Starting phenix.real_space_refine on Mon Aug 25 02:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yp9_33996/08_2025/7yp9_33996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp9_33996/08_2025/7yp9_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_2025/7yp9_33996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2025/7yp9_33996.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2025/7yp9_33996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp9_33996/08_2025/7yp9_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-2.0-5787/lib/python3.9/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: {'RNA': 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: 4.70, per 1000 atoms: 0.19 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: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.47 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: 5.15 Time building geometry restraints manager: 2.15 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=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.61e+00 bond pdb=" N ASN D 962 " pdb=" CA ASN D 962 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.35e+00 bond pdb=" C3' DG G 10 " pdb=" O3' DG G 10 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.69e+00 bond pdb=" N GLY D 231 " pdb=" CA GLY D 231 " ideal model delta sigma weight residual 1.449 1.471 -0.022 1.45e-02 4.76e+03 2.31e+00 bond pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.27e+00 ... (remaining 25024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 33185 1.76 - 3.52: 768 3.52 - 5.28: 88 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=" C GLY C 64 " pdb=" N ASN C 65 " pdb=" CA ASN C 65 " ideal model delta sigma weight residual 122.08 128.09 -6.01 1.47e+00 4.63e-01 1.67e+01 angle pdb=" C ARG B 158 " pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.49e+01 ... (remaining 34086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 14488 27.87 - 55.75: 689 55.75 - 83.62: 72 83.62 - 111.50: 9 111.50 - 139.37: 1 Dihedral angle restraints: 15259 sinusoidal: 6612 harmonic: 8647 Sorted by residual: dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DG G 10 " pdb=" C3' DG G 10 " pdb=" O3' DG G 10 " pdb=" P DT G 11 " ideal model delta sinusoidal sigma weight residual 220.00 80.63 139.37 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 15256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2964 0.046 - 0.092: 713 0.092 - 0.137: 236 0.137 - 0.183: 38 0.183 - 0.229: 7 Chirality restraints: 3958 Sorted by residual: chirality pdb=" CA ASP D 129 " pdb=" N ASP D 129 " pdb=" C ASP D 129 " pdb=" CB ASP D 129 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE B 183 " pdb=" CA ILE B 183 " pdb=" CG1 ILE B 183 " pdb=" CG2 ILE B 183 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE D 22 " pdb=" CA ILE D 22 " pdb=" CG1 ILE D 22 " pdb=" CG2 ILE D 22 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 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= 0.196 Angle : 0.657 8.803 34091 Z= 0.357 Chirality : 0.047 0.229 3958 Planarity : 0.005 0.070 4218 Dihedral : 14.963 139.371 9683 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 aren 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 covalent geometry : bond 0.00288 (25029) covalent geometry : angle 0.65677 (34091) hydrogen bonds : bond 0.30932 ( 726) hydrogen bonds : angle 10.39846 ( 2024) metal coordination : bond 0.27997 ( 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 : 0.824 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: 0.1847 time to fit residues: 183.9234 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 : 0.808 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 208 ASN C 276 GLN C 343 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 686 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 762 ASN C 766 ASN C 799 ASN C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1135 GLN C1236 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 157 GLN D 164 GLN D 341 ASN D 665 GLN D 667 GLN D 736 GLN D 865 HIS D1252 HIS D1366 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169440 restraints weight = 34026.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.169630 restraints weight = 26006.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171172 restraints weight = 22617.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171959 restraints weight = 17557.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172090 restraints weight = 15291.722| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25034 Z= 0.170 Angle : 0.598 9.975 34091 Z= 0.309 Chirality : 0.042 0.274 3958 Planarity : 0.005 0.067 4218 Dihedral : 13.571 140.107 4019 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.92 % Allowed : 14.34 % Favored : 82.74 % 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 aren not related in a simple way. whole: -3.31 (0.13), residues: 2965 helix: -2.83 (0.12), residues: 994 sheet: -1.73 (0.29), residues: 275 loop : -1.87 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1149 TYR 0.014 0.002 TYR C 291 PHE 0.019 0.002 PHE D 437 TRP 0.023 0.003 TRP D 868 HIS 0.009 0.001 HIS D1252 Details of bonding type rmsd covalent geometry : bond 0.00382 (25029) covalent geometry : angle 0.59795 (34091) hydrogen bonds : bond 0.03897 ( 726) hydrogen bonds : angle 5.58164 ( 