Starting phenix.real_space_refine on Tue Sep 15 04:10:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xl9_22236/09_2026/6xl9_22236.map" } resolution = 2.5 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= 0.138 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 111 5.49 5 Mg 2 5.21 5 S 154 5.16 5 C 21741 2.51 5 N 6169 2.21 5 O 6931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.25s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35113 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1774 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} 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: 10398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10398 Classifications: {'peptide': 1338} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1282} Chain breaks: 2 Chain: "F" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3789 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 1 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: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" A R 2 " Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1104 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} 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: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'118': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14569 SG CYS D 70 85.132 87.457 57.321 1.00102.31 S ATOM 14583 SG CYS D 72 82.276 86.475 56.855 1.00105.68 S ATOM 14691 SG CYS D 85 83.243 88.215 53.580 1.00108.22 S ATOM 14715 SG CYS D 88 82.079 89.678 56.335 1.00106.02 S ATOM 20403 SG CYS D 814 120.941 146.289 69.170 1.00 91.18 S ATOM 20968 SG CYS D 888 118.088 144.384 70.703 1.00 80.10 S ATOM 21019 SG CYS D 895 121.672 143.432 71.232 1.00 78.81 S ATOM 21040 SG CYS D 898 120.509 146.033 72.789 1.00 75.95 S Time building chain proxies: 8.25, per 1000 atoms: 0.23 Number of scatterers: 35113 At special positions: 0 Unit cell: (186.16, 213.01, 164.68, 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 154 16.00 P 111 15.00 Mg 2 11.99 O 6931 8.00 N 6169 7.00 C 21741 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: 3.33 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7706 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 49 sheets defined 41.3% alpha, 17.0% beta 41 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.882A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (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 154 through 159 removed outlier: 3.749A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.559A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.703A pdb=" N ASN B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.635A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (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 161 removed outlier: 3.545A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.994A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.754A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.648A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 4.516A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.935A pdb=" N MET C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.766A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'C' and resid 460 through 479 removed outlier: 4.001A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.609A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 removed outlier: 3.551A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.778A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.708A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.528A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.917A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 711 removed outlier: 3.761A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 958 Processing helix chain 'C' and resid 960 through 980 removed outlier: 4.490A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN C 965 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 1004 through 1037 removed outlier: 4.019A pdb=" N ALA C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.657A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.888A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.548A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C1119 " --> pdb=" O THR C1115 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C1120 " --> pdb=" O HIS C1116 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.795A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.771A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.794A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.721A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1299 through 1310 removed outlier: 4.075A pdb=" N TYR C1305 " --> pdb=" O ARG C1301 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 4.101A 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 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.520A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.569A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.195A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) 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: 4.404A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.739A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.533A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.671A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.723A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.680A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.504A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.532A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.805A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 