Starting phenix.real_space_refine on Fri Oct 30 11:48:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlj_22245/10_2026/6xlj_22245.cif" } resolution = 2.7 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= 0.004 sd= 0.152 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: 8 Type Number sf(0) Gaussians Sb 3 10.97 5 Zn 2 6.06 5 P 112 5.49 5 Mg 2 5.21 5 S 155 5.16 5 C 22278 2.51 5 N 6287 2.21 5 O 7063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35902 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1726 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10387 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3878 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 461} Chain breaks: 2 Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "N" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1109 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "R" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 97 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 3, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" C R 2 " Chain: "T" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1099 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" 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 14528 SG CYS D 70 47.649 79.945 127.927 1.00 93.81 S ATOM 14542 SG CYS D 72 49.454 79.125 130.609 1.00 96.27 S ATOM 14650 SG CYS D 85 45.729 80.345 130.745 1.00 94.52 S ATOM 14674 SG CYS D 88 49.491 82.446 129.666 1.00 92.96 S ATOM 20362 SG CYS D 814 30.328 109.990 71.120 1.00 79.78 S ATOM 20927 SG CYS D 888 33.422 109.229 72.719 1.00 78.38 S ATOM 20978 SG CYS D 895 31.663 106.922 70.654 1.00 70.69 S ATOM 20999 SG CYS D 898 33.335 109.560 69.143 1.00 71.66 S Time building chain proxies: 8.60, per 1000 atoms: 0.24 Number of scatterers: 35902 At special positions: 0 Unit cell: (149.296, 181.288, 201.283, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Sb 3 50.95 Zn 2 29.99 S 155 16.00 P 112 15.00 Mg 2 11.99 O 7063 8.00 N 6287 7.00 C 22278 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7868 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 52 sheets defined 43.7% alpha, 17.0% beta 43 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.759A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 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 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.887A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.735A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.830A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.640A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.072A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 3.932A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.776A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.323A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.611A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.790A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.648A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.502A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 860 through 864' Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 993 through 999 removed outlier: 3.506A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1037 removed outlier: 3.688A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.542A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1261 through 1265 removed outlier: 3.678A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.545A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.044A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.576A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.558A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.607A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 removed outlier: 4.106A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 206 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.072A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.953A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.040A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.892A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (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 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.782A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.618A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.103A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.823A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.949A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.579A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1063 through 1067 removed outlier: 3.755A pdb=" N GLU D1066 " --> pdb=" O ASP D1063 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG D1067 " --> pdb=" O SER D1064 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1063 through 1067' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.839A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.699A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.505A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.841A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.546A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.685A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 135 removed outlier: 3.773A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.119A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 160 Processing helix chain 'F' and resid 213 through 233 removed outlier: 4.507A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.645A pdb=" N GLN F 246 " --> pdb=" O ALA F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 257 Processing helix chain 'F' and resid 262 through 289 Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.586A pdb=" N PHE F 306 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 302 through 307' Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.953A pdb=" N ALA F 318 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 332 removed outlier: 3.808A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 343 through 351 removed outlier: 4.199A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 382 removed outlier: 3.572A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.685A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.517A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 4.118A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 447 " --> pdb=" O ILE F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.513A pdb=" N GLN F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.513A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.695A pdb=" N ALA F 501 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 514 removed outlier: 3.608A pdb=" N ASP F 513 " --> pdb=" O PRO F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.692A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.617A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.633A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.953A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 109 removed outlier: 3.804A pdb=" N ILE G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 removed outlier: 3.921A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 154 removed outlier: 3.713A pdb=" N ILE G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 removed outlier: 3.723A pdb=" N SER G 218 " --> pdb=" O PRO G 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 215 through 218' Processing helix chain 'G' and resid 219 through 233 removed outlier: 3.561A pdb=" N TYR G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 14 through 25 Processing helix chain 'H' and resid 42 through 57 removed outlier: 3.719A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 75 through 109 removed outlier: 3.625A pdb=" N GLU H 79 " --> pdb=" O CYS H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 154 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 215 through 218 Processing helix chain 'H' and resid 219 through 233 removed outlier: 3.504A pdb=" N TYR H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 257 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.911A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.557A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.467A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.869A pdb=" N GLN B 18 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS B 25 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 23 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.637A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.562A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.420A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.311A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 161 removed outlier: 5.013A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.081A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.102A 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: 3.568A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.408A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.645A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.655A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) 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 1209 through 1210 removed outlier: 7.357A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.210A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.723A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AD3, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.388A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.392A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD6, first strand: chain 'D' and resid 350 through 356 removed outlier: 6.480A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 709 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.562A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 848 through 849 Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.057A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.366A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AE8, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.523A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 162 through 165 removed outlier: 6.979A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AF3, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.240A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 117 through 121 removed outlier: 5.240A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AF6, first strand: chain 'H' and resid 117 through 121 removed outlier: 4.611A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET H 259 " --> pdb=" O ILE H 246 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 117 through 121 removed outlier: 4.611A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 1513 hydrogen bonds defined for protein. 