2024) metal coordination : bond 0.01254 ( 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 581 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 508 time to evaluate : 0.746 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 76 GLU cc_start: 0.7102 (tp30) cc_final: 0.6765 (tp30) REVERT: A 181 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 212 ASP cc_start: 0.7441 (t70) cc_final: 0.7140 (t0) REVERT: B 39 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 51 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6328 (ttm) REVERT: C 72 SER cc_start: 0.6690 (t) cc_final: 0.6092 (m) REVERT: C 407 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.6985 (mmm-85) REVERT: C 614 TYR cc_start: 0.7553 (m-10) cc_final: 0.7341 (m-10) REVERT: C 653 MET cc_start: 0.7454 (tmm) cc_final: 0.6810 (ttt) REVERT: C 807 TRP cc_start: 0.6557 (t60) cc_final: 0.6192 (t60) REVERT: C 810 TYR cc_start: 0.8939 (m-80) cc_final: 0.8708 (m-80) REVERT: C 828 PHE cc_start: 0.9022 (m-80) cc_final: 0.8754 (m-80) REVERT: C 1232 MET cc_start: 0.6781 (mmt) cc_final: 0.6469 (mmt) REVERT: C 1278 LEU cc_start: 0.8947 (tp) cc_final: 0.8645 (tp) REVERT: C 1290 MET cc_start: 0.7973 (tpp) cc_final: 0.7709 (mmp) REVERT: C 1336 ASN cc_start: 0.8364 (t0) cc_final: 0.7994 (t0) REVERT: D 133 ARG cc_start: 0.7430 (mpt-90) cc_final: 0.6462 (tpt170) REVERT: D 622 ASP cc_start: 0.6988 (t0) cc_final: 0.6569 (t0) REVERT: D 626 TYR cc_start: 0.7225 (m-10) cc_final: 0.6887 (m-10) REVERT: D 760 THR cc_start: 0.8086 (p) cc_final: 0.7856 (p) outliers start: 73 outliers final: 47 residues processed: 545 average time/residue: 0.1527 time to fit residues: 131.3397 Evaluate side-chains 468 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 419 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 118 ASP 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 51 MET 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 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 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 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 1233 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 217 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1163 VAL 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 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 251 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 0.0270 chunk 205 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN A 132 HIS C 343 HIS C 462 ASN C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C 811 ASN C1061 GLN C1116 HIS ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 736 GLN D 897 HIS E 72 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.193885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169674 restraints weight = 34121.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168919 restraints weight = 31426.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170039 restraints weight = 30810.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170704 restraints weight = 24864.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.171002 restraints weight = 21250.238| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25034 Z= 0.112 Angle : 0.526 9.810 34091 Z= 0.266 Chirality : 0.040 0.175 3958 Planarity : 0.004 0.062 4218 Dihedral : 13.451 138.496 4018 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.68 % Allowed : 16.98 % Favored : 79.34 % 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 aren not related in a simple way. whole: -2.46 (0.14), residues: 2965 helix: -1.67 (0.15), residues: 1000 sheet: -1.59 (0.29), residues: 278 loop : -1.60 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 368 TYR 0.023 0.001 TYR B 177 PHE 0.014 0.001 PHE D 172 TRP 0.020 0.002 TRP D 236 HIS 0.007 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00254 (25029) covalent geometry : angle 0.52635 (34091) hydrogen bonds : bond 0.03492 ( 726) hydrogen bonds : angle 5.05883 ( 2024) metal coordination : bond 0.00147 ( 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 564 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 472 time to evaluate : 0.842 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: B 39 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8645 (mm) REVERT: C 618 GLN cc_start: 0.6338 (tt0) cc_final: 0.5900 (tt0) REVERT: C 653 MET cc_start: 0.7324 (tmm) cc_final: 0.6766 (ttt) REVERT: C 699 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 807 TRP cc_start: 0.7178 (t60) cc_final: 0.6749 (t60) REVERT: C 808 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7224 (t0) REVERT: C 1107 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6404 (mmp) REVERT: C 1232 MET cc_start: 0.6814 (mmt) cc_final: 0.6454 (mmt) REVERT: C 1278 LEU cc_start: 0.8899 (tp) cc_final: 0.8493 (tp) REVERT: C 1336 ASN cc_start: 0.8342 (t0) cc_final: 0.7954 (t0) REVERT: D 35 PHE cc_start: 0.5228 (m-80) cc_final: 0.5018 (m-80) REVERT: D 78 LEU cc_start: 0.3217 (OUTLIER) cc_final: 0.2559 (mp) REVERT: D 133 ARG cc_start: 0.7350 (mpt-90) cc_final: 0.6420 (tpt170) REVERT: D 432 LEU cc_start: 0.9137 (mm) cc_final: 0.8861 (mt) REVERT: D 475 GLU cc_start: 0.7478 (pt0) cc_final: 0.7271 (mt-10) REVERT: D 571 ASP cc_start: 0.7197 (t70) cc_final: 0.6935 (p0) REVERT: D 622 ASP cc_start: 0.7052 (t0) cc_final: 0.6736 (t0) REVERT: D 760 THR cc_start: 