666 removed outlier: 3.708A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.162A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 4.629A 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: 3.555A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 4.095A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.528A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.675A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1070 through 1074 removed outlier: 4.100A pdb=" N ASP D1073 " --> pdb=" O GLY D1070 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D1074 " --> pdb=" O GLY D1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1070 through 1074' Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.766A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.537A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1293 removed outlier: 3.892A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 removed outlier: 3.661A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.545A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1353 removed outlier: 3.569A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) 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 1376 removed outlier: 3.587A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.542A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 134 removed outlier: 3.621A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN F 131 " --> pdb=" O ILE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 213 through 220 removed outlier: 3.690A pdb=" N LYS F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 232 removed outlier: 4.395A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 236 removed outlier: 4.233A pdb=" N LYS F 236 " --> pdb=" O ASP F 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 236' Processing helix chain 'F' and resid 242 through 257 Processing helix chain 'F' and resid 264 through 289 removed outlier: 3.612A pdb=" N SER F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG F 279 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 309 removed outlier: 3.843A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 315 removed outlier: 3.776A pdb=" N TRP F 315 " --> pdb=" O SER F 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 312 through 315' Processing helix chain 'F' and resid 316 through 321 removed outlier: 3.975A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 321 " --> pdb=" O ASN F 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 321' Processing helix chain 'F' and resid 333 through 352 removed outlier: 3.630A pdb=" N VAL F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.814A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG F 364 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.733A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 400 through 419 removed outlier: 4.058A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.742A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.038A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.613A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 3.941A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 498 removed outlier: 3.565A pdb=" N LEU F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.572A pdb=" N PHE F 522 " --> pdb=" O LEU F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 548 Processing helix chain 'F' and resid 552 through 564 removed outlier: 3.607A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 4.375A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.857A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 611 removed outlier: 3.898A pdb=" N VAL F 606 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG F 608 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER F 609 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.691A pdb=" N LYS G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.580A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.616A pdb=" N LEU G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 3.521A 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 75 through 110 removed outlier: 3.809A pdb=" N GLU G 79 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 153 Proline residue: G 144 - end of helix removed outlier: 3.797A pdb=" N VAL G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 removed outlier: 4.056A 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: 3.508A pdb=" N TYR G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN G 228 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 231 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN G 233 " --> pdb=" O TRP G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 Processing helix chain 'H' and resid 3 through 12 removed outlier: 3.556A pdb=" N LYS H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.987A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 4.023A 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 76 through 109 removed outlier: 3.638A pdb=" N GLU H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU H 109 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 154 Proline residue: H 144 - end of helix