4239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 230 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 11.24 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 14413 1.39 - 1.57: 21811 1.57 - 1.76: 233 1.76 - 1.95: 256 1.95 - 2.13: 12 Bond restraints: 36725 Sorted by residual: bond pdb=" N1 DC T 31 " pdb=" C6 DC T 31 " ideal model delta sigma weight residual 1.367 1.339 0.028 6.00e-03 2.78e+04 2.23e+01 bond pdb=" N1 DC T 36 " pdb=" C6 DC T 36 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.66e+01 bond pdb=" N1 DC T 33 " pdb=" C6 DC T 33 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.60e+01 bond pdb=" C3' DC N 42 " pdb=" O3' DC N 42 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" C3' DA T 10 " pdb=" O3' DA T 10 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.52e+01 ... (remaining 36720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 48311 2.46 - 4.92: 1603 4.92 - 7.38: 172 7.38 - 9.84: 27 9.84 - 12.30: 8 Bond angle restraints: 50121 Sorted by residual: angle pdb=" N VAL A 192 " pdb=" CA VAL A 192 " pdb=" C VAL A 192 " ideal model delta sigma weight residual 107.99 120.29 -12.30 1.46e+00 4.69e-01 7.09e+01 angle pdb=" N ASP C1296 " pdb=" CA ASP C1296 " pdb=" C ASP C1296 " ideal model delta sigma weight residual 112.90 122.93 -10.03 1.31e+00 5.83e-01 5.86e+01 angle pdb=" N GLN D 504 " pdb=" CA GLN D 504 " pdb=" C GLN D 504 " ideal model delta sigma weight residual 111.37 121.62 -10.25 1.64e+00 3.72e-01 3.91e+01 angle pdb=" C GLY C1260 " pdb=" N GLY C1261 " pdb=" CA GLY C1261 " ideal model delta sigma weight residual 122.47 116.93 5.54 8.90e-01 1.26e+00 3.88e+01 angle pdb=" O4' DG N 59 " pdb=" C4' DG N 59 " pdb=" C3' DG N 59 " ideal model delta sigma weight residual 106.00 102.52 3.48 6.00e-01 2.78e+00 3.37e+01 ... (remaining 50116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 21234 35.25 - 70.51: 865 70.51 - 105.76: 39 105.76 - 141.01: 1 141.01 - 176.27: 3 Dihedral angle restraints: 22142 sinusoidal: 9936 harmonic: 12206 Sorted by residual: dihedral pdb=" C SER D 503 " pdb=" N SER D 503 " pdb=" CA SER D 503 " pdb=" CB SER D 503 " ideal model delta harmonic sigma weight residual -122.60 -143.61 21.01 0 2.50e+00 1.60e-01 7.06e+01 dihedral pdb=" N SER D 503 " pdb=" C SER D 503 " pdb=" CA SER D 503 " pdb=" CB SER D 503 " ideal model delta harmonic sigma weight residual 122.80 140.69 -17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" CA GLU C1005 " pdb=" C GLU C1005 " pdb=" N GLU C1006 " pdb=" CA GLU C1006 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 22139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 5622 0.178 - 0.355: 74 0.355 - 0.533: 4 0.533 - 0.710: 0 0.710 - 0.888: 1 Chirality restraints: 5701 Sorted by residual: chirality pdb=" CA SER D 503 " pdb=" N SER D 503 " pdb=" C SER D 503 " pdb=" CB SER D 503 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CA GLN D 504 " pdb=" N GLN D 504 " pdb=" C GLN D 504 " pdb=" CB GLN D 504 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA LEU D 139 " pdb=" N LEU D 139 " pdb=" C LEU D 139 " pdb=" CB LEU D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 5698 not shown) Planarity restraints: 6101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " 0.077 2.00e-02 2.50e+03 4.13e-02 3.40e+01 pdb=" CG TYR D 75 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 178 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" CG ASN G 178 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN G 178 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN G 178 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 77 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ILE H 77 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE H 77 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE H 78 " 0.022 2.00e-02 2.50e+03 ... (remaining 6098 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 170 2.46 - 3.07: 23722 3.07 - 3.68: 55428 3.68 - 4.29: 83828 4.29 - 4.90: 140069 Nonbonded interactions: 303217 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.853 2.170 nonbonded pdb=" O3' G R 4 " pdb="MG MG D1501 " model vdw 1.859 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 1.874 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.093 2.170 nonbonded pdb=" OG1 THR G 209 " pdb=" OE1 GLU G 261 " model vdw 2.208 3.040 ... (remaining 303212 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 5 through 159 or resid 167 through 234)) selection = (chain 'B' and resid 5 through 234) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.050 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 47.710 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.015 0.402 36734 Z= 0.676 Angle : 1.060 19.351 50133 Z= 0.616 Chirality : 0.069 0.888 5701 Planarity : 0.006 0.076 6101 Dihedral : 17.265 176.267 14274 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.69 % Favored : 98.28 % Rotamer: Outliers : 0.16 % Allowed : 7.52 % Favored : 92.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.11), residues: 4195 helix: -2.05 (0.10), residues: 1657 sheet: -2.01 (0.21), residues: 473 loop : -1.83 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 220 TYR 0.077 0.004 TYR D 75 PHE 0.040 0.003 PHE H 166 TRP 0.036 0.004 TRP G 258 HIS 0.017 0.003 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.01424 / 0.67 (36725) covalent geometry : angle 1.04774 / 0.62 (50121) hydrogen bonds : bond 0.15075 / 9.94 ( 1600) hydrogen bonds : angle 7.13748 / 4.91 ( 4469) metal coordination : bond 0.22894 / 11.93 ( 8) metal coordination : angle 10.65267 / 5.63 ( 12) Misc. bond : bond 0.02702 / 1.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 412 time to evaluate : 1.307 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: A 9 LEU cc_start: 0.8688 (mp) cc_final: 0.8425 (mt) REVERT: A 147 GLN cc_start: 0.8350 (tt0) cc_final: 0.8123 (tt0) REVERT: A 185 TYR cc_start: 0.9045 (p90) cc_final: 0.8845 (p90) REVERT: B 13 LEU cc_start: 0.6618 (mm) cc_final: 0.6406 (mt) REVERT: B 25 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7783 (mtpp) REVERT: B 68 TYR cc_start: 0.8325 (m-80) cc_final: 0.8075 (m-80) REVERT: B 93 GLN cc_start: 0.7328 (mp-120) cc_final: 0.7116 (mp10) REVERT: B 95 LYS cc_start: 0.8782 (mttt) cc_final: 0.8529 (mtpp) REVERT: B 145 LYS cc_start: 0.8403 (tttt) cc_final: 0.7800 (tttp) REVERT: B 174 ASP cc_start: 0.8053 (m-30) cc_final: 0.7737 (m-30) REVERT: B 186 ASN cc_start: 0.7955 (m-40) cc_final: 0.7694 (m110) REVERT: B 200 LYS cc_start: 0.8532 (tttt) cc_final: 0.8293 (ttpp) REVERT: C 116 ASP cc_start: 0.7725 (t0) cc_final: 0.7418 (t0) REVERT: C 127 ILE cc_start: 0.8407 (pt) cc_final: 0.8155 (pp) REVERT: C 191 LYS cc_start: 0.8521 (mttp) cc_final: 0.8184 (mtmp) REVERT: C 200 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8168 (mmp-170) REVERT: C 239 MET cc_start: 0.5281 (ttt) cc_final: 0.4911 (ttm) REVERT: C 285 ILE cc_start: 0.7019 (mm) cc_final: 0.6801 (mm) REVERT: C 295 LYS cc_start: 0.5939 (mmtt) cc_final: 0.5598 (mttm) REVERT: C 429 MET cc_start: 0.8312 (mtp) cc_final: 0.7887 (mtp) REVERT: C 465 ARG cc_start: 0.7661 (ttp-110) cc_final: 0.7306 (ttp-170) REVERT: C 515 MET cc_start: 0.9109 (ttp) cc_final: 0.8830 (ttm) REVERT: C 681 MET cc_start: 0.7886 (mtt) cc_final: 0.7660 (mtt) REVERT: C 685 MET cc_start: 0.8544 (mtm) cc_final: 0.8317 (mtp) REVERT: C 778 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7145 (mm-30) REVERT: C 951 MET cc_start: 0.7778 (ttm) cc_final: 0.7543 (ttp) REVERT: C 1020 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 1024 GLU cc_start: 0.8117 (tp30) cc_final: 0.7896 (tp30) REVERT: C 1025 PHE cc_start: 0.8263 (t80) cc_final: 0.8042 (t80) REVERT: C 1131 MET cc_start: 0.8751 (mtt) cc_final: 0.8461 (mtp) REVERT: C 1140 LYS cc_start: 0.8584 (mttt) cc_final: 0.8338 (mtpp) REVERT: C 1178 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8527 (mtmm) REVERT: C 1180 MET cc_start: 0.8641 (ttp) cc_final: 0.8385 (ttt) REVERT: D 137 ARG cc_start: 0.7409 (mtp180) cc_final: 0.6788 (mtp-110) REVERT: D 237 MET cc_start: 0.9357 (mtm) cc_final: 0.8750 (mtp) REVERT: D 484 MET cc_start: 0.9344 (mtp) cc_final: 0.8982 (mtm) REVERT: D 725 MET cc_start: 0.8812 (mtt) cc_final: 0.8365 (mtt) REVERT: D 747 MET cc_start: 0.8336 (mmm) cc_final: 0.8127 (mmp) REVERT: D 785 ASP cc_start: 0.7377 (t0) cc_final: 0.7110 (t70) REVERT: D 1025 MET cc_start: 0.6761 (tpt) cc_final: 0.6551 (mmm) REVERT: D 1040 MET cc_start: 0.2037 (tmm) cc_final: 0.1704 (tmm) REVERT: D 1149 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8073 (mtt-85) REVERT: D 1189 MET cc_start: 0.7541 (tpp) cc_final: 0.7259 (tpp) REVERT: D 1196 LEU cc_start: 0.8940 (tt) cc_final: 0.8711 (tm) REVERT: D 1197 ASN cc_start: 0.6919 (m-40) cc_final: 0.6559 (m110) REVERT: E 18 ASP cc_start: 0.8188 (m-30) cc_final: 0.7969 (m-30) REVERT: E 43 ASN cc_start: 0.7818 (t0) cc_final: 0.7319 (t0) REVERT: E 72 GLN cc_start: 0.8131 (tt0) cc_final: 0.7735 (tm-30) REVERT: F 160 ASP cc_start: 0.7996 (t70) cc_final: 0.7631 (t0) REVERT: F 273 MET cc_start: 0.8898 (tmm) cc_final: 0.8690 (tmt) REVERT: F 364 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.8024 (ptp90) REVERT: F 485 GLU cc_start: 0.8084 (mp0) cc_final: 0.7684 (mp0) REVERT: F 487 MET cc_start: 0.8219 (mtp) cc_final: 0.7861 (mtp) REVERT: F 491 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7001 (tm-30) REVERT: G 73 ASN cc_start: 0.7001 (m-40) cc_final: 0.6256 (t0) REVERT: G 105 HIS cc_start: 0.7141 (m-70) cc_final: 0.6806 (m90) REVERT: G 151 MET cc_start: 0.8839 (ppp) cc_final: 0.8615 (ppp) REVERT: H 47 MET cc_start: 0.8049 (tmm) cc_final: 0.7609 (tmm) REVERT: H 253 GLN cc_start: 0.7999 (mp-120) cc_final: 0.7734 (pm20) outliers start: 6 outliers final: 4 residues processed: 418 average time/residue: 0.7936 time to fit residues: 390.0352 Evaluate side-chains 298 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 294 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain D residue 174 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 424, 155] chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 75 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 339 ASN C 518 ASN C 620 ASN C 649 GLN C 965 GLN C1237 HIS C1244 HIS C1268 GLN D 157 GLN D 274 ASN D 665 GLN D 762 ASN D1114 GLN D1366 HIS E 15 ASN E 70 GLN F 258 GLN F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN F 383 ASN G 22 ASN G 45 GLN G 51 GLN G 86 GLN G 105 HIS G 154 ASN ** G 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN G 233 ASN G 239 ASN H 3 GLN H 22 ASN H 50 HIS H 154 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.154370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097146 restraints weight = 48669.671| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.26 r_work: 0.3182 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36734 Z= 0.170 Angle : 0.663 14.359 50133 Z= 0.355 Chirality : 0.046 0.398 5701 Planarity : 0.005 0.057 6101 Dihedral : 16.171 174.221 5868 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.84 % Allowed : 12.46 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.12), residues: 4195 helix: -0.59 (0.12), residues: 1682 sheet: -1.68 (0.22), residues: 456 loop : -1.47 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 12 TYR 0.020 0.001 TYR C1281 PHE 0.028 0.002 PHE D 172 TRP 0.015 0.001 TRP G 258 HIS 0.015 0.001 HIS H 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (36725) covalent geometry : angle 0.65360 / 0.35 (50121) hydrogen bonds : bond 0.04864 / 3.24 ( 1600) hydrogen bonds : angle 5.41560 / 3.68 ( 4469) metal coordination : bond 0.01837 / 0.94 ( 8) metal coordination : angle 7.13485 / 3.71 ( 12) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 1.187 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: A 9 LEU cc_start: 0.8407 (mp) cc_final: 0.8139 (mt) REVERT: A 62 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7536 (p0) REVERT: A 127 GLN cc_start: 0.8707 (mp10) cc_final: 0.8428 (mp10) REVERT: A 147 GLN cc_start: 0.8506 (tt0) cc_final: 0.8221 (tt0) REVERT: A 185 TYR cc_start: 0.9158 (p90) cc_final: 0.8878 (p90) REVERT: B 86 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8427 (ttpt) REVERT: B 95 LYS cc_start: 0.8486 (mttt) cc_final: 0.8127 (mtpp) REVERT: B 125 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7814 (ttmt) REVERT: B 147 GLN cc_start: 0.8166 (tt0) cc_final: 0.7946 (tt0) REVERT: B 174 ASP cc_start: 0.8184 (m-30) cc_final: 0.7677 (m-30) REVERT: B 186 ASN cc_start: 0.8166 (m-40) cc_final: 0.7884 (m110) REVERT: B 200 LYS cc_start: 0.8267 (tttt) cc_final: 0.7892 (tttp) REVERT: B 204 GLU cc_start: 0.8081 (tt0) cc_final: 0.7870 (tt0) REVERT: C 36 GLN cc_start: 0.7627 (tp40) cc_final: 0.7254 (mm-40) REVERT: C 60 GLN cc_start: 0.7399 (mp10) cc_final: 0.7014 (mm-40) REVERT: C 127 ILE cc_start: 0.8310 (pt) cc_final: 0.7975 (pp) REVERT: C 191 LYS cc_start: 0.8302 (mttp) cc_final: 0.7956 (mtmp) REVERT: C 200 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8283 (mmp-170) REVERT: C 295 LYS cc_start: 0.5895 (mmtt) cc_final: 0.5580 (mttm) REVERT: C 315 MET cc_start: 0.8260 (mtp) cc_final: 0.7891 (mtm) REVERT: C 337 PHE cc_start: 0.8267 (t80) cc_final: 0.7797 (t80) REVERT: C 515 MET cc_start: 0.9187 (ttp) cc_final: 0.8937 (ttm) REVERT: C 778 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7122 (mm-30) REVERT: C 844 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7868 (ptmm) REVERT: C 951 MET cc_start: 0.8132 (ttm) cc_final: 0.7720 (ttp) REVERT: C 1020 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 1131 MET cc_start: 0.8247 (mtt) cc_final: 0.7898 (mtm) REVERT: C 1161 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7271 (pp) REVERT: C 1178 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8464 (mtmm) REVERT: C 1180 MET cc_start: 0.8870 (ttp) cc_final: 0.8608 (ttt) REVERT: C 1230 MET cc_start: 0.9367 (ttp) cc_final: 0.8976 (ttp) REVERT: D 29 MET cc_start: 0.7942 (tpp) cc_final: 0.7577 (ttp) REVERT: D 69 GLU cc_start: 0.8918 (tt0) cc_final: 0.8565 (mt-10) REVERT: D 137 ARG cc_start: 0.7192 (mtp180) cc_final: 0.6742 (mtp-110) REVERT: D 147 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7525 (pp) REVERT: D 151 MET cc_start: 0.8249 (mtp) cc_final: 0.7939 (mpt) REVERT: D 237 MET cc_start: 0.9341 (mtm) cc_final: 0.8834 (mtp) REVERT: D 321 LYS cc_start: 0.8453 (mmtm) cc_final: 0.7242 (ttpm) REVERT: D 484 MET cc_start: 0.9396 (mtp) cc_final: 0.9033 (mtm) REVERT: D 720 ASN cc_start: 0.8564 (t0) cc_final: 0.8336 (t0) REVERT: D 725 MET cc_start: 0.8572 (mtt) cc_final: 0.8230 (mtt) REVERT: D 769 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8468 (t) REVERT: D 785 ASP cc_start: 0.7740 (t0) cc_final: 0.7461 (t70) REVERT: D 832 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7498 (mmmt) REVERT: D 1025 MET cc_start: 0.6987 (tpt) cc_final: 0.6589 (mmm) REVERT: D 1040 MET cc_start: 0.1367 (tmm) cc_final: 0.1043 (tmm) REVERT: D 1149 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7971 (mtt-85) REVERT: D 1189 MET cc_start: 0.7339 (tpp) cc_final: 0.7002 (tpp) REVERT: D 1196 LEU cc_start: 0.8862 (tt) cc_final: 0.8614 (tm) REVERT: D 1197 ASN cc_start: 0.6658 (m-40) cc_final: 0.6271 (m110) REVERT: E 43 ASN cc_start: 0.7739 (t0) cc_final: 0.7232 (t0) REVERT: F 160 ASP cc_start: 0.7480 (t70) cc_final: 0.7197 (t0) REVERT: F 273 MET cc_start: 0.8757 (tmm) cc_final: 0.8489 (tmt) REVERT: F 364 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7950 (ptp90) REVERT: F 485 GLU cc_start: 0.8346 (mp0) cc_final: 0.8075 (mp0) REVERT: F 491 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6652 (tm-30) REVERT: F 567 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7247 (mtp) REVERT: G 73 ASN cc_start: 0.7235 (m110) cc_final: 0.6371 (t0) REVERT: G 88 GLN cc_start: 0.8468 (mt0) cc_final: 0.8241 (mp10) REVERT: G 95 MET cc_start: 0.8359 (mmt) cc_final: 0.8068 (mmt) REVERT: G 105 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6859 (m90) REVERT: G 151 MET cc_start: 0.8799 (ppp) cc_final: 0.8574 (ppp) REVERT: G 179 MET cc_start: 0.7078 (pmm) cc_final: 0.6771 (pmm) REVERT: G 261 GLU cc_start: 0.7932 (pp20) cc_final: 0.7623 (pp20) REVERT: H 47 MET cc_start: 0.8133 (tmm) cc_final: 0.7689 (tmm) REVERT: H 60 PHE cc_start: 0.7191 (m-80) cc_final: 0.6946 (m-80) REVERT: H 151 MET cc_start: 0.8118 (ptm) cc_final: 0.7857 (ppp) REVERT: H 253 GLN cc_start: 0.8059 (mp-120) cc_final: 0.7858 (pm20) REVERT: H 261 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6638 (tp30) outliers start: 67 outliers final: 17 residues processed: 364 average time/residue: 0.7369 time to fit residues: 317.0818 Evaluate side-chains 310 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 56 ARG Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain H residue 261 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [396, 239, 157, 151, 89, 379, 21, 83, 205, 297, 362] chunk 396 optimal weight: 8.9990 chunk 239 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 89 optimal weight: 0.0970 chunk 379 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 205 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN C 41 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 894 GLN D 365 GLN D 875 ASN E 15 ASN E 70 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 105 HIS G 178 ASN G 196 ASN H 50 HIS H 188 ASN ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096425 restraints weight = 48784.888| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.26 r_work: 0.3195 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36734 Z= 0.148 Angle : 0.594 11.056 50133 Z= 0.318 Chirality : 0.044 0.394 5701 Planarity : 0.004 0.051 6101 Dihedral : 15.894 175.766 5864 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 14.60 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 4195 helix: 0.14 (0.13), residues: 1688 sheet: -1.48 (0.22), residues: 461 loop : -1.15 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1034 TYR 0.018 0.001 TYR C1281 PHE 0.030 0.001 PHE H 183 TRP 0.010 0.001 TRP G 258 HIS 0.017 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (36725) covalent geometry : angle 0.58852 / 0.32 (50121) hydrogen bonds : bond 0.04188 / 2.83 ( 1600) hydrogen bonds : angle 4.96213 / 3.37 ( 4469) metal coordination : bond 0.01146 / 0.61 ( 8) metal coordination : angle 5.01191 / 2.57 ( 12) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 325 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8399 (mp) cc_final: 0.8139 (mt) REVERT: A 127 GLN cc_start: 0.8724 (mp10) cc_final: 0.8426 (mp10) REVERT: A 147 GLN cc_start: 0.8456 (tt0) cc_final: 0.8245 (tt0) REVERT: A 185 TYR cc_start: 0.9151 (p90) cc_final: 0.8878 (p90) REVERT: B 93 GLN cc_start: 0.7042 (mp10) cc_final: 0.6772 (mp10) REVERT: B 95 LYS cc_start: 0.8452 (mttt) cc_final: 0.8197 (mtpp) REVERT: B 125 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7643 (ttmt) REVERT: B 145 LYS cc_start: 0.8114 (tttt) cc_final: 0.7833 (ttpp) REVERT: B 147 GLN cc_start: 0.8249 (tt0) cc_final: 0.7719 (tt0) REVERT: B 186 ASN cc_start: 0.8150 (m-40) cc_final: 0.7829 (m110) REVERT: B 200 LYS cc_start: 0.8252 (tttt) cc_final: 0.7880 (tttp) REVERT: C 36 GLN cc_start: 0.7540 (tp40) cc_final: 0.7170 (mm-40) REVERT: C 60 GLN cc_start: 0.7305 (mp10) cc_final: 0.6994 (mm-40) REVERT: C 127 ILE cc_start: 0.8288 (pt) cc_final: 0.8009 (pp) REVERT: C 191 LYS cc_start: 0.8281 (mttp) cc_final: 0.7902 (mtmp) REVERT: C 200 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8240 (mmp-170) REVERT: C 315 MET cc_start: 0.8091 (mtp) cc_final: 0.7785 (mtp) REVERT: C 515 MET cc_start: 0.9213 (ttp) cc_final: 0.8947 (ttm) REVERT: C 681 MET cc_start: 0.7637 (mtt) cc_final: 0.7432 (mtt) REVERT: C 742 TYR cc_start: 0.6723 (m-80) cc_final: 0.6486 (m-80) REVERT: C 778 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7190 (mm-30) REVERT: C 844 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7510 (ptmm) REVERT: C 951 MET cc_start: 0.8238 (ttm) cc_final: 0.7822 (ttp) REVERT: C 1020 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 1131 MET cc_start: 0.8158 (mtt) cc_final: 0.7842 (mtm) REVERT: C 1161 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7350 (pp) REVERT: C 1178 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8533 (mtmm) REVERT: C 1180 MET cc_start: 0.8885 (ttp) cc_final: 0.8650 (ttt) REVERT: C 1296 ASP cc_start: 0.8503 (t0) cc_final: 0.8298 (t0) REVERT: D 18 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: D 29 MET cc_start: 