERT: D 754 ILE cc_start: 0.8924 (mm) cc_final: 0.8655 (mt) REVERT: D 822 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7052 (mmm) REVERT: D 957 SER cc_start: 0.8174 (m) cc_final: 0.7783 (t) REVERT: D 996 LYS cc_start: 0.7243 (tmtt) cc_final: 0.6960 (tttt) outliers start: 105 outliers final: 82 residues processed: 507 average time/residue: 0.1574 time to fit residues: 128.9461 Evaluate side-chains 501 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 412 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 32 optimal weight: 0.3980 chunk 257 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 chunk 241 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 274 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS A 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C1061 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN D 594 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1019 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.189423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160344 restraints weight = 33281.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162152 restraints weight = 23993.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163221 restraints weight = 18022.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163666 restraints weight = 14870.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163821 restraints weight = 13702.185| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25034 Z= 0.145 Angle : 0.595 11.787 34091 Z= 0.294 Chirality : 0.043 0.199 3958 Planarity : 0.004 0.055 4218 Dihedral : 13.050 130.660 3976 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.00 % Allowed : 22.77 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 2965 helix: -0.48 (0.16), residues: 1008 sheet: -1.04 (0.32), residues: 282 loop : -1.11 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1242 TYR 0.014 0.001 TYR C 810 PHE 0.028 0.002 PHE C 828 TRP 0.022 0.002 TRP D 236 HIS 0.004 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (25029) covalent geometry : angle 0.59470 / 0.29 (34091) hydrogen bonds : bond 0.03322 / 2.18 ( 726) hydrogen bonds : angle 4.91788 / 3.41 ( 2024) metal coordination : bond 0.00272 / 0.17 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 435 time to evaluate : 0.858 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: B 39 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8667 (mm) REVERT: C 32 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7316 (mm) REVERT: C 44 GLU cc_start: 0.6485 (pm20) cc_final: 0.6077 (tm-30) REVERT: C 72 SER cc_start: 0.6522 (t) cc_final: 0.5991 (m) REVERT: C 129 LEU cc_start: 0.8771 (mm) cc_final: 0.8426 (mp) REVERT: C 179 TYR cc_start: 0.7422 (t80) cc_final: 0.7160 (t80) REVERT: C 611 GLU cc_start: 0.7826 (tt0) cc_final: 0.7565 (tt0) REVERT: C 653 MET cc_start: 0.7664 (tmm) cc_final: 0.7319 (ttt) REVERT: C 657 THR cc_start: 0.8447 (t) cc_final: 0.8183 (p) REVERT: C 761 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: C 865 LEU cc_start: 0.7040 (mt) cc_final: 0.6714 (mt) REVERT: C 1107 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6746 (mmp) REVERT: C 1291 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7988 (pp) REVERT: D 133 ARG cc_start: 0.7649 (mpt-90) cc_final: 0.6624 (tpt170) REVERT: D 172 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5757 (t80) REVERT: D 347 VAL cc_start: 0.9367 (t) cc_final: 0.9110 (m) REVERT: D 362 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7386 (mtp85) REVERT: D 571 ASP cc_start: 0.7108 (t70) cc_final: 0.6824 (p0) REVERT: D 719 PHE cc_start: 0.7501 (m-80) cc_final: 0.7235 (m-80) REVERT: D 754 ILE cc_start: 0.8895 (mm) cc_final: 0.8651 (mt) REVERT: D 822 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: D 957 SER cc_start: 0.8158 (m) cc_final: 0.7773 (t) REVERT: D 996 LYS cc_start: 0.7291 (tmtt) cc_final: 0.7013 (tttt) outliers start: 100 outliers final: 82 residues processed: 498 average time/residue: 0.1503 time to fit residues: 121.9844 Evaluate side-chains 497 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 408 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 262 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 273 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 299 optimal weight: 40.0000 chunk 292 optimal weight: 6.9990 chunk 219 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN D 458 ASN D 594 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.193011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163776 restraints weight = 33480.