removed outlier: 3.681A pdb=" N GLY H 147 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 233 removed outlier: 3.893A pdb=" N ALA H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU H 231 " --> pdb=" O MET H 227 " (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 18 removed outlier: 6.887A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.986A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (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: 6.663A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.712A 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: 6.504A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 111 removed outlier: 12.992A pdb=" N VAL B 98 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 13.011A pdb=" N MET B 142 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 13.171A pdb=" N LEU B 100 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 13.092A pdb=" N ILE B 140 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N LEU B 102 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 13.283A pdb=" N ALA B 138 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N LYS B 104 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU B 136 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLY B 106 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR B 134 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (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 152 through 153 removed outlier: 3.547A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.666A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.918A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.936A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.732A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.517A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.556A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.556A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.488A 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: 6.237A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.474A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.786A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.768A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.645A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.547A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.710A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 252 through 254 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 809 through 811 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 949 through 950 removed outlier: 3.702A pdb=" N ILE D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 995 removed outlier: 3.991A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1024 through 1028 Processing sheet with id=AE4, first strand: chain 'D' and resid 1034 through 1036 Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.743A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 1187 through 1189 Processing sheet with id=AE7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.845A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.509A pdb=" N TYR G 31 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 117 through 121 removed outlier: 4.872A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET G 259 " --> pdb=" O ILE G 246 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 117 through 121 removed outlier: 4.872A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AF3, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.667A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL H 266 " --> pdb=" O THR H 206 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.667A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL H 266 " --> pdb=" O THR H 206 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 10.16 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 14155 1.39 - 1.58: 21245 1.58 - 1.76: 220 1.76 - 1.95: 267 1.95 - 2.13: 12 Bond restraints: 35899 Sorted by residual: bond pdb=" C1' DT N 77 " pdb=" N1 DT N 77 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.81e+01 bond pdb=" C3' DT T 48 " pdb=" C2' DT T 48 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DT N 38 " pdb=" C2' DT N 38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC T 4 " pdb=" C2' DC T 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" O3' DG T 19 " pdb=" P DG T 20 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.20e-02 6.94e+03 1.07e+01 ... (remaining 35894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 47996 2.66 - 5.33: 866 5.33 - 7.99: 87 7.99 - 10.66: 15 10.66 - 13.32: 3 Bond angle restraints: 48967 Sorted by residual: angle pdb=" N GLU F 585 " pdb=" CA GLU F 585 " pdb=" C GLU F 585 " ideal model delta sigma weight residual 112.90 120.54 -7.64 1.31e+00 5.83e-01 3.40e+01 angle pdb=" O4' DA T 12 " pdb=" C4' DA T 12 " pdb=" C3' DA T 12 " ideal model delta sigma weight residual 106.00 102.55 3.45 6.00e-01 2.78e+00 3.31e+01 angle pdb=" O4' DT N 61 " pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.79e+01 angle pdb=" N LEU C 397 " pdb=" CA LEU C 397 " pdb=" C LEU C 397 " ideal model delta sigma weight residual 109.25 101.44 7.81 1.53e+00 4.27e-01 2.61e+01 angle pdb=" O4' DG T 16 " pdb=" C4' DG T 16 " pdb=" C3' DG T 16 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.53e+01 ... (remaining 48962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 20857 