0.7971 (tpp) cc_final: 0.7623 (ttp) REVERT: D 69 GLU cc_start: 0.8801 (tt0) cc_final: 0.8539 (tt0) REVERT: D 137 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6711 (mtp-110) REVERT: D 147 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7618 (pp) REVERT: D 151 MET cc_start: 0.8120 (mtp) cc_final: 0.7871 (mpt) REVERT: D 159 ILE cc_start: 0.8527 (pp) cc_final: 0.8215 (mp) REVERT: D 180 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8412 (ttp) REVERT: D 237 MET cc_start: 0.9397 (mtm) cc_final: 0.8849 (mtp) REVERT: D 321 LYS cc_start: 0.8615 (mmtm) cc_final: 0.7344 (ttpm) REVERT: D 484 MET cc_start: 0.9379 (mtp) cc_final: 0.9052 (mtm) REVERT: D 720 ASN cc_start: 0.8591 (t0) cc_final: 0.8376 (t0) REVERT: D 725 MET cc_start: 0.8548 (mtt) cc_final: 0.8241 (mtp) REVERT: D 832 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7409 (mmmt) REVERT: D 992 LYS cc_start: 0.7464 (mptt) cc_final: 0.7249 (mptt) REVERT: D 1025 MET cc_start: 0.7098 (tpt) cc_final: 0.6683 (mmm) REVERT: D 1040 MET cc_start: 0.0974 (tmm) cc_final: 0.0576 (tmm) REVERT: D 1143 ASP cc_start: 0.7849 (p0) cc_final: 0.7483 (p0) REVERT: D 1149 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.7981 (mtt-85) REVERT: D 1189 MET cc_start: 0.7643 (tpp) cc_final: 0.7402 (tpp) REVERT: D 1196 LEU cc_start: 0.8887 (tt) cc_final: 0.8641 (tm) REVERT: D 1197 ASN cc_start: 0.6786 (m-40) cc_final: 0.6390 (m110) REVERT: E 43 ASN cc_start: 0.7914 (t0) cc_final: 0.7435 (t0) REVERT: E 70 GLN cc_start: 0.7323 (mt0) cc_final: 0.7036 (mt0) REVERT: F 160 ASP cc_start: 0.7473 (t70) cc_final: 0.7173 (t0) REVERT: F 273 MET cc_start: 0.8935 (tmm) cc_final: 0.8575 (tmt) REVERT: F 364 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7942 (ptp90) REVERT: F 485 GLU cc_start: 0.8250 (mp0) cc_final: 0.7800 (mp0) REVERT: F 491 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6701 (tm-30) REVERT: F 529 GLU cc_start: 0.8404 (pt0) cc_final: 0.7944 (pm20) REVERT: G 73 ASN cc_start: 0.7134 (m110) cc_final: 0.6218 (t0) REVERT: G 88 GLN cc_start: 0.8443 (mt0) cc_final: 0.8179 (mt0) REVERT: G 95 MET cc_start: 0.8306 (mmt) cc_final: 0.8028 (mmt) REVERT: G 179 MET cc_start: 0.6953 (pmm) cc_final: 0.6747 (pmm) REVERT: G 212 HIS cc_start: 0.6581 (OUTLIER) cc_final: 0.6164 (t-90) REVERT: G 261 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: H 47 MET cc_start: 0.7962 (tmm) cc_final: 0.7573 (tmm) REVERT: H 60 PHE cc_start: 0.7301 (m-80) cc_final: 0.7086 (m-80) REVERT: H 95 MET cc_start: 0.8310 (ttp) cc_final: 0.7407 (tpp) REVERT: H 151 MET cc_start: 0.8135 (ptm) cc_final: 0.7921 (ppp) REVERT: H 253 GLN cc_start: 0.8136 (mp-120) cc_final: 0.7897 (pm20) REVERT: H 261 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6625 (tp30) outliers start: 84 outliers final: 28 residues processed: 377 average time/residue: 0.7112 time to fit residues: 319.6650 Evaluate side-chains 321 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 261 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [146, 12, 48, 57, 400, 44, 424, 280, 397, 405, 391] chunk 146 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 400 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 424 optimal weight: 20.0000 chunk 280 optimal weight: 1.9990 chunk 397 optimal weight: 0.9980 chunk 405 optimal weight: 6.9990 chunk 391 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 894 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 489 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN H 50 HIS H 188 ASN ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094407 restraints weight = 48593.181| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 36734 Z= 0.242 Angle : 0.626 12.817 50133 Z= 0.333 Chirality : 0.046 0.402 5701 Planarity : 0.004 0.050 6101 Dihedral : 15.861 173.915 5864 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.47 % Allowed : 16.27 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4195 helix: 0.25 (0.13), residues: 1709 sheet: -1.35 (0.22), residues: 507 loop : -1.07 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 388 TYR 0.019 0.002 TYR C1281 PHE 0.028 0.002 PHE H 183 TRP 0.020 0.002 TRP D1020 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (36725) covalent geometry : angle 0.62223 / 0.33 (50121) hydrogen bonds : bond 0.04312 / 2.94 ( 1600) hydrogen bonds : angle 4.88610 / 3.30 ( 4469) metal coordination : bond 0.01192 / 0.63 ( 8) metal coordination : angle 4.69502 / 2.42 ( 12) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 299 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7679 (p0) REVERT: A 127 GLN cc_start: 0.8742 (mp10) cc_final: 0.8449 (mp10) REVERT: A 185 TYR cc_start: 0.9191 (p90) cc_final: 0.8941 (p90) REVERT: B 25 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7655 (mtpp) REVERT: B 93 GLN cc_start: 0.7062 (mp10) cc_final: 0.6587 (mp10) REVERT: B 95 LYS cc_start: 0.8457 (mttt) cc_final: 0.8160 (mtpp) REVERT: B 145 LYS cc_start: 0.8168 (tttt) cc_final: 0.7846 (ttpp) REVERT: B 147 GLN cc_start: 0.8057 (tt0) cc_final: 0.7819 (tt0) REVERT: B 174 ASP cc_start: 0.8233 (m-30) cc_final: 0.7815 (m-30) REVERT: B 183 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 186 ASN cc_start: 0.8229 (m-40) cc_final: 0.7915 (m110) REVERT: B 200 LYS cc_start: 0.8267 (tttt) cc_final: 0.8012 (ttpp) REVERT: C 36 GLN cc_start: 0.7683 (tp40) cc_final: 0.7260 (mm-40) REVERT: C 127 ILE cc_start: 0.8456 (pt) cc_final: 0.8176 (pp) REVERT: C 191 LYS cc_start: 0.8353 (mttp) cc_final: 0.7985 (mtmp) REVERT: C 200 ARG cc_start: 0.8604 (mmm160) cc_final: 0.8250 (mmp-170) REVERT: C 315 MET cc_start: 0.8091 (mtp) cc_final: 0.7744 (mtp) REVERT: C 337 PHE cc_start: 0.8160 (t80) cc_final: 0.7728 (t80) REVERT: C 515 MET cc_start: 0.9266 (ttp) cc_final: 0.8997 (ttm) REVERT: C 681 MET cc_start: 0.7861 (mtt) cc_final: 0.7651 (mtt) REVERT: C 742 TYR cc_start: 0.6856 (m-80) cc_final: 0.6631 (m-80) REVERT: C 778 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7294 (mm-30) REVERT: C 844 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7584 (ptmm) REVERT: C 859 GLU cc_start: 0.7712 (pp20) cc_final: 0.6850 (tm-30) REVERT: C 951 MET cc_start: 0.8309 (ttm) cc_final: 0.7890 (ttp) REVERT: C 1020 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 1022 LYS cc_start: 0.7454 (mtpt) cc_final: 0.6990 (mtpt) REVERT: C 1024 GLU cc_start: 0.7415 (pp20) cc_final: 0.7155 (pp20) REVERT: C 1034 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7614 (ttp-110) REVERT: C 1131 MET cc_start: 0.8200 (mtt) cc_final: 0.7878 (mtm) REVERT: C 1154 ASP cc_start: 0.7514 (t70) cc_final: 0.7107 (t0) REVERT: C 1178 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8561 (mtmm) REVERT: C 1180 MET cc_start: 0.8798 (ttp) cc_final: 0.8497 (ttt) REVERT: C 1230 MET cc_start: 0.9352 (ttp) cc_final: 0.9049 (ttp) REVERT: D 18 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: D 29 MET cc_start: 0.8106 (tpp) cc_final: 0.7746 (ttp) REVERT: D 69 GLU cc_start: 0.8913 (tt0) cc_final: 0.8709 (tt0) REVERT: D 137 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6843 (mtp-110) REVERT: D 147 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7761 (pp) REVERT: D 151 MET cc_start: 0.8116 (mtp) cc_final: 0.7864 (mpt) REVERT: D 180 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8584 (ttp) REVERT: D 237 MET cc_start: 0.9462 (mtm) cc_final: 0.8825 (mtp) REVERT: D 321 LYS cc_start: 0.8661 (mmtm) cc_final: 0.7381 (ttpm) REVERT: D 484 MET cc_start: 0.9414 (mtp) cc_final: 0.9118 (mtm) REVERT: D 525 MET cc_start: 0.9061 (ptm) cc_final: 0.8809 (ptm) REVERT: D 725 MET cc_start: 0.8631 (mtt) cc_final: 0.8305 (mtt) REVERT: D 785 ASP cc_start: 0.7870 (t0) cc_final: 0.7618 (t70) REVERT: D 992 LYS cc_start: 0.7450 (mptt) cc_final: 0.7212 (mptt) REVERT: D 1025 MET cc_start: 0.6997 (tpt) cc_final: 0.6609 (mmm) REVERT: D 1040 MET cc_start: 0.1006 (tmm) cc_final: 0.0564 (tmm) REVERT: D 1143 ASP cc_start: 0.8106 (p0) cc_final: 0.7732 (p0) REVERT: D 1149 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8147 (mtt-85) REVERT: D 1189 MET cc_start: 0.8035 (tpp) cc_final: 0.7747 (tpp) REVERT: D 1196 LEU cc_start: 0.8874 (tt) cc_final: 0.8598 (tm) REVERT: D 1197 ASN cc_start: 0.6785 (m-40) cc_final: 0.6431 (m110) REVERT: E 43 ASN cc_start: 0.7989 (t0) cc_final: 0.7493 (t0) REVERT: F 160 ASP cc_start: 0.7508 (t70) cc_final: 0.7256 (t0) REVERT: F 276 MET cc_start: 0.8202 (pp-130) cc_final: 0.7997 (pp-130) REVERT: F 294 GLN cc_start: 0.3374 (OUTLIER) cc_final: 0.2329 (pt0) REVERT: F 364 ARG cc_start: 0.8205 (mtp-110) cc_final: 0.7930 (ptp90) REVERT: F 485 GLU cc_start: 0.8260 (mp0) cc_final: 0.8044 (mp0) REVERT: F 491 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6695 (tm-30) REVERT: F 529 GLU cc_start: 0.8332 (pt0) cc_final: 0.7977 (pm20) REVERT: F 567 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7355 (mtp) REVERT: G 73 ASN cc_start: 0.7102 (m110) cc_final: 0.6124 (t0) REVERT: G 88 GLN cc_start: 0.8404 (mt0) cc_final: 0.8176 (mt0) REVERT: G 95 MET cc_start: 0.8290 (mmt) cc_final: 0.7976 (mmt) REVERT: G 212 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.6069 (t-90) REVERT: G 261 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: H 47 MET cc_start: 0.8057 (tmm) cc_final: 0.7723 (tmm) REVERT: H 105 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7598 (m-70) REVERT: H 253 GLN cc_start: 0.8313 (mp-120) cc_final: 0.7981 (pm20) REVERT: H 261 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6702 (tp30) outliers start: 90 outliers final: 44 residues processed: 361 average time/residue: 0.7044 time to fit residues: 303.4952 Evaluate side-chains 341 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain F residue 507 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 261 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [161, 94, 313, 23, 133, 315, 312, 16, 152, 104, 24] chunk 161 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 313 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 315 optimal weight: 0.8980 chunk 312 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN C 69 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 894 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN E 70 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN H 50 HIS H 193 ASN ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.155439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098369 restraints weight = 48685.262| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.25 