0.8100 (p) cc_final: 0.7896 (p) REVERT: E 44 ASP cc_start: 0.5600 (p0) cc_final: 0.5395 (p0) outliers start: 92 outliers final: 48 residues processed: 520 average time/residue: 0.1426 time to fit residues: 119.1491 Evaluate side-chains 473 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 420 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE 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 193 GLU 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 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 700 VAL 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 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR 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 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU 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 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 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 736 GLN 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 1250 ASP Chi-restraints excluded: chain E residue 4 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: 8.9990 chunk 271 optimal weight: 20.0000 chunk 125 optimal weight: 0.0870 chunk 176 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 64 optimal weight: 0.0770 chunk 302 optimal weight: 4.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN C 69 GLN C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C1061 GLN C1116 HIS ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 435 GLN D 817 HIS D 897 HIS D 962 ASN D1098 GLN D1326 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.191736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163302 restraints weight = 33542.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163055 restraints weight = 25060.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.164543 restraints weight = 21878.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165097 restraints weight = 18255.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.165397 restraints weight = 16017.142| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25034 Z= 0.209 Angle : 0.617 13.359 34091 Z= 0.311 Chirality : 0.043 0.178 3958 Planarity : 0.005 0.068 4218 Dihedral : 13.577 137.921 4018 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.00 % Allowed : 18.38 % Favored : 77.63 % 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 aren not related in a simple way. whole: -1.95 (0.14), residues: 2965 helix: -1.16 (0.15), residues: 999 sheet: -1.45 (0.29), residues: 285 loop : -1.32 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 647 TYR 0.024 0.002 TYR C1213 PHE 0.016 0.002 PHE C 157 TRP 0.035 0.003 TRP D 236 HIS 0.006 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00481 (25029) covalent geometry : angle 0.61674 (34091) hydrogen bonds : bond 0.03558 ( 726) hydrogen bonds : angle 5.01644 ( 2024) metal coordination : bond 0.00220 ( 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 585 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 485 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8727 (mm) REVERT: B 84 ASN cc_start: 0.8774 (m110) cc_final: 0.8086 (m110) REVERT: B 101 THR cc_start: 0.5173 (OUTLIER) cc_final: 0.4483 (p) REVERT: C 44 GLU cc_start: 0.6605 (pm20) cc_final: 0.6284 (tm-30) REVERT: C 133 ASN cc_start: 0.7303 (t0) cc_final: 0.6958 (t0) REVERT: C 465 ARG cc_start: 0.7592 (ttp-170) cc_final: 0.7272 (ttp-110) REVERT: C 653 MET cc_start: 0.7785 (tmm) cc_final: 0.7450 (ttt) REVERT: C 1107 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6836 (mmp) REVERT: C 1265 PHE cc_start: 0.7385 (t80) cc_final: 0.7014 (t80) REVERT: C 1274 GLU cc_start: 0.7016 (mp0) cc_final: 0.6669 (mp0) REVERT: C 1278 LEU cc_start: 0.9114 (tp) cc_final: 0.8760 (tp) REVERT: C 1291 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7780 (pp) REVERT: D 133 ARG cc_start: 0.7707 (mpt-90) cc_final: 0.6701 (tpt170) REVERT: D 347 VAL cc_start: 0.9337 (t) cc_final: 0.9049 (m) REVERT: D 475 GLU cc_start: 0.7737 (pt0) cc_final: 0.7325 (pm20) REVERT: D 571 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7093 (p0) REVERT: D 754 ILE cc_start: 0.8778 (mm) cc_final: 0.8506 (mt) REVERT: D 957 SER cc_start: 0.8162 (m) cc_final: 0.7786 (t) REVERT: D 996 LYS cc_start: 0.7325 (tmtt) cc_final: 0.7057 (tttt) REVERT: D 1250 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7252 (m-30) outliers start: 100 outliers final: 74 residues processed: 541 average time/residue: 0.1427 time to fit residues: 123.1513 Evaluate side-chains 497 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 417 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 118 ASP 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 35 PHE 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 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 137 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 400 VAL Chi-restraints excluded: chain C residue 442 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 700 VAL 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 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 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 1247 SER Chi-restraints excluded: chain C residue 1291 LEU 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 223 LEU 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 327 LEU Chi-restraints excluded: chain D residue 330 MET 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 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 642 ASP 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 882 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 113 optimal weight: 0.0070 chunk 180 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C1061 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** 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 = 0.4131 r_free = 0.4131 target = 0.187880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157600 restraints weight = 33371.