35.46 - 70.92: 791 70.92 - 106.39: 42 106.39 - 141.85: 1 141.85 - 177.31: 3 Dihedral angle restraints: 21694 sinusoidal: 9731 harmonic: 11963 Sorted by residual: dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL C 261 " pdb=" C VAL C 261 " pdb=" N TYR C 262 " pdb=" CA TYR C 262 " ideal model delta harmonic sigma weight residual 180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS D 850 " pdb=" C LYS D 850 " pdb=" N PRO D 851 " pdb=" CA PRO D 851 " ideal model delta harmonic sigma weight residual 180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 21691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4405 0.071 - 0.142: 1026 0.142 - 0.212: 83 0.212 - 0.283: 13 0.283 - 0.354: 2 Chirality restraints: 5529 Sorted by residual: chirality pdb=" CA LYS H 141 " pdb=" N LYS H 141 " pdb=" C LYS H 141 " pdb=" CB LYS H 141 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB VAL H 126 " pdb=" CA VAL H 126 " pdb=" CG1 VAL H 126 " pdb=" CG2 VAL H 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LEU B 65 " pdb=" N LEU B 65 " pdb=" C LEU B 65 " pdb=" CB LEU B 65 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 5526 not shown) Planarity restraints: 5981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 851 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C PRO D 851 " 0.060 2.00e-02 2.50e+03 pdb=" O PRO D 851 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY D 852 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 131 " 0.022 2.00e-02 2.50e+03 2.28e-02 9.07e+00 pdb=" CG PHE G 131 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE G 131 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE G 131 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 131 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE G 131 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE G 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 881 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" C LYS D 881 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS D 881 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL D 882 " 0.017 2.00e-02 2.50e+03 ... (remaining 5978 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 261 2.60 - 3.18: 27885 3.18 - 3.75: 49438 3.75 - 4.32: 72013 4.32 - 4.90: 118208 Nonbonded interactions: 267805 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.025 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.102 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.121 2.170 nonbonded pdb=" N7 GTP R 1 " pdb="MG MG R 101 " model vdw 2.123 2.250 nonbonded pdb=" O ASP G 135 " pdb=" OG SER G 138 " model vdw 2.204 3.040 ... (remaining 267800 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 6 through 233) selection = (chain 'B' and resid 6 through 233) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.890 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 43.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.008 0.183 35908 Z= 0.411 Angle : 0.948 32.463 48979 Z= 0.560 Chirality : 0.058 0.354 5529 Planarity : 0.006 0.065 5981 Dihedral : 17.103 177.311 13988 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.04 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -3.38 (0.11), residues: 4117 helix: -2.40 (0.11), residues: 1540 sheet: -0.76 (0.22), residues: 473 loop : -2.48 (0.11), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 352 TYR 0.025 0.002 TYR G 127 PHE 0.051 0.003 PHE G 131 TRP 0.016 0.002 TRP G 258 HIS 0.021 0.002 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.41 (35899) covalent geometry : angle 0.91759 / 0.56 (48967) hydrogen bonds : bond 0.17384 / 11.58 ( 1416) hydrogen bonds : angle 6.89670 / 4.67 ( 3946) metal coordination : bond 0.10286 / 6.71 ( 8) metal coordination : angle 15.28204 / 8.30 ( 12) Misc. bond : bond 0.03964 / 2.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.7831 (m-30) cc_final: 0.7600 (t0) REVERT: B 25 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7451 (mtmm) REVERT: B 69 SER cc_start: 0.7307 (t) cc_final: 0.7047 (t) REVERT: C 60 GLN cc_start: 0.7665 (mt0) cc_final: 0.7322 (mt0) REVERT: C 371 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7556 (mtp-110) REVERT: C 378 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7558 (ttt-90) REVERT: C 473 ARG cc_start: 0.7013 (mtp-110) cc_final: 0.6802 (ttm-80) REVERT: C 541 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6633 (tp30) REVERT: C 598 VAL cc_start: 0.7963 (t) cc_final: 0.7741 (p) REVERT: C 768 MET cc_start: 0.8232 (ptm) cc_final: 0.8013 (ptp) REVERT: C 1041 ASP cc_start: 0.8107 (p0) cc_final: 0.7791 (p0) REVERT: C 1085 MET cc_start: 0.8675 (mmm) cc_final: 0.8373 (mmm) REVERT: D 322 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7610 (mtt-85) REVERT: D 724 MET cc_start: 0.7702 (mtp) cc_final: 0.7401 (mtp) REVERT: D 743 MET cc_start: 0.8069 (ptp) cc_final: 0.7690 (ptm) REVERT: D 1334 GLU cc_start: 0.7476 (tp30) cc_final: 0.7266 (tp30) REVERT: D 1369 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6890 (mpt180) REVERT: F 100 MET cc_start: 0.8028 (mtm) cc_final: 0.7805 (mtm) REVERT: F 109 GLU cc_start: 0.6867 (tp30) cc_final: 0.6587 (tp30) REVERT: H 47 MET cc_start: 0.7052 (tmm) cc_final: 0.6740 (tmm) REVERT: H 209 THR cc_start: 0.7361 (m) cc_final: 0.7091 (p) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.8799 time to fit residues: 418.5839 Evaluate side-chains 276 