r_work: 0.3210 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36734 Z= 0.129 Angle : 0.554 11.565 50133 Z= 0.298 Chirality : 0.043 0.383 5701 Planarity : 0.004 0.048 6101 Dihedral : 15.723 175.328 5864 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.50 % Allowed : 16.74 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4195 helix: 0.59 (0.13), residues: 1707 sheet: -1.23 (0.22), residues: 485 loop : -0.93 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 3 TYR 0.018 0.001 TYR D 679 PHE 0.023 0.001 PHE F 256 TRP 0.013 0.001 TRP D1020 HIS 0.013 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (36725) covalent geometry : angle 0.55075 / 0.30 (50121) hydrogen bonds : bond 0.03798 / 2.59 ( 1600) hydrogen bonds : angle 4.68729 / 3.16 ( 4469) metal coordination : bond 0.00697 / 0.37 ( 8) metal coordination : angle 3.68558 / 1.88 ( 12) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 307 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8784 (mttp) cc_final: 0.8507 (mmtt) REVERT: A 127 GLN cc_start: 0.8730 (mp10) cc_final: 0.8420 (mp10) REVERT: A 185 TYR cc_start: 0.9166 (p90) cc_final: 0.8825 (p90) REVERT: B 93 GLN cc_start: 0.7083 (mp10) cc_final: 0.6567 (mp10) REVERT: B 95 LYS cc_start: 0.8421 (mttt) cc_final: 0.8131 (mtpp) REVERT: B 145 LYS cc_start: 0.8107 (tttt) cc_final: 0.7789 (ttpp) REVERT: B 174 ASP cc_start: 0.8261 (m-30) cc_final: 0.8046 (m-30) REVERT: B 183 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8591 (tp) REVERT: B 186 ASN cc_start: 0.8163 (m-40) cc_final: 0.7859 (m110) REVERT: B 200 LYS cc_start: 0.8225 (tttt) cc_final: 0.8004 (ttpp) REVERT: C 36 GLN cc_start: 0.7562 (tp40) cc_final: 0.7254 (mm-40) REVERT: C 127 ILE cc_start: 0.8312 (pt) cc_final: 0.8056 (pp) REVERT: C 191 LYS cc_start: 0.8295 (mttp) cc_final: 0.7923 (mtmp) REVERT: C 200 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8147 (mmp-170) REVERT: C 315 MET cc_start: 0.8082 (mtp) cc_final: 0.7732 (mtp) REVERT: C 337 PHE cc_start: 0.8207 (t80) cc_final: 0.7794 (t80) REVERT: C 515 MET cc_start: 0.9201 (ttp) cc_final: 0.8921 (ttm) REVERT: C 628 HIS cc_start: 0.7400 (m170) cc_final: 0.7167 (m-70) REVERT: C 641 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: C 742 TYR cc_start: 0.6830 (m-80) cc_final: 0.6603 (m-80) REVERT: C 778 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7299 (mm-30) REVERT: C 844 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7937 (mtmm) REVERT: C 859 GLU cc_start: 0.7683 (pp20) cc_final: 0.6823 (tm-30) REVERT: C 951 MET cc_start: 0.8088 (ttm) cc_final: 0.7670 (ttp) REVERT: C 1020 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 1024 GLU cc_start: 0.7507 (pp20) cc_final: 0.7266 (pp20) REVERT: C 1034 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7521 (ttp-110) REVERT: C 1131 MET cc_start: 0.7996 (mtt) cc_final: 0.7721 (mtm) REVERT: C 1154 ASP cc_start: 0.7521 (t70) cc_final: 0.7104 (t0) REVERT: C 1178 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8543 (mtmm) REVERT: C 1180 MET cc_start: 0.8848 (ttp) cc_final: 0.8623 (ttt) REVERT: C 1230 MET cc_start: 0.9350 (ttp) cc_final: 0.9036 (ttp) REVERT: D 18 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: D 29 MET cc_start: 0.8001 (tpp) cc_final: 0.7668 (ttm) REVERT: D 69 GLU cc_start: 0.8764 (tt0) cc_final: 0.8541 (tt0) REVERT: D 80 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6243 (p90) REVERT: D 137 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6753 (mtp-110) REVERT: D 147 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7620 (pp) REVERT: D 237 MET cc_start: 0.9425 (mtm) cc_final: 0.8882 (mtp) REVERT: D 321 LYS cc_start: 0.8619 (mmtm) cc_final: 0.7349 (ttpm) REVERT: D 484 MET cc_start: 0.9376 (mtp) cc_final: 0.9063 (mtm) REVERT: D 525 MET cc_start: 0.8961 (ptm) cc_final: 0.8705 (ptm) REVERT: D 720 ASN cc_start: 0.8587 (t0) cc_final: 0.8376 (t0) REVERT: D 725 MET cc_start: 0.8545 (mtt) cc_final: 0.8245 (mtt) REVERT: D 992 LYS cc_start: 0.7405 (mptt) cc_final: 0.7148 (mptt) REVERT: D 1025 MET cc_start: 0.6945 (tpt) cc_final: 0.6516 (mmm) REVERT: D 1040 MET cc_start: 0.0976 (tmm) cc_final: 0.0527 (tmm) REVERT: D 1143 ASP cc_start: 0.7825 (p0) cc_final: 0.7430 (p0) REVERT: D 1149 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8013 (mtt-85) REVERT: D 1189 MET cc_start: 0.8070 (tpp) cc_final: 0.7752 (tpp) REVERT: D 1195 GLN cc_start: 0.8506 (pm20) cc_final: 0.8092 (pt0) REVERT: D 1196 LEU cc_start: 0.8875 (tt) cc_final: 0.8628 (tm) REVERT: D 1197 ASN cc_start: 0.6797 (m-40) cc_final: 0.6432 (m110) REVERT: E 43 ASN cc_start: 0.7937 (t0) cc_final: 0.7426 (t0) REVERT: F 105 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8101 (ptm) REVERT: F 160 ASP cc_start: 0.7526 (t70) cc_final: 0.7267 (t0) REVERT: F 379 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8198 (ttp) REVERT: F 485 GLU cc_start: 0.8254 (mp0) cc_final: 0.7997 (mp0) REVERT: F 491 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6636 (tm-30) REVERT: F 529 GLU cc_start: 0.8389 (pt0) cc_final: 0.7945 (pm20) REVERT: F 596 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7692 (mtm110) REVERT: G 56 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5605 (ttm-80) REVERT: G 73 ASN cc_start: 0.7073 (m110) cc_final: 0.6104 (t0) REVERT: G 88 GLN cc_start: 0.8474 (mt0) cc_final: 0.8251 (mt0) REVERT: G 95 MET cc_start: 0.8418 (mmt) cc_final: 0.8096 (mmt) REVERT: G 212 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.6054 (t-90) REVERT: G 261 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: H 47 MET cc_start: 0.8040 (tmm) cc_final: 0.7760 (tmm) REVERT: H 60 PHE cc_start: 0.7188 (m-80) cc_final: 0.6948 (m-80) REVERT: H 95 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7405 (tpp) REVERT: H 112 MET cc_start: 0.4351 (OUTLIER) cc_final: 0.4122 (mpt) REVERT: H 151 MET cc_start: 0.8251 (ptm) cc_final: 0.7912 (ppp) REVERT: H 253 GLN cc_start: 0.8299 (mp-120) cc_final: 0.7981 (pm20) outliers start: 91 outliers final: 41 residues processed: 369 average time/residue: 0.6938 time to fit residues: 307.3418 Evaluate side-chains 342 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 827 GLU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 56 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 212 HIS Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 246 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [157, 256, 84, 352, 26, 140, 335, 75, 236, 190, 131] chunk 157 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 352 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 137 ASN B 75 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN D 712 GLN E 70 GLN E 72 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093431 restraints weight = 46703.118| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.24 r_work: 0.3097 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36734 Z= 0.197 Angle : 0.589 12.677 50133 Z= 0.312 Chirality : 0.045 0.394 5701 Planarity : 0.004 0.048 6101 Dihedral : 15.696 174.843 5864 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.72 % Allowed : 17.53 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4195 helix: 0.64 (0.13), residues: 1710 sheet: -1.19 (0.22), residues: 490 loop : -0.86 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 3 TYR 0.018 0.001 TYR F 148 PHE 0.025 0.002 PHE F 256 TRP 0.014 0.001 TRP D1020 HIS 0.010 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (36725) covalent geometry : angle 0.58653 / 0.31 (50121) hydrogen bonds : bond 0.03935 / 2.70 ( 1600) hydrogen bonds : angle 4.64541 / 3.13 ( 4469) metal coordination : bond 0.00893 / 0.47 ( 8) metal coordination : angle 3.51102 / 1.79 ( 12) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 294 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8606 (mp10) cc_final: 0.8256 (mp10) REVERT: A 185 TYR cc_start: 0.9122 (p90) cc_final: 0.8767 (p90) REVERT: B 25 LYS cc_start: 0.7405 (mtpt) cc_final: 0.7204 (mtpp) REVERT: B 86 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8047 (ttpt) REVERT: B 93 GLN cc_start: 0.7024 (mp10) cc_final: 0.6557 (mp10) REVERT: B 95 LYS cc_start: 0.8200 (mttt) cc_final: 0.7851 (mtpp) REVERT: B 145 LYS cc_start: 0.7856 (tttt) cc_final: 0.7541 (ttpp) REVERT: B 174 ASP cc_start: 0.8124 (m-30) cc_final: 0.7550 (m-30) REVERT: B 183 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 186 ASN cc_start: 0.7971 (m-40) cc_final: 0.7680 (m110) REVERT: B 200 LYS cc_start: 0.7896 (tttt) cc_final: 0.7650 (ttpp) REVERT: C 36 GLN cc_start: 0.7369 (tp40) cc_final: 0.7043 (mm-40) REVERT: C 127 ILE cc_start: 0.8249 (pt) cc_final: 0.7955 (pp) REVERT: C 191 LYS cc_start: 0.8186 (mttp) cc_final: 0.7802 (mtmp) REVERT: C 200 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8048 (mmp-170) REVERT: C 315 MET cc_start: 0.7966 (mtp) cc_final: 0.7597 (mtp) REVERT: C 337 PHE cc_start: 0.8095 (t80) cc_final: 0.7657 (t80) REVERT: C 515 MET cc_start: 0.9218 (ttp) cc_final: 0.8916 (ttm) REVERT: C 641 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: C 778 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7034 (mm-30) REVERT: C 844 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7580 (ptmm) REVERT: C 859 GLU cc_start: 0.7577 (pp20) cc_final: 0.6657 (tm-30) REVERT: C 951 MET cc_start: 0.8120 (ttm) cc_final: 0.7719 (ttp) REVERT: C 1020 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7881 (tm-30) REVERT: C 1131 MET cc_start: 0.7607 (mtt) cc_final: 0.7306 (mtm) REVERT: C 1154 ASP cc_start: 0.7441 (t70) cc_final: 0.7007 (t0) REVERT: C 1178 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8430 (mtmm) REVERT: C 1180 MET cc_start: 0.8682 (ttp) cc_final: 0.8374 (ttt) REVERT: C 1230 MET cc_start: 0.9321 (ttp) cc_final: 0.8998 (ttp) REVERT: D 29 MET cc_start: 0.7835 (tpp) cc_final: 0.7536 (ttm) REVERT: D 80 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.6054 (p90) REVERT: D 137 ARG cc_start: 0.6990 (mtp180) cc_final: 0.6528 (mtp-110) REVERT: D 147 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7498 (pp) REVERT: D 237 MET cc_start: 0.9391 (mtm) cc_final: 0.8697 (mtp) REVERT: D 321 LYS cc_start: 0.8541 (mmtm) cc_final: 0.7188 (ttpm) REVERT: D 484 MET cc_start: 0.9371 (mtp) cc_final: 0.9009 (mtm) REVERT: D 485 MET cc_start: 0.8525 (tpp) cc_final: 0.8014 (tpp) REVERT: D 677 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: D 720 ASN cc_start: 0.8463 (t0) cc_final: 0.8120 (t0) REVERT: D 725 MET cc_start: 0.8139 (mtt) cc_final: 0.7820 (mtt) REVERT: D 785 ASP cc_start: 0.7590 (t0) cc_final: 0.7371 (t70) REVERT: D 832 LYS cc_start: 0.7522 (mmtt) cc_final: 0.7258 (mmmt) REVERT: D 992 LYS cc_start: 0.7304 (mptt) cc_final: 0.7013 (mptt) REVERT: D 1025 MET cc_start: 0.6976 (tpt) cc_final: 0.6303 (mmm) REVERT: D 1040 MET cc_start: 0.1285 (tmm) cc_final: 0.0838 (tmm) REVERT: D 1046 ILE cc_start: 0.4514 (OUTLIER) cc_final: 0.4247 (pp) REVERT: D 1149 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8041 (mtt-85) REVERT: D 1189 MET cc_start: 0.8094 (tpp) cc_final: 0.7832 (tpp) REVERT: D 1195 GLN cc_start: 0.8434 (pm20) cc_final: 0.8160 (pt0) REVERT: D 1196 LEU cc_start: 0.8814 (tt) cc_final: 0.8538 (tm) REVERT: D 1197 ASN cc_start: 0.6565 (m-40) cc_final: 0.6226 (m110) REVERT: E 43 ASN cc_start: 0.8151 (t0) cc_final: 0.7825 (t0) REVERT: F 102 MET cc_start: 0.8544 (mmm) cc_final: 0.8234 (mtp) REVERT: F 105 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7891 (ptm) REVERT: F 160 ASP cc_start: 0.7434 (t70) cc_final: 0.7201 (t0) REVERT: F 365 MET cc_start: 0.8521 (ttm) cc_final: 0.8270 (ttm) REVERT: F 379 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8043 (ttp) REVERT: F 485 GLU cc_start: 0.8182 (mp0) cc_final: 0.7626 (mp0) REVERT: F 491 GLU cc_start: 0.6514 (tm-30) cc_final: 0.6290 (tm-30) REVERT: F 529 GLU cc_start: 0.8357 (pt0) cc_final: 0.7888 (pm20) REVERT: F 596 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7670 (mtm110) REVERT: G 73 ASN cc_start: 0.7496 (m110) cc_final: 0.6443 (t0) REVERT: G 88 GLN cc_start: 0.8358 (mt0) cc_final: 0.8109 (mt0) REVERT: G 95 MET cc_start: 0.8371 (mmt) cc_final: 0.8099 (mmt) REVERT: G 258 TRP cc_start: 0.7045 (m-10) cc_final: 0.6546 (m-10) REVERT: G 261 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: H 47 MET cc_start: 0.7909 (tmm) cc_final: 0.7606 (tmm) REVERT: H 95 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7408 (tpp) REVERT: H 112 MET cc_start: 0.4367 (OUTLIER) cc_final: 0.4103 (mpt) REVERT: H 253 GLN cc_start: 0.8351 (mp-120) cc_final: 0.8035 (pm20) outliers start: 99 outliers final: 54 residues processed: 369 average time/residue: 0.6842 time to fit residues: 302.1444 Evaluate side-chains 353 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 827 GLU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 246 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [266, 186, 258, 3, 256, 156, 351, 39, 345, 162, 154] chunk 266 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 351 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 345 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN B 127 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS E 70 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN F 446 GLN H 50 HIS ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094882 restraints weight = 46985.869| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.24 r_work: 0.3120 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36734 Z= 0.141 Angle : 0.555 11.926 50133 Z= 0.295 Chirality : 0.043 0.384 5701 Planarity : 0.004 0.049 6101 Dihedral : 15.619 175.672 5864 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.77 % Allowed : 18.16 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4195 helix: 0.86 (0.13), residues: 1710 sheet: -1.09 (0.22), residues: 491 loop : -0.75 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 3 TYR 0.021 0.001 TYR F 148 PHE 0.026 0.001 PHE H 183 TRP 0.020 0.001 TRP D1020 HIS 0.010 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (36725) covalent geometry : angle 0.55321 / 0.30 (50121) hydrogen bonds : bond 0.03650 / 2.50 ( 1600) hydrogen bonds : angle 4.53704 / 3.05 ( 4469) metal coordination : bond 0.00669 / 0.36 ( 8) metal coordination : angle 2.92612 / 1.50 ( 12) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 302 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8632 (mttp) cc_final: 0.8294 (mmtt) REVERT: A 127 GLN cc_start: 0.8604 (mp10) cc_final: 0.8253 (mp10) REVERT: A 185 TYR cc_start: 0.9118 (p90) cc_final: 0.8759 (p90) REVERT: B 86 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8045 (ttpt) REVERT: B 93 GLN cc_start: 0.6831 (mp10) cc_final: 0.6364 (mp10) REVERT: B 95 LYS cc_start: 0.8137 (mttt) cc_final: 0.7801 (mtpp) REVERT: B 145 LYS cc_start: 0.7800 (tttt) cc_final: 0.7470 (ttpp) REVERT: B 174 ASP cc_start: 0.8054 (m-30) cc_final: 0.7605 (m-30) REVERT: B 183 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 186 ASN cc_start: 0.7971 (m-40) cc_final: 0.7679 (m110) REVERT: B 200 LYS cc_start: 0.7865 (tttt) cc_final: 0.7652 (ttpp) REVERT: C 36 GLN cc_start: 0.7317 (tp40) cc_final: 0.7031 (mm-40) REVERT: C 127 ILE cc_start: 0.8208 (pt) cc_final: 0.7920 (pp) REVERT: C 191 LYS cc_start: 0.8147 (mttp) cc_final: 0.7781 (mtmp) REVERT: C 200 ARG cc_start: 0.8386 (mmm160) cc_final: 0.8179 (mmp-170) REVERT: C 315 MET cc_start: 0.7956 (mtp) cc_final: 0.7582 (mtp) REVERT: C 337 PHE cc_start: 0.8170 (t80) cc_final: 0.7744 (t80) REVERT: C 515 MET cc_start: 0.9177 (ttp) cc_final: 0.8872 (ttm) REVERT: C 641 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: C 778 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7080 (mm-30) REVERT: C 844 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7902 (mtmm) REVERT: C 859 GLU cc_start: 0.7582 (pp20) cc_final: 0.6656 (tm-30) REVERT: C 951 MET cc_start: 0.7908 (ttm) cc_final: 0.7517 (ttp) REVERT: C 955 GLN cc_start: 0.7429 (tp40) cc_final: 0.6890 (tm-30) REVERT: C 1020 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7457 (tm-30) REVERT: C 1024 GLU cc_start: 0.7497 (pp20) cc_final: 0.6096 (pt0) REVERT: C 1025 PHE cc_start: 0.7752 (t80) cc_final: 0.7139 (t80) REVERT: C 1131 MET cc_start: 0.7536 (mtt) cc_final: 0.7302 (mtm) REVERT: C 1154 ASP cc_start: 0.7438 (t70) cc_final: 0.7001 (t0) REVERT: C 1178 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8060 (mttp) REVERT: C 1180 MET cc_start: 0.8738 (ttp) cc_final: 0.8475 (ttt) REVERT: C 1230 MET cc_start: 0.9327 (ttp) cc_final: 0.8987 (ttp) REVERT: D 29 MET cc_start: 0.7785 (tpp) cc_final: 0.7522 (ttm) REVERT: D 137 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6510 (mtp-110) REVERT: D 147 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7335 (pp) REVERT: D 237 MET cc_start: 0.9379 (mtm) cc_final: 0.8814 (mtp) REVERT: D 321 LYS cc_start: 0.8537 (mmtm) cc_final: 0.7186 (ttpm) REVERT: D 388 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7790 (mtm-85) REVERT: D 484 MET cc_start: 0.9330 (mtp) cc_final: 0.8975 (mtm) REVERT: D 677 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: D 720 ASN cc_start: 0.8480 (t0) cc_final: 0.8172 (t0) REVERT: D 725 MET cc_start: 0.8105 (mtt) cc_final: 0.7809 (mtt) REVERT: D 992 LYS cc_start: 0.7253 (mptt) cc_final: 0.6953 (mptt) REVERT: D 1025 MET cc_start: 0.7002 (tpt) cc_final: 0.6285 (mmm) REVERT: D 1040 MET cc_start: 0.1258 (tmm) cc_final: 0.0820 (tmm) REVERT: D 1046 ILE cc_start: 0.4475 (OUTLIER) cc_final: 0.4211 (pp) REVERT: D 1149 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7949 (mtt-85) REVERT: D 1189 MET cc_start: 0.8095 (tpp) cc_final: 0.7811 (tpp) REVERT: D 1195 GLN cc_start: 0.8452 (pm20) cc_final: 0.8164 (pt0) REVERT: D 1196 LEU cc_start: 0.8859 (tt) cc_final: 0.8605 (tm) REVERT: D 1197 ASN cc_start: 0.6563 (m-40) cc_final: 0.6197 (m110) REVERT: E 43 ASN cc_start: 0.8132 (t0) cc_final: 0.7808 (t0) REVERT: E 71 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: F 102 MET cc_start: 0.8549 (mmm) cc_final: 0.8229 (mtp) REVERT: F 105 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7891 (ptm) REVERT: F 294 GLN cc_start: 0.3428 (OUTLIER) cc_final: 0.2755 (pt0) REVERT: F 365 MET cc_start: 0.8354 (ttm) cc_final: 0.8135 (ttm) REVERT: F 446 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: F 485 GLU cc_start: 0.8170 (mp0) cc_final: 0.7608 (mp0) REVERT: F 491 GLU cc_start: 0.6497 (tm-30) cc_final: 0.6249 (tm-30) REVERT: F 529 GLU cc_start: 0.8346 (pt0) cc_final: 0.7876 (pm20) REVERT: F 596 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7654 (mtm110) REVERT: G 73 ASN cc_start: 0.7468 (m110) cc_final: 0.6385 (t0) REVERT: G 88 GLN cc_start: 0.8420 (mt0) cc_final: 0.8199 (mt0) REVERT: G 95 MET cc_start: 0.8384 (mmt) cc_final: 0.8110 (mmt) REVERT: G 261 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: H 47 MET cc_start: 0.7892 (tmm) cc_final: 0.7602 (tmm) REVERT: H 60 PHE cc_start: 0.7117 (m-80) cc_final: 0.6884 (m-80) REVERT: H 95 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: H 105 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7717 (m-70) REVERT: H 112 MET cc_start: 0.4208 (OUTLIER) cc_final: 0.3942 (mpt) REVERT: H 151 MET cc_start: 0.8178 (ptm) cc_final: 0.7870 (ppp) REVERT: H 253 GLN cc_start: 0.8348 (mp-120) cc_final: 0.8041 (pm20) outliers start: 101 outliers final: 51 residues processed: 379 average time/residue: 0.6932 time to fit residues: 314.6422 Evaluate side-chains 349 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 827 GLU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 246 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [425, 299, 391, 99, 291, 394, 376, 404, 277, 286, 86] chunk 425 optimal weight: 10.0000 chunk 299 optimal weight: 0.9990 chunk 391 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 291 optimal weight: 30.0000 chunk 394 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 404 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS D 365 GLN E 70 GLN E 72 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.092192 restraints weight = 46539.881| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.21 r_work: 0.3079 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 36734 Z= 0.284 Angle : 0.639 13.591 50133 Z= 0.335 Chirality : 0.047 0.396 5701 Planarity : 0.004 0.056 6101 Dihedral : 15.702 174.856 5864 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.69 % Allowed : 18.74 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4195 helix: 0.70 (0.13), residues: 1715 sheet: -1.16 (0.22), residues: 493 loop : -0.79 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 3 TYR 0.020 0.002 TYR F 148 PHE 0.025 0.002 PHE F 256 TRP 0.022 0.002 TRP D1020 HIS 0.012 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.28 (36725) covalent geometry : angle 0.63694 / 0.34 (50121) hydrogen bonds : bond 0.04133 / 2.84 ( 1600) hydrogen bonds : angle 4.64618 / 3.13 ( 4469) metal