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158842 restraints weight = 25286.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159817 restraints weight = 20301.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160866 restraints weight = 16217.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160895 restraints weight = 14657.000| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25034 Z= 0.188 Angle : 0.610 13.765 34091 Z= 0.305 Chirality : 0.043 0.245 3958 Planarity : 0.004 0.055 4218 Dihedral : 13.628 133.297 4018 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.51 % Allowed : 20.46 % Favored : 75.03 % 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 aren not related in a simple way. whole: -1.59 (0.15), residues: 2965 helix: -0.78 (0.16), residues: 995 sheet: -1.16 (0.31), residues: 281 loop : -1.17 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 547 TYR 0.020 0.002 TYR C1229 PHE 0.015 0.002 PHE C 157 TRP 0.040 0.002 TRP D 236 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00441 (25029) covalent geometry : angle 0.60967 (34091) hydrogen bonds : bond 0.03314 ( 726) hydrogen bonds : angle 4.97736 ( 2024) metal coordination : bond 0.00322 ( 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 575 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 462 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8742 (mm) REVERT: C 44 GLU cc_start: 0.6535 (pm20) cc_final: 0.6169 (tm-30) REVERT: C 129 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 133 ASN cc_start: 0.7235 (t0) cc_final: 0.6886 (t0) REVERT: C 465 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7358 (ttp80) REVERT: C 490 GLN cc_start: 0.6736 (tp40) cc_final: 0.6480 (tt0) REVERT: C 611 GLU cc_start: 0.7457 (tt0) cc_final: 0.7256 (tt0) REVERT: C 653 MET cc_start: 0.7673 (tmm) cc_final: 0.7444 (ttt) REVERT: C 657 THR cc_start: 0.8473 (t) cc_final: 0.8229 (p) REVERT: C 711 ASP cc_start: 0.6793 (m-30) cc_final: 0.6294 (m-30) REVERT: C 808 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7869 (t0) REVERT: C 1107 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7041 (mmp) REVERT: C 1180 MET cc_start: 0.8186 (tpp) cc_final: 0.7442 (ttm) REVERT: C 1232 MET cc_start: 0.6995 (mmt) cc_final: 0.6747 (mmt) REVERT: D 133 ARG cc_start: 0.7838 (mpt-90) cc_final: 0.6760 (tpt170) REVERT: D 172 PHE cc_start: 0.6199 (t80) cc_final: 0.5857 (t80) REVERT: D 347 VAL cc_start: 0.9313 (t) cc_final: 0.8977 (m) REVERT: D 362 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7329 (mtp85) REVERT: D 432 LEU cc_start: 0.9301 (mm) cc_final: 0.9082 (mt) REVERT: D 475 GLU cc_start: 0.7718 (pt0) cc_final: 0.7244 (pm20) REVERT: D 484 MET cc_start: 0.8827 (mmm) cc_final: 0.8623 (mtt) REVERT: D 547 ARG cc_start: 0.6829 (mtt-85) cc_final: 0.6588 (mtm110) REVERT: D 754 ILE cc_start: 0.8860 (mm) cc_final: 0.8608 (mt) REVERT: D 822 MET cc_start: 0.7686 (mmp) cc_final: 0.7403 (mmm) REVERT: D 957 SER cc_start: 0.8209 (m) cc_final: 0.7843 (t) REVERT: D 996 LYS cc_start: 0.7446 (tmtt) cc_final: 0.7171 (tttt) REVERT: E 47 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8148 (p) outliers start: 113 outliers final: 70 residues processed: 540 average time/residue: 0.1523 time to fit residues: 130.7061 Evaluate side-chains 477 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 402 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 6 THR 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 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU 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 348 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 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 935 THR 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 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR 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 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 454 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 495 ASN 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 624 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 803 VAL 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 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 1250 ASP Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 16 optimal weight: 0.1980 chunk 246 optimal weight: 7.9990 chunk 186 optimal weight: 0.0010 chunk 154 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 243 optimal weight: 0.3980 chunk 264 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN A 227 GLN C 343 HIS C 462 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 808 ASN C1061 GLN C1220 GLN D 458 ASN D 465 GLN D 594 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162024 restraints weight = 33362.