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.0060 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 84 ASN A 137 ASN A 147 GLN A 160 HIS B 23 HIS B 66 HIS B 75 GLN B 147 GLN C 139 ASN C 447 HIS C 462 ASN C 518 ASN C 519 ASN C 620 ASN C 894 GLN C 932 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D 186 GLN D 200 GLN D 209 ASN D 266 ASN D 364 HIS D 419 HIS D 430 HIS D 465 GLN D 667 GLN D 680 ASN D 720 ASN D 736 GLN D 979 ASN D1235 ASN D1350 ASN F 128 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN F 400 GLN F 461 ASN F 472 GLN F 579 GLN G 22 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 ASN H 50 HIS H 76 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.176403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105781 restraints weight = 40864.319| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.82 r_work: 0.3162 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35908 Z= 0.144 Angle : 0.661 13.406 48979 Z= 0.357 Chirality : 0.046 0.411 5529 Planarity : 0.005 0.057 5981 Dihedral : 15.856 175.824 5746 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 1.37 % Allowed : 12.57 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4117 helix: -1.06 (0.13), residues: 1573 sheet: -0.21 (0.23), residues: 498 loop : -1.94 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 12 TYR 0.021 0.001 TYR G 127 PHE 0.019 0.001 PHE G 131 TRP 0.017 0.001 TRP D1020 HIS 0.010 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (35899) covalent geometry : angle 0.65747 / 0.36 (48967) hydrogen bonds : bond 0.05791 / 3.89 ( 1416) hydrogen bonds : angle 5.09471 / 3.48 ( 3946) metal coordination : bond 0.00524 / 0.32 ( 8) metal coordination : angle 4.25160 / 2.23 ( 12) Misc. bond : bond 0.00584 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.7779 (m-30) cc_final: 0.7497 (t0) REVERT: B 25 LYS cc_start: 0.7343 (mtpt) cc_final: 0.6988 (mtmm) REVERT: C 46 GLN cc_start: 0.7453 (pm20) cc_final: 0.7136 (pm20) REVERT: C 60 GLN cc_start: 0.7554 (mt0) cc_final: 0.6958 (mm-40) REVERT: C 126 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 343 HIS cc_start: 0.6638 (m90) cc_final: 0.6326 (m90) REVERT: C 371 ARG cc_start: 0.7337 (mtt-85) cc_final: 0.7059 (mtp-110) REVERT: C 378 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7614 (ttt-90) REVERT: C 473 ARG cc_start: 0.7038 (mtp-110) cc_final: 0.6811 (ttm-80) REVERT: C 510 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: C 541 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6739 (tp30) REVERT: C 628 HIS cc_start: 0.6881 (m-70) cc_final: 0.6626 (m-70) REVERT: C 899 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 1041 ASP cc_start: 0.8365 (p0) cc_final: 0.8078 (p0) REVERT: C 1085 MET cc_start: 0.8782 (mmm) cc_final: 0.8456 (mmm) REVERT: C 1135 GLN cc_start: 0.8492 (tp40) cc_final: 0.7804 (mp10) REVERT: D 133 ARG cc_start: 0.7225 (mmm160) cc_final: 0.6469 (mtm-85) REVERT: D 196 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6651 (tm-30) REVERT: D 322 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7624 (mtt-85) REVERT: D 724 MET cc_start: 0.7335 (mtp) cc_final: 0.7081 (mtp) REVERT: D 1189 MET cc_start: 0.7319 (tmt) cc_final: 0.6401 (ttm) REVERT: D 1334 GLU cc_start: 0.8182 (tp30) cc_final: 0.7903 (tp30) REVERT: D 1369 ARG cc_start: 0.6838 (ttm170) cc_final: 0.6563 (mpt180) REVERT: F 100 MET cc_start: 0.7857 (mtm) cc_final: 0.7656 (mtm) REVERT: G 94 ASP cc_start: 0.8593 (p0) cc_final: 0.8285 (p0) REVERT: H 47 MET cc_start: 0.6542 (tmm) cc_final: 0.6246 (tmm) REVERT: H 143 ILE cc_start: 0.8655 (mp) cc_final: 0.8132 (tt) REVERT: H 209 THR cc_start: 0.6808 (m) cc_final: 0.6530 (p) outliers start: 49 outliers final: 20 residues processed: 333 average time/residue: 0.8146 time to fit residues: 319.3337 Evaluate side-chains 300 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 95 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 20 optimal weight: 1.9990 chunk 368 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 320 optimal weight: 50.0000 chunk 408 optimal weight: 30.0000 chunk 294 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 147 GLN B 18 GLN B 103 ASN B 117 HIS C 20 GLN C 568 ASN C 620 ASN C 894 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1134 GLN C1307 ASN D 200 GLN D 294 ASN D 680 ASN D 690 ASN D 736 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.174011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103749 restraints weight = 40609.018| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.64 r_work: 0.3178 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35908 Z= 0.226 Angle : 0.681 12.710 48979 Z= 0.365 Chirality : 0.049 0.419 5529 Planarity : 0.005 0.076 5981 Dihedral : 15.892 174.183 5746 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.18 % Allowed : 13.52 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.82 (0.12), residues: 4117 helix: -0.76 (0.13), residues: 1585 sheet: -0.21 (0.23), residues: 493 loop : -1.81 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1173 TYR 0.019 0.002 TYR D 631 PHE 0.018 0.002 PHE H 183 TRP 0.015 0.001 TRP D1020 HIS 0.012 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (35899) covalent geometry : angle 0.67832 / 0.37 (48967) hydrogen bonds : bond 0.06477 / 4.35 ( 1416) hydrogen bonds : angle 4.89681 / 3.36 ( 3946) metal coordination : bond 0.00858 / 0.56 ( 8) metal coordination : angle 4.10458 / 2.17 ( 12) Misc. bond : bond 