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163688 restraints weight = 25101.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.165202 restraints weight = 20957.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.165852 restraints weight = 16456.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166544 restraints weight = 14976.749| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25034 Z= 0.134 Angle : 0.591 11.191 34091 Z= 0.293 Chirality : 0.042 0.189 3958 Planarity : 0.004 0.053 4218 Dihedral : 13.036 129.726 3976 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.76 % Allowed : 22.85 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2965 helix: -0.41 (0.16), residues: 1006 sheet: -1.08 (0.32), residues: 275 loop : -1.06 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1216 TYR 0.016 0.001 TYR C 810 PHE 0.026 0.001 PHE C 828 TRP 0.027 0.002 TRP D 236 HIS 0.004 0.001 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (25029) covalent geometry : angle 0.59148 / 0.29 (34091) hydrogen bonds : bond 0.03250 / 2.13 ( 726) hydrogen bonds : angle 4.88738 / 3.39 ( 2024) metal coordination : bond 0.00222 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 423 time to evaluate : 0.865 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: B 39 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8688 (mm) REVERT: C 44 GLU cc_start: 0.6434 (pm20) cc_final: 0.6059 (tm-30) REVERT: C 72 SER cc_start: 0.6661 (t) cc_final: 0.6133 (m) REVERT: C 129 LEU cc_start: 0.8756 (mm) cc_final: 0.8520 (mt) REVERT: C 179 TYR cc_start: 0.7494 (t80) cc_final: 0.7118 (t80) REVERT: C 611 GLU cc_start: 0.7661 (tt0) cc_final: 0.7426 (tt0) REVERT: C 653 MET cc_start: 0.7610 (tmm) cc_final: 0.7275 (ttt) REVERT: C 657 THR cc_start: 0.8394 (t) cc_final: 0.8117 (p) REVERT: C 711 ASP cc_start: 0.6155 (m-30) cc_final: 0.5775 (m-30) REVERT: C 760 ASN cc_start: 0.7953 (m-40) cc_final: 0.7675 (m-40) REVERT: C 761 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: C 810 TYR cc_start: 0.8729 (m-80) cc_final: 0.8496 (m-80) REVERT: C 865 LEU cc_start: 0.7033 (mt) cc_final: 0.6712 (mt) REVERT: C 1107 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6736 (mmp) REVERT: C 1291 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7952 (pp) REVERT: D 133 ARG cc_start: 0.7661 (mpt-90) cc_final: 0.6589 (tpt170) REVERT: D 172 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5766 (t80) REVERT: D 347 VAL cc_start: 0.9363 (t) cc_final: 0.9118 (m) REVERT: D 362 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7446 (mtp85) REVERT: D 571 ASP cc_start: 0.7074 (t70) cc_final: 0.6804 (p0) REVERT: D 719 PHE cc_start: 0.7539 (m-80) cc_final: 0.7318 (m-80) REVERT: D 754 ILE cc_start: 0.8883 (mm) cc_final: 0.8651 (mt) REVERT: D 822 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7150 (mmm) REVERT: D 957 SER cc_start: 0.8138 (m) cc_final: 0.7758 (t) REVERT: D 996 LYS cc_start: 0.7320 (tmtt) cc_final: 0.7053 (tttt) outliers start: 94 outliers final: 80 residues processed: 483 average time/residue: 0.1556 time to fit residues: 121.8676 Evaluate side-chains 496 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 410 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 243 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 260 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C1061 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D1019 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.188883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159513 restraints weight = 33304.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161770 restraints weight = 24848.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.162934 restraints weight = 18644.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163070 restraints weight = 14045.