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163171 restraints weight = 23604.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164360 restraints weight = 18828.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165020 restraints weight = 14676.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165115 restraints weight = 13311.115| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25034 Z= 0.124 Angle : 0.568 12.081 34091 Z= 0.283 Chirality : 0.042 0.273 3958 Planarity : 0.004 0.055 4218 Dihedral : 13.525 132.228 4018 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.84 % Allowed : 22.09 % Favored : 74.07 % 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 aren not related in a simple way. whole: -1.37 (0.15), residues: 2965 helix: -0.52 (0.16), residues: 1000 sheet: -1.24 (0.31), residues: 285 loop : -1.04 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 195 TYR 0.018 0.001 TYR D 537 PHE 0.024 0.001 PHE C 545 TRP 0.025 0.002 TRP D 236 HIS 0.004 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00292 (25029) covalent geometry : angle 0.56840 (34091) hydrogen bonds : bond 0.03020 ( 726) hydrogen bonds : angle 4.78353 ( 2024) metal coordination : bond 0.00182 ( 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 525 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 429 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8760 (m-80) cc_final: 0.8555 (m-80) REVERT: B 39 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8740 (mm) REVERT: C 39 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.6553 (mt) REVERT: C 44 GLU cc_start: 0.6536 (pm20) cc_final: 0.6182 (tm-30) REVERT: C 129 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8450 (mt) REVERT: C 490 GLN cc_start: 0.6668 (tp40) cc_final: 0.6451 (tt0) REVERT: C 653 MET cc_start: 0.7752 (tmm) cc_final: 0.7425 (ttt) REVERT: C 657 THR cc_start: 0.8359 (t) cc_final: 0.8143 (p) REVERT: C 711 ASP cc_start: 0.6573 (m-30) cc_final: 0.6247 (m-30) REVERT: C 808 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7634 (t0) REVERT: C 1107 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7131 (mmp) REVERT: C 1146 GLN cc_start: 0.8582 (tp40) cc_final: 0.8106 (tp40) REVERT: C 1180 MET cc_start: 0.8029 (tpp) cc_final: 0.7389 (ttm) REVERT: C 1232 MET cc_start: 0.6832 (mmt) cc_final: 0.6595 (mmt) REVERT: C 1274 GLU cc_start: 0.6996 (mp0) cc_final: 0.6648 (mp0) REVERT: D 133 ARG cc_start: 0.7837 (mpt-90) cc_final: 0.6771 (tpt170) REVERT: D 347 VAL cc_start: 0.9291 (t) cc_final: 0.9016 (m) REVERT: D 432 LEU cc_start: 0.9292 (mm) cc_final: 0.8959 (mt) REVERT: D 738 ARG cc_start: 0.7422 (ttm170) cc_final: 0.6963 (ttm110) REVERT: D 822 MET cc_start: 0.7515 (mmp) cc_final: 0.7135 (mmm) REVERT: D 957 SER cc_start: 0.8155 (m) cc_final: 0.7806 (t) REVERT: D 996 LYS cc_start: 0.7386 (tmtt) cc_final: 0.7153 (tttt) REVERT: D 1020 TRP cc_start: 0.5062 (p90) cc_final: 0.4727 (p90) REVERT: D 1250 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: E 47 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8229 (p) outliers start: 96 outliers final: 67 residues processed: 489 average time/residue: 0.1399 time to fit residues: 109.8772 Evaluate side-chains 475 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 401 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 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 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 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 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 935 THR 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 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 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 161 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 454 CYS Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 483 LEU 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 624 ILE Chi-restraints excluded: chain D residue 642 ASP 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 1230 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 4 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: 2.9990 chunk 162 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 343 HIS C 462 ASN ** C 513 GLN ** 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 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.189904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159861 restraints weight = 33357.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161498 restraints weight = 23203.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162793 restraints weight = 18152.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163503 restraints weight = 14374.