coordination : bond 0.01114 / 0.59 ( 8) metal coordination : angle 3.38644 / 1.73 ( 12) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 286 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7560 (p0) REVERT: A 127 GLN cc_start: 0.8549 (mp10) cc_final: 0.8238 (mp10) REVERT: A 147 GLN cc_start: 0.8381 (mt0) cc_final: 0.8148 (mt0) REVERT: A 185 TYR cc_start: 0.9146 (p90) cc_final: 0.8856 (p90) REVERT: B 86 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8260 (ttpp) REVERT: B 93 GLN cc_start: 0.6883 (mp10) cc_final: 0.6402 (mp10) REVERT: B 95 LYS cc_start: 0.8133 (mttt) cc_final: 0.7775 (mtpp) REVERT: B 145 LYS cc_start: 0.7897 (tttt) cc_final: 0.7560 (ttpp) REVERT: B 174 ASP cc_start: 0.8045 (m-30) cc_final: 0.7579 (m-30) REVERT: B 183 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 186 ASN cc_start: 0.7982 (m-40) cc_final: 0.7693 (m110) REVERT: B 200 LYS cc_start: 0.7874 (tttt) cc_final: 0.7599 (ttpp) REVERT: C 36 GLN cc_start: 0.7418 (tp40) cc_final: 0.7072 (mm-40) REVERT: C 124 MET cc_start: 0.8887 (ptp) cc_final: 0.8685 (ptm) REVERT: C 127 ILE cc_start: 0.8289 (pt) cc_final: 0.8009 (pp) REVERT: C 191 LYS cc_start: 0.8216 (mttp) cc_final: 0.7838 (mtmp) REVERT: C 200 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8031 (mmp-170) REVERT: C 315 MET cc_start: 0.8008 (mtp) cc_final: 0.7631 (mtp) REVERT: C 515 MET cc_start: 0.9231 (ttp) cc_final: 0.8926 (ttm) REVERT: C 641 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: C 778 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7020 (mm-30) REVERT: C 844 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7628 (ptmm) REVERT: C 859 GLU cc_start: 0.7666 (pp20) cc_final: 0.6715 (tm-30) REVERT: C 951 MET cc_start: 0.7885 (ttm) cc_final: 0.7478 (ttp) REVERT: C 955 GLN cc_start: 0.7413 (tp40) cc_final: 0.6963 (tm-30) REVERT: C 1020 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7820 (tm-30) REVERT: C 1024 GLU cc_start: 0.7607 (pp20) cc_final: 0.7333 (pp20) REVERT: C 1131 MET cc_start: 0.7576 (mtt) cc_final: 0.7271 (mtm) REVERT: C 1154 ASP cc_start: 0.7464 (t70) cc_final: 0.7049 (t0) REVERT: C 1178 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8416 (mtmm) REVERT: C 1180 MET cc_start: 0.8723 (ttp) cc_final: 0.8465 (ttt) REVERT: C 1230 MET cc_start: 0.9321 (ttp) cc_final: 0.9005 (ttp) REVERT: D 29 MET cc_start: 0.7861 (tpp) cc_final: 0.7567 (ttm) REVERT: D 80 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6072 (p90) REVERT: D 137 ARG cc_start: 0.7022 (mtp180) cc_final: 0.6536 (mtp-110) REVERT: D 147 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7448 (pp) REVERT: D 237 MET cc_start: 0.9407 (mtm) cc_final: 0.8682 (mtp) REVERT: D 388 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7921 (mtm-85) REVERT: D 484 MET cc_start: 0.9387 (mtp) cc_final: 0.9031 (mtm) REVERT: D 603 LYS cc_start: 0.7464 (tttt) cc_final: 0.6943 (tmmt) REVERT: D 677 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: D 725 MET cc_start: 0.8160 (mtt) cc_final: 0.7844 (mtt) REVERT: D 785 ASP cc_start: 0.7569 (t0) cc_final: 0.7343 (t70) REVERT: D 832 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7176 (mmmt) REVERT: D 992 LYS cc_start: 0.7302 (mptt) cc_final: 0.6983 (mptt) REVERT: D 1025 MET cc_start: 0.7010 (tpt) cc_final: 0.6243 (mmm) REVERT: D 1040 MET cc_start: 0.1344 (tmm) cc_final: 0.0879 (tmm) REVERT: D 1046 ILE cc_start: 0.4443 (OUTLIER) cc_final: 0.4182 (pp) REVERT: D 1149 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8127 (mtt-85) REVERT: D 1189 MET cc_start: 0.8106 (tpp) cc_final: 0.7838 (tpp) REVERT: D 1195 GLN cc_start: 0.8467 (pm20) cc_final: 0.8155 (pt0) REVERT: D 1197 ASN cc_start: 0.6569 (m-40) cc_final: 0.6337 (m110) REVERT: E 43 ASN cc_start: 0.8181 (t0) cc_final: 0.7858 (t0) REVERT: F 102 MET cc_start: 0.8560 (mmm) cc_final: 0.8305 (mtp) REVERT: F 105 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7492 (ptt) REVERT: F 365 MET cc_start: 0.8357 (ttm) cc_final: 0.8145 (ttm) REVERT: F 485 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: F 491 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6313 (tm-30) REVERT: F 529 GLU cc_start: 0.8360 (pt0) cc_final: 0.7826 (pm20) REVERT: F 596 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7713 (mtm110) REVERT: G 73 ASN cc_start: 0.7492 (m110) cc_final: 0.6407 (t0) REVERT: G 88 GLN cc_start: 0.8309 (mt0) cc_final: 0.8056 (mt0) REVERT: G 95 MET cc_start: 0.8389 (mmt) cc_final: 0.8128 (mmt) REVERT: G 258 TRP cc_start: 0.7146 (m-10) cc_final: 0.6644 (m-10) REVERT: G 261 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7537 (pp20) REVERT: H 47 MET cc_start: 0.7921 (tmm) cc_final: 0.7632 (tmm) REVERT: H 60 PHE cc_start: 0.7220 (m-80) cc_final: 0.6964 (m-80) REVERT: H 95 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7860 (tpp) REVERT: H 109 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: H 112 MET cc_start: 0.4853 (OUTLIER) cc_final: 0.4604 (mpt) REVERT: H 151 MET cc_start: 0.8181 (ptm) cc_final: 0.7870 (ppp) REVERT: H 253 GLN cc_start: 0.8356 (mp-120) cc_final: 0.8048 (pm20) outliers start: 98 outliers final: 61 residues processed: 357 average time/residue: 0.7110 time to fit residues: 305.9144 Evaluate side-chains 351 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 275 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 911 SER Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 827 GLU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 246 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [360, 143, 353, 185, 183, 125, 162, 170, 255, 310, 206] chunk 360 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 353 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 chunk 310 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS D 365 GLN E 70 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS F 342 GLN F 446 GLN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.153432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095262 restraints weight = 46782.908| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.25 r_work: 0.3128 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36734 Z= 0.128 Angle : 0.563 11.441 50133 Z= 0.299 Chirality : 0.043 0.377 5701 Planarity : 0.004 0.050 6101 Dihedral : 15.605 176.317 5864 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.22 % Allowed : 19.48 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4195 helix: 0.96 (0.13), residues: 1707 sheet: -1.05 (0.23), residues: 474 loop : -0.70 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 3 TYR 0.018 0.001 TYR D 679 PHE 0.033 0.001 PHE C 337 TRP 0.026 0.001 TRP D1020 HIS 0.012 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (36725) covalent geometry : angle 0.56202 / 0.30 (50121) hydrogen bonds : bond 0.03570 / 2.44 ( 1600) hydrogen bonds : angle 4.50051 / 3.03 ( 4469) metal coordination : bond 0.00581 / 0.31 ( 8) metal coordination : angle 2.67936 / 1.37 ( 12) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 1.252 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: A 10 LYS cc_start: 0.8640 (mttp) cc_final: 0.8301 (mmtt) REVERT: A 127 GLN cc_start: 0.8544 (mp10) cc_final: 0.8237 (mp10) REVERT: A 147 GLN cc_start: 0.8299 (mt0) cc_final: 0.8064 (mt0) REVERT: A 185 TYR cc_start: 0.9140 (p90) cc_final: 0.8844 (p90) REVERT: B 93 GLN cc_start: 0.6920 (mp10) cc_final: 0.6416 (mp10) REVERT: B 95 LYS cc_start: 0.8073 (mttt) cc_final: 0.7722 (mtpp) REVERT: B 145 LYS cc_start: 0.7800 (tttt) cc_final: 0.7465 (ttpp) REVERT: B 174 ASP cc_start: 0.8032 (m-30) cc_final: 0.7607 (m-30) REVERT: B 183 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 186 ASN cc_start: 0.7915 (m-40) cc_final: 0.7617 (m110) REVERT: B 200 LYS cc_start: 0.7878 (tttt) cc_final: 0.7505 (tttp) REVERT: C 36 GLN cc_start: 0.7309 (tp40) cc_final: 0.7016 (mm-40) REVERT: C 124 MET cc_start: 0.8859 (ptp) cc_final: 0.8633 (ptm) REVERT: C 127 ILE cc_start: 0.8198 (pt) cc_final: 0.7952 (pp) REVERT: C 191 LYS cc_start: 0.8136 (mttp) cc_final: 0.7792 (mtmp) REVERT: C 200 ARG cc_start: 0.8376 (mmm160) cc_final: 0.8014 (mmp-170) REVERT: C 315 MET cc_start: 0.7954 (mtp) cc_final: 0.7598 (mtp) REVERT: C 337 PHE cc_start: 0.7850 (t80) cc_final: 0.7480 (t80) REVERT: C 515 MET cc_start: 0.9160 (ttp) cc_final: 0.8843 (ttm) REVERT: C 641 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7171 (pt0) REVERT: C 778 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7010 (mm-30) REVERT: C 844 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7870 (mtmm) REVERT: C 859 GLU cc_start: 0.7703 (pp20) cc_final: 0.6748 (tm-30) REVERT: C 951 MET cc_start: 0.7914 (ttm) cc_final: 0.7523 (ttp) REVERT: C 955 GLN cc_start: 0.7359 (tp40) cc_final: 0.6883 (tm-30) REVERT: C 1020 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 1024 GLU cc_start: 0.7568 (pp20) cc_final: 0.7280 (pp20) REVERT: C 1025 PHE cc_start: 0.7714 (t80) cc_final: 0.7493 (t80) REVERT: C 1131 MET cc_start: 0.7572 (mtt) cc_final: 0.7350 (mtm) REVERT: C 1154 ASP cc_start: 0.7452 (t70) cc_final: 0.7032 (t0) REVERT: C 1178 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8066 (mttp) REVERT: C 1180 MET cc_start: 0.8781 (ttp) cc_final: 0.8548 (ttt) REVERT: C 1230 MET cc_start: 0.9302 (ttp) cc_final: 0.8959 (ttp) REVERT: D 29 MET cc_start: 0.7778 (tpp) cc_final: 0.7511 (ttm) REVERT: D 80 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6047 (p90) REVERT: D 137 ARG cc_start: 0.7019 (mtp180) cc_final: 0.6606 (mtp-110) REVERT: D 147 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7290 (pp) REVERT: D 237 MET cc_start: 0.9361 (mtm) cc_final: 0.8833 (mtp) REVERT: D 321 LYS cc_start: 0.8447 (mmtm) cc_final: 0.7068 (ttpm) REVERT: D 484 MET cc_start: 0.9321 (mtp) cc_final: 0.8975 (mtm) REVERT: D 625 MET cc_start: 0.8681 (ttp) cc_final: 0.8309 (tmm) REVERT: D 626 TYR cc_start: 0.8213 (m-10) cc_final: 0.7957 (m-80) REVERT: D 677 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: D 720 ASN cc_start: 0.8462 (t0) cc_final: 0.8167 (t0) REVERT: D 725 MET cc_start: 0.8092 (mtt) cc_final: 0.7810 (mtp) REVERT: D 992 LYS cc_start: 0.7229 (mptt) cc_final: 0.6909 (mptt) REVERT: D 1025 MET cc_start: 0.7023 (tpt) cc_final: 0.6236 (mmm) REVERT: D 1040 MET cc_start: 0.1597 (tmm) cc_final: 0.0859 (tmm) REVERT: D 1046 ILE cc_start: 0.4411 (OUTLIER) cc_final: 0.4037 (pp) REVERT: D 1149 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.7958 (mtt-85) REVERT: D 1189 MET cc_start: 0.8169 (tpp) cc_final: 0.7886 (tpp) REVERT: D 1195 GLN cc_start: 0.8440 (pm20) cc_final: 0.8123 (pt0) REVERT: D 1197 ASN cc_start: 0.6589 (m-40) cc_final: 0.6279 (m110) REVERT: E 43 ASN cc_start: 0.8157 (t0) cc_final: 0.7835 (t0) REVERT: E 71 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: F 105 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7509 (ptt) REVERT: F 162 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.4635 (tp) REVERT: F 365 MET cc_start: 0.8369 (ttm) cc_final: 0.8142 (ttm) REVERT: F 446 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8624 (pt0) REVERT: F 491 GLU cc_start: 0.6488 (tm-30) cc_final: 0.6174 (tm-30) REVERT: F 529 GLU cc_start: 0.8370 (pt0) cc_final: 0.7898 (pm20) REVERT: F 596 ARG cc_start: 0.8077 (mtm180) cc_final: 0.7723 (mtm110) REVERT: G 73 ASN cc_start: 0.7498 (m110) cc_final: 0.6415 (t0) REVERT: G 88 GLN cc_start: 0.8358 (mt0) cc_final: 0.8111 (mt0) REVERT: G 95 MET cc_start: 0.8384 (mmt) cc_final: 0.8120 (mmt) REVERT: G 261 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: H 47 MET cc_start: 0.7917 (tmm) cc_final: 0.7622 (tmm) REVERT: H 60 PHE cc_start: 0.7212 (m-80) cc_final: 0.6973 (m-80) REVERT: H 95 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7418 (tpp) REVERT: H 109 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: H 112 MET cc_start: 0.4141 (OUTLIER) cc_final: 0.3851 (mpt) REVERT: H 151 MET cc_start: 0.8094 (ptm) cc_final: 0.7824 (ppp) REVERT: H 253 GLN cc_start: 0.8383 (mp-120) cc_final: 0.8057 (pm20) outliers start: 81 outliers final: 45 residues processed: 349 average time/residue: 0.6880 time to fit residues: 288.7475 Evaluate side-chains 341 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 827 GLU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 246 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [22, 180, 208, 262, 44, 95, 390, 190, 178, 195, 387] chunk 22 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 chunk 387 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS E 70 GLN E 72 GLN E 73 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094479 restraints weight = 46730.592| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.24 r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36734 Z= 0.162 Angle : 0.584 13.918 50133 Z= 0.308 Chirality : 0.044 0.384 5701 Planarity : 0.004 0.050 6101 Dihedral : 15.572 176.234 5864 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 19.86 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4195 helix: 0.96 (0.13), residues: 1709 sheet: -1.03 (0.23), residues: 474 loop : -0.68 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 3 TYR 0.016 0.001 TYR C1281 PHE 0.030 0.001 PHE F 256 TRP 0.022 0.001 TRP D1020 HIS 0.017 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (36725) covalent geometry : angle 0.58288 / 0.31 (50121) hydrogen bonds : bond 0.03675 / 2.52 ( 1600) hydrogen bonds : angle 4.49869 / 3.02 ( 4469) metal coordination : bond 0.00673 / 0.36 ( 8) metal coordination : angle 2.61160 / 1.32 ( 12) Misc. bond : bond 0.00084 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8390 Ramachandran restraints generated. 4195 Oldfield, 0 Emsley, 4195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 1.395 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: A 10 LYS cc_start: 0.8655 (mttp) cc_final: 0.8317 (mmtt) REVERT: A 127 GLN cc_start: 0.8540 (mp10) cc_final: 0.8239 (mp10) REVERT: A 147 GLN cc_start: 0.8308 (mt0) cc_final: 0.8080 (mt0) REVERT: A 185 TYR cc_start: 0.9119 (p90) cc_final: 0.8810 (p90) REVERT: B 86 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8211 (ttpp) REVERT: B 93 GLN cc_start: 0.6972 (mp10) cc_final: 0.6456 (mp10) REVERT: B 95 LYS cc_start: 0.8048 (mttt) cc_final: 0.7747 (mtpp) REVERT: B 145 LYS cc_start: 0.7822 (tttt) cc_final: 0.7491 (ttpp) REVERT: B 174 ASP cc_start: 0.8087 (m-30) cc_final: 0.7432 (m-30) REVERT: B 183 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 186 ASN cc_start: 0.7938 (m-40) cc_final: 0.7658 (m110) REVERT: B 200 LYS cc_start: 0.7903 (tttt) cc_final: 0.7663 (ttpp) REVERT: C 36 GLN cc_start: 0.7366 (tp40) cc_final: 0.7034 (mm-40) REVERT: C 124 MET cc_start: 0.8737 (ptp) cc_final: 0.8512 (ptm) REVERT: C 127 ILE cc_start: 0.8230 (pt) cc_final: 0.7987 (pp) REVERT: C 191 LYS cc_start: 0.8111 (mttp) cc_final: 0.7761 (mtmp) REVERT: C 200 ARG cc_start: 0.8357 (mmm160) cc_final: 0.7984 (mmp-170) REVERT: C 315 MET cc_start: 0.7955 (mtp) cc_final: 0.7598 (mtp) REVERT: C 337 PHE cc_start: 0.7830 (t80) cc_final: 0.7454 (t80) REVERT: C 515 MET cc_start: 0.9173 (ttp) cc_final: 0.8869 (ttm) REVERT: C 641 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: C 778 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7007 (mm-30) REVERT: C 800 MET cc_start: 0.8813 (mmm) cc_final: 0.8581 (mmm) REVERT: C 844 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7866 (mtmm) REVERT: C 859 GLU cc_start: 0.7708 (pp20) cc_final: 0.6747 (tm-30) REVERT: C 951 MET cc_start: 0.7922 (ttm) cc_final: 0.7525 (ttp) REVERT: C 955 GLN cc_start: 0.7364 (tp40) cc_final: 0.6953 (tm-30) REVERT: C 1020 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 1024 GLU cc_start: 0.7599 (pp20) cc_final: 0.7336 (pp20) REVERT: C 1025 PHE cc_start: 0.7774 (t80) cc_final: 0.7560 (t80) REVERT: C 1131 MET cc_start: 0.7577 (mtt) cc_final: 0.7353 (mtm) REVERT: C 1154 ASP cc_start: 0.7329 (t70) cc_final: 0.6901 (t0) REVERT: C 1178 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8070 (mttp) REVERT: C 1180 MET cc_start: 0.8671 (ttp) cc_final: 0.8388 (ttt) REVERT: C 1230 MET cc_start: 0.9302 (ttp) cc_final: 0.8976 (ttp) REVERT: D 29 MET cc_start: 0.7803 (tpp) cc_final: 0.7539 (ttm) REVERT: D 80 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6026 (p90) REVERT: D 137 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6610 (mtp-110) REVERT: D 147 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7456 (pp) REVERT: D 237 MET cc_start: 0.9395 (mtm) cc_final: 0.8673 (mtp) REVERT: D 321 LYS cc_start: 0.8424 (mmtm) cc_final: 0.7113 (ttpm) REVERT: D 372 MET cc_start: 0.8415 (mtm) cc_final: 0.8214 (mtp) REVERT: D 484 MET cc_start: 0.9333 (mtp) cc_final: 0.8979 (mtm) REVERT: D 677 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: D 720 ASN cc_start: 0.8427 (t0) cc_final: 0.8111 (t0) REVERT: D 725 MET cc_start: 0.8107 (mtt) cc_final: 0.7809 (mtt) REVERT: D 805 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: D 832 LYS cc_start: 0.7432 (mmtt) cc_final: 0.7158 (mmmt) REVERT: D 992 LYS cc_start: 0.7266 (mptt) cc_final: 0.6935 (mptt) REVERT: D 1025 MET cc_start: 0.7019 (tpt) cc_final: 0.6227 (mmm) REVERT: D 1040 MET cc_start: 0.1593 (tmm) cc_final: 0.0856 (tmm) REVERT: D 1046 ILE cc_start: 0.4381 (OUTLIER) cc_final: 0.4011 (pp) REVERT: D 1149 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.7927 (mtt-85) REVERT: D 1189 MET cc_start: 0.8180 (tpp) cc_final: 0.7892 (tpp) REVERT: D 1195 GLN cc_start: 0.8433 (pm20) cc_final: 0.8072 (pt0) REVERT: D 1197 ASN cc_start: 0.6635 (m-40) cc_final: 0.6323 (m110) REVERT: E 43 ASN cc_start: 0.8179 (t0) cc_final: 0.7861 (t0) REVERT: F 102 MET cc_start: 0.8546 (mmm) cc_final: 0.8264 (mtp) REVERT: F 105 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7922 (ptm) REVERT: F 162 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.4878 (tp) REVERT: F 365 MET cc_start: 0.8372 (ttm) cc_final: 0.8136 (ttm) REVERT: F 446 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: F 491 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6290 (tm-30) REVERT: F 529 GLU cc_start: 0.8376 (pt0) cc_final: 0.7909 (pm20) REVERT: F 567 MET cc_start: 0.7610 (mtm) cc_final: 0.7134 (ptp) REVERT: F 596 ARG cc_start: 0.8077 (mtm180) cc_final: 0.7721 (mtm110) REVERT: F 604 SER cc_start: 0.7960 (p) cc_final: 0.7716 (m) REVERT: G 73 ASN cc_start: 0.7498 (m110) cc_final: 0.6421 (t0) REVERT: G 88 GLN cc_start: 0.8361 (mt0) cc_final: 0.8156 (mt0) REVERT: G 95 MET cc_start: 0.8419 (mmt) cc_final: 0.8084 (mmt) REVERT: G 261 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7569 (pp20) REVERT: H 47 MET cc_start: 0.7977 (tmm) cc_final: 0.7648 (tmm) REVERT: H 60 PHE cc_start: 0.7119 (m-80) cc_final: 0.6907 (m-80) REVERT: H 95 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7907 (tpp) REVERT: H 105 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7684 (m-70) REVERT: H 109 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: H 112 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4571 (mpt) REVERT: H 151 MET cc_start: 0.8101 (ptm) cc_final: 0.7835 (ppp) REVERT: H 253 GLN cc_start: 0.8382 (mp-120) cc_final: 0.8061 (pm20) outliers start: 73 outliers final: 49 residues processed: 336 average time/residue: 0.7119 time to fit residues: 286.2076 Evaluate side-chains 341 residues out of total 3645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 827 GLU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 246 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: [412, 417, 365, 110, 99, 34, 116, 3, 185, 371, 379] chunk 412 optimal weight: 2.9990 chunk 417 optimal weight: 30.0000 chunk 365 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 371 optimal weight: 6.9990 chunk 379 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS E 70 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094126 restraints weight = 46547.866| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.23 r_work: 0.3112 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36734 Z= 0.177 Angle : 0.585 14.022 50133 Z= 0.308 Chirality : 0.044 0.383 5701 Planarity : 0.004 0.050 6101 Dihedral : 15.576 176.117 5864 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.98 % Allowed : 20.00 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4195 helix: 0.97 (0.13), residues: 1701 sheet: -1.07 (0.22), residues: 496 loop : -0.67 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 3 TYR 0.017 0.001 TYR C1281 PHE 0.031 0.001 PHE F 256 TRP 0.020 0.001 TRP D1020 HIS 0.016 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (36725) covalent geometry : angle 0.58405 / 0.31 (50121) hydrogen bonds : bond 0.03712 / 2.55 ( 1600) hydrogen bonds : angle 4.50264 / 3.03 ( 4469) metal coordination : bond 0.00714 / 0.38 ( 8) metal coordination : angle 2.64292 / 1.33 ( 12) Misc. bond : bond 0.00052 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17442.50 seconds wall clock time: 295 minutes 55.74 seconds (17755.74 seconds total)