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163204 restraints weight = 13330.713| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25034 Z= 0.164 Angle : 0.614 11.547 34091 Z= 0.305 Chirality : 0.043 0.193 3958 Planarity : 0.004 0.061 4218 Dihedral : 13.060 128.341 3976 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.64 % Allowed : 22.61 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 2965 helix: -0.38 (0.16), residues: 1007 sheet: -0.95 (0.32), residues: 285 loop : -1.06 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 647 TYR 0.014 0.001 TYR C 751 PHE 0.019 0.002 PHE C 545 TRP 0.029 0.002 TRP D 236 HIS 0.004 0.001 HIS D1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (25029) covalent geometry : angle 0.61385 / 0.30 (34091) hydrogen bonds : bond 0.03344 / 2.18 ( 726) hydrogen bonds : angle 4.92084 / 3.40 ( 2024) metal coordination : bond 0.00346 / 0.20 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 427 time to evaluate : 0.883 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: B 39 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8698 (mm) REVERT: C 44 GLU cc_start: 0.6403 (pm20) cc_final: 0.6051 (tm-30) REVERT: C 72 SER cc_start: 0.6764 (t) cc_final: 0.6218 (m) REVERT: C 129 LEU cc_start: 0.8763 (mm) cc_final: 0.8445 (mp) REVERT: C 179 TYR cc_start: 0.7548 (t80) cc_final: 0.7036 (t80) REVERT: C 490 GLN cc_start: 0.6647 (tp40) cc_final: 0.6433 (tt0) REVERT: C 611 GLU cc_start: 0.7672 (tt0) cc_final: 0.7407 (tt0) REVERT: C 653 MET cc_start: 0.7700 (tmm) cc_final: 0.7384 (ttt) REVERT: C 657 THR cc_start: 0.8419 (t) cc_final: 0.8162 (p) REVERT: C 711 ASP cc_start: 0.6359 (m-30) cc_final: 0.5934 (m-30) REVERT: C 761 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: C 865 LEU cc_start: 0.7183 (mt) cc_final: 0.6893 (mt) REVERT: D 133 ARG cc_start: 0.7681 (mpt-90) cc_final: 0.6663 (tpt170) REVERT: D 172 PHE cc_start: 0.6097 (OUTLIER) cc_final: 0.5767 (t80) REVERT: D 347 VAL cc_start: 0.9363 (t) cc_final: 0.9093 (m) REVERT: D 362 ARG cc_start: 0.7757 (ttp-110) cc_final: 0.7441 (mtp85) REVERT: D 571 ASP cc_start: 0.7050 (t70) cc_final: 0.6827 (p0) REVERT: D 719 PHE cc_start: 0.7641 (m-80) cc_final: 0.7425 (m-80) REVERT: D 754 ILE cc_start: 0.8902 (mm) cc_final: 0.8666 (mt) REVERT: D 822 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7145 (mmm) REVERT: D 957 SER cc_start: 0.8131 (m) cc_final: 0.7762 (t) REVERT: D 996 LYS cc_start: 0.7353 (tmtt) cc_final: 0.7110 (tttt) outliers start: 91 outliers final: 84 residues processed: 486 average time/residue: 0.1570 time to fit residues: 123.9825 Evaluate side-chains 500 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 412 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 107 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 181 optimal weight: 0.0670 chunk 247 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 284 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C1061 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D1019 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.184332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153941 restraints weight = 33204.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153557 restraints weight = 25872.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155124 restraints weight = 22952.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155702 restraints weight = 17057.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155887 restraints weight = 15972.488| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25034 Z= 0.228 Angle : 0.675 13.861 34091 Z= 0.337 Chirality : 0.045 0.259 3958 Planarity : 0.005 0.066 4218 Dihedral : 13.179 125.632 3976 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.68 % Allowed : 22.85 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 2965 helix: -0.50 (0.16), residues: 1011 sheet: -0.97 (0.32), residues: 281 loop : -1.11 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1242 TYR 0.026 0.002 TYR D 537 PHE 0.022 0.002 PHE D 437 TRP 0.035 0.002 TRP D 236 HIS 0.007 0.001 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (25029) covalent geometry : angle 0.67484 / 0.34 (34091) hydrogen bonds : bond 0.03581 / 2.35 ( 726) hydrogen bonds : angle 5.05189 / 3.49 ( 2024) metal coordination : bond 0.00699 / 0.41 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.64 seconds wall clock time: 70 minutes 45.64 seconds (4245.64 seconds total)