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163428 restraints weight = 13441.341| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25034 Z= 0.140 Angle : 0.579 13.371 34091 Z= 0.287 Chirality : 0.042 0.259 3958 Planarity : 0.004 0.060 4218 Dihedral : 13.500 132.268 4018 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.12 % Allowed : 22.01 % Favored : 73.87 % 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 aren not related in a simple way. whole: -1.24 (0.15), residues: 2965 helix: -0.40 (0.16), residues: 999 sheet: -1.12 (0.31), residues: 293 loop : -0.99 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 195 TYR 0.012 0.001 TYR D 360 PHE 0.016 0.001 PHE C 545 TRP 0.027 0.002 TRP D 236 HIS 0.004 0.001 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00334 (25029) covalent geometry : angle 0.57937 (34091) hydrogen bonds : bond 0.03056 ( 726) hydrogen bonds : angle 4.68637 ( 2024) metal coordination : bond 0.00313 ( 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 518 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 415 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8828 (mm) REVERT: C 44 GLU cc_start: 0.6564 (pm20) cc_final: 0.6216 (tm-30) REVERT: C 129 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8492 (mt) REVERT: C 653 MET cc_start: 0.7758 (tmm) cc_final: 0.7450 (ttt) REVERT: C 657 THR cc_start: 0.8405 (t) cc_final: 0.8183 (p) REVERT: C 711 ASP cc_start: 0.6709 (m-30) cc_final: 0.6360 (m-30) REVERT: C 1107 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7158 (mmp) REVERT: C 1180 MET cc_start: 0.8069 (tpp) cc_final: 0.7413 (ttm) REVERT: C 1274 GLU cc_start: 0.7078 (mp0) cc_final: 0.6690 (mp0) REVERT: C 1307 ASN cc_start: 0.6499 (t0) cc_final: 0.6233 (t0) REVERT: D 133 ARG cc_start: 0.7868 (mpt-90) cc_final: 0.6910 (tpt170) REVERT: D 172 PHE cc_start: 0.5986 (t80) cc_final: 0.5779 (t80) REVERT: D 347 VAL cc_start: 0.9292 (t) cc_final: 0.9021 (m) REVERT: D 362 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7268 (mtp85) REVERT: D 432 LEU cc_start: 0.9224 (mm) cc_final: 0.8971 (mt) REVERT: D 475 GLU cc_start: 0.7766 (pt0) cc_final: 0.7481 (mt-10) REVERT: D 897 HIS cc_start: 0.7662 (m90) cc_final: 0.7428 (m90) REVERT: D 957 SER cc_start: 0.8204 (m) cc_final: 0.7896 (t) REVERT: D 996 LYS cc_start: 0.7410 (tmtt) cc_final: 0.7163 (tttt) REVERT: D 1250 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: E 47 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8164 (p) outliers start: 103 outliers final: 79 residues processed: 483 average time/residue: 0.1381 time to fit residues: 107.5116 Evaluate side-chains 480 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 396 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 6 THR 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 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER 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 660 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR 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 1212 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR 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 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 478 LEU Chi-restraints excluded: chain D residue 483 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 572 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS 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 1230 THR Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 4 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: 7.9990 chunk 257 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 65 optimal weight: 0.0070 chunk 241 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.192753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163202 restraints weight = 33484.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.164237 restraints weight = 23930.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165457 restraints weight = 19104.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166088 restraints weight = 15606.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166256 restraints weight = 13714.574| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25034 Z= 0.116 Angle : 0.565 12.202 34091 Z= 0.280 Chirality : 0.041 0.228 3958 Planarity : 0.004 0.058 4218 Dihedral : 13.442 132.517 4018 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.84 % Allowed : 22.53 % Favored : 73.63 % 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 aren not related in a simple way. whole: -1.08 (0.15), residues: 2965 helix: -0.23 (0.17), residues: 997 sheet: -1.07 (0.32), residues: 279 loop : -0.91 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 195 TYR 0.012 0.001 TYR D 360 PHE 0.012 0.001 PHE C 337 TRP 0.034 0.002 TRP D 236 HIS 0.005 0.001 HIS D1227 Details of bonding type rmsd covalent geometry : bond 0.00271 (25029) covalent geometry : angle 0.56457 (34091) hydrogen bonds : bond 0.02912 ( 726) hydrogen bonds : angle 4.56787 ( 2024) metal coordination : bond 0.00197 ( 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 524 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 428 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.8628 (m-40) cc_final: 0.8279 (m-40) REVERT: C 44 GLU cc_start: 0.6575 (pm20) cc_final: 0.6264 (tm-30) REVERT: C 129 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8454 (mt) REVERT: C 383 SER cc_start: 0.8616 (t) cc_final: 0.8394 (p) REVERT: C 653 MET cc_start: 0.7787 (tmm) cc_final: 0.7475 (ttt) REVERT: C 657 THR cc_start: 0.8370 (t) cc_final: 0.8146 (p) REVERT: C 711 ASP cc_start: 0.6583 (m-30) cc_final: 0.6212 (m-30) REVERT: C 807 TRP cc_start: 0.7590 (t60) cc_final: 0.7141 (t60) REVERT: C 1180 MET cc_start: 0.8022 (tpp) cc_final: 0.7405 (ttm) REVERT: C 1274 GLU cc_start: 0.7025 (mp0) cc_final: 0.6654 (mp0) REVERT: D 133 ARG cc_start: 0.7873 (mpt-90) cc_final: 0.6903 (tpt170) REVERT: D 347 VAL cc_start: 0.9288 (t) cc_final: 0.9052 (m) REVERT: D 362 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7116 (mtp85) REVERT: D 432 LEU cc_start: 0.9190 (mm) cc_final: 0.8925 (mt) REVERT: D 738 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6900 (ttm110) REVERT: D 822 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6960 (mmm) REVERT: D 897 HIS cc_start: 0.7813 (m90) cc_final: 0.7489 (m90) REVERT: D 957 SER cc_start: 0.8155 (m) cc_final: 0.7920 (t) REVERT: D 996 LYS cc_start: 0.7400 (tmtt) cc_final: 0.7159 (tttt) REVERT: E 47 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8216 (p) REVERT: E 69 ARG cc_start: 0.7651 (ptp-110) cc_final: 0.7227 (mtt-85) outliers start: 96 outliers final: 74 residues processed: 498 average time/residue: 0.1500 time to fit residues: 119.4792 Evaluate side-chains 479 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 402 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR 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 C residue 11 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER 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 660 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 935 THR 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 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR 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 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 478 LEU Chi-restraints excluded: chain D residue 483 LEU 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 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 930 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1011 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 1230 THR 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: 20.0000 chunk 109 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 513 GLN ** 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 628 HIS C 686 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150550 restraints weight = 33208.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150972 restraints weight = 25937.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152364 restraints weight = 20950.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152701 restraints weight = 16781.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153044 restraints weight = 14731.013| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25034 Z= 0.249 Angle : 0.694 18.267 34091 Z= 0.347 Chirality : 0.046 0.200 3958 Planarity : 0.005 0.070 4218 Dihedral : 13.696 133.317 4018 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.80 % Allowed : 22.81 % 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 aren not related in a simple way. whole: -1.30 (0.15), residues: 2965 helix: -0.47 (0.16), residues: 1010 sheet: -1.14 (0.33), residues: 276 loop : -1.02 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 143 TYR 0.027 0.002 TYR A 185 PHE 0.021 0.002 PHE C 828 TRP 0.044 0.003 TRP D 236 HIS 0.010 0.001 HIS D1227 Details of bonding type rmsd covalent geometry : bond 0.00587 (25029) covalent geometry : angle 0.69367 (34091) hydrogen bonds : bond 0.03651 ( 726) hydrogen bonds : angle 4.93166 ( 2024) metal coordination : bond 0.00762 ( 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 527 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 432 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.8838 (m-40) cc_final: 0.8405 (m-40) REVERT: C 179 TYR cc_start: 0.7321 (t80) cc_final: 0.6883 (t80) REVERT: C 383 SER cc_start: 0.8650 (t) cc_final: 0.8437 (p) REVERT: C 461 GLU cc_start: 0.7373 (tt0) cc_final: 0.7140 (tt0) REVERT: C 542 ARG cc_start: 0.6355 (mpt180) cc_final: 0.5560 (mmt180) REVERT: C 711 ASP cc_start: 0.7112 (m-30) cc_final: 0.6841 (m-30) REVERT: C 1180 MET cc_start: 0.8269 (tpp) cc_final: 0.8007 (ttm) REVERT: C 1332 SER cc_start: 0.9022 (p) cc_final: 0.8593 (p) REVERT: D 347 VAL cc_start: 0.9335 (t) cc_final: 0.9030 (m) REVERT: D 362 ARG cc_start: 0.7632 (ttp-110) cc_final: 0.7223 (mtp85) REVERT: D 432 LEU cc_start: 0.9303 (mm) cc_final: 0.9090 (mt) REVERT: D 822 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6824 (mmm) REVERT: D 957 SER cc_start: 0.8225 (m) cc_final: 0.7902 (t) REVERT: D 996 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7316 (tttt) outliers start: 95 outliers final: 75 residues processed: 500 average time/residue: 0.1515 time to fit residues: 120.7455 Evaluate side-chains 477 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 401 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR 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 C residue 11 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 VAL 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 284 LEU Chi-restraints excluded: chain C residue 348 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 660 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS 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 1176 LEU Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR 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 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 279 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 483 LEU 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 624 ILE Chi-restraints excluded: chain D residue 642 ASP 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 865 HIS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 138 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 222 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 206 optimal weight: 0.4980 chunk 67 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 343 HIS C 447 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.189996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160588 restraints weight = 33257.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161719 restraints weight = 24188.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163459 restraints weight = 19763.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163642 restraints weight = 15073.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163779 restraints weight = 13675.168| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25034 Z= 0.129 Angle : 0.617 16.269 34091 Z= 0.305 Chirality : 0.042 0.246 3958 Planarity : 0.004 0.055 4218 Dihedral : 13.560 132.066 4018 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.88 % Allowed : 24.17 % Favored : 72.95 % 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 aren not related in a simple way. whole: -1.12 (0.15), residues: 2965 helix: -0.28 (0.17), residues: 1002 sheet: -1.14 (0.32), residues: 277 loop : -0.91 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 143 TYR 0.024 0.001 TYR A 185 PHE 0.016 0.001 PHE C1025 TRP 0.031 0.002 TRP D 236 HIS 0.004 0.001 HIS C1070 Details of bonding type rmsd covalent geometry : bond 0.00306 (25029) covalent geometry : angle 0.61747 (34091) hydrogen bonds : bond 0.03108 ( 726) hydrogen bonds : angle 4.74094 ( 2024) metal coordination : bond 0.00238 ( 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 503 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 431 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.8618 (m-40) cc_final: 0.8102 (m110) REVERT: C 711 ASP cc_start: 0.6836 (m-30) cc_final: 0.6550 (m-30) REVERT: C 1180 MET cc_start: 0.8060 (tpp) cc_final: 0.7424 (ttm) REVERT: C 1332 SER cc_start: 0.9010 (p) cc_final: 0.8595 (p) REVERT: D 133 ARG cc_start: 0.7919 (mpt-90) cc_final: 0.6756 (tpt170) REVERT: D 159 ILE cc_start: 0.8135 (mp) cc_final: 0.7731 (mt) REVERT: D 347 VAL cc_start: 0.9270 (t) cc_final: 0.9028 (m) REVERT: D 432 LEU cc_start: 0.9104 (mm) cc_final: 0.8840 (mm) REVERT: D 680 ASN cc_start: 0.7310 (m-40) cc_final: 0.7105 (m-40) REVERT: D 738 ARG cc_start: 0.7476 (ttm170) cc_final: 0.7125 (ttm110) REVERT: D 822 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6631 (mmm) REVERT: D 957 SER cc_start: 0.8178 (m) cc_final: 0.7883 (t) REVERT: D 996 LYS cc_start: 0.7469 (tmtt) cc_final: 0.7240 (tttt) REVERT: E 69 ARG cc_start: 0.7612 (ptp-110) cc_final: 0.7185 (mtt-85) outliers start: 72 outliers final: 65 residues processed: 480 average time/residue: 0.1493 time to fit residues: 113.4817 Evaluate side-chains 469 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 403 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL 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 C residue 11 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 VAL 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 284 LEU Chi-restraints excluded: chain C residue 348 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 660 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 764 CYS 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 1176 LEU Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL 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 279 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 483 LEU 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 572 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 642 ASP 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 865 HIS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1230 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: 9.9990 chunk 181 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN D 736 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.183731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153299 restraints weight = 33107.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153726 restraints weight = 24610.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155129 restraints weight = 20346.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155731 restraints weight = 15834.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155875 restraints weight = 14662.832| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25034 Z= 0.200 Angle : 0.663 17.683 34091 Z= 0.330 Chirality : 0.044 0.241 3958 Planarity : 0.004 0.065 4218 Dihedral : 13.626 133.413 4018 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.20 % Allowed : 24.09 % Favored : 72.71 % 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 aren not related in a simple way. whole: -1.15 (0.15), residues: 2965 helix: -0.32 (0.16), residues: 1004 sheet: -1.12 (0.32), residues: 277 loop : -0.92 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 202 TYR 0.021 0.002 TYR A 185 PHE 0.016 0.002 PHE C1025 TRP 0.035 0.002 TRP D 236 HIS 0.005 0.001 HIS D1252 Details of bonding type rmsd covalent geometry : bond 0.00477 (25029) covalent geometry : angle 0.66346 (34091) hydrogen bonds : bond 0.03326 ( 726) hydrogen bonds : angle 4.82731 ( 2024) metal coordination : bond 0.00554 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3687.76 seconds wall clock time: 64 minutes 35.77 seconds (3875.77 seconds total)