0.00316 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 281 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: B 15 ASP cc_start: 0.7852 (m-30) cc_final: 0.7565 (t0) REVERT: B 25 LYS cc_start: 0.7538 (mtpt) cc_final: 0.7174 (mtmm) REVERT: B 51 MET cc_start: 0.8244 (mmp) cc_final: 0.7969 (mmm) REVERT: B 86 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7845 (mtmt) REVERT: C 60 GLN cc_start: 0.7658 (mt0) cc_final: 0.7136 (mm-40) REVERT: C 343 HIS cc_start: 0.6840 (m90) cc_final: 0.6540 (m90) REVERT: C 371 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.7172 (mtp-110) REVERT: C 378 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7676 (ttt-90) REVERT: C 473 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6938 (ttm-80) REVERT: C 510 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: C 541 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6753 (tp30) REVERT: C 859 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7118 (tp30) REVERT: C 899 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 903 ARG cc_start: 0.7521 (mmt90) cc_final: 0.7262 (mmt90) REVERT: C 1041 ASP cc_start: 0.8323 (p0) cc_final: 0.8057 (p0) REVERT: C 1085 MET cc_start: 0.8816 (mmm) cc_final: 0.8546 (mmm) REVERT: C 1135 GLN cc_start: 0.8625 (tp40) cc_final: 0.7791 (mp10) REVERT: D 80 HIS cc_start: 0.6134 (OUTLIER) cc_final: 0.5853 (p90) REVERT: D 133 ARG cc_start: 0.7384 (mmm160) cc_final: 0.6641 (mtm110) REVERT: D 140 TYR cc_start: 0.8093 (m-10) cc_final: 0.7866 (m-10) REVERT: D 196 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6927 (tm-30) REVERT: D 200 GLN cc_start: 0.6809 (tt0) cc_final: 0.6447 (tm-30) REVERT: D 312 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.7408 (ttt180) REVERT: D 322 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7732 (mtt-85) REVERT: D 724 MET cc_start: 0.7525 (mtp) cc_final: 0.7285 (mtp) REVERT: D 993 GLU cc_start: 0.4619 (mm-30) cc_final: 0.4313 (mm-30) REVERT: D 1189 MET cc_start: 0.6989 (tmt) cc_final: 0.6158 (ttm) REVERT: D 1334 GLU cc_start: 0.8250 (tp30) cc_final: 0.8008 (tp30) REVERT: F 100 MET cc_start: 0.7988 (mtm) cc_final: 0.7765 (mtt) REVERT: H 47 MET cc_start: 0.6501 (tmm) cc_final: 0.6219 (tmm) REVERT: H 95 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8084 (mmt) REVERT: H 209 THR cc_start: 0.6895 (m) cc_final: 0.6576 (p) outliers start: 78 outliers final: 41 residues processed: 331 average time/residue: 0.7780 time to fit residues: 304.6284 Evaluate side-chains 309 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 578 LYS Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 211 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 229 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 185 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 23 HIS A 137 ASN C 628 HIS C 894 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.173711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102797 restraints weight = 40648.987| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.76 r_work: 0.3166 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 35908 Z= 0.234 Angle : 0.678 12.691 48979 Z= 0.363 Chirality : 0.049 0.416 5529 Planarity : 0.005 0.058 5981 Dihedral : 15.897 173.940 5746 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.69 % Allowed : 14.75 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.64 (0.12), residues: 4117 helix: -0.58 (0.13), residues: 1581 sheet: -0.14 (0.23), residues: 493 loop : -1.74 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 12 TYR 0.020 0.002 TYR D 631 PHE 0.021 0.002 PHE H 183 TRP 0.015 0.001 TRP D1020 HIS 0.012 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 (35899) covalent geometry : angle 0.67501 / 0.36 (48967) hydrogen bonds : bond 0.06318 / 4.24 ( 1416) hydrogen bonds : angle 4.80252 / 3.29 ( 3946) metal coordination : bond 0.00739 / 0.48 ( 8) metal coordination : angle 3.79471 / 2.02 ( 12) Misc. bond : bond 0.00411 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 272 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: B 15 ASP cc_start: 0.7849 (m-30) cc_final: 0.7580 (t0) REVERT: B 25 LYS cc_start: 0.7549 (mtpt) cc_final: 0.7182 (mtmm) REVERT: B 51 MET cc_start: 0.8257 (mmp) cc_final: 0.7987 (mmm) REVERT: B 226 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: C 5 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.7018 (m-10) REVERT: C 60 GLN cc_start: 0.7607 (mt0) cc_final: 0.7119 (mm-40) REVERT: C 371 ARG cc_start: 0.7440 (mtt-85) cc_final: 0.7152 (mtp-110) REVERT: C 378 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7608 (ttt-90) REVERT: C 473 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6931 (ttm-80) REVERT: C 510 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: C 541 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6686 (tp30) REVERT: C 859 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7169 (tp30) REVERT: C 899 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6877 (tm-30) REVERT: C 1041 ASP cc_start: 0.8339 (p0) cc_final: 0.8094 (p0) REVERT: C 1085 MET cc_start: 0.8795 (mmm) cc_final: 0.8519 (mmm) REVERT: C 1135 GLN cc_start: 0.8655 (tp40) cc_final: 0.7848 (mp10) REVERT: C 1233 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8156 (mt) REVERT: D 133 ARG cc_start: 0.7422 (mmm160) cc_final: 0.6684 (mtm110) REVERT: D 196 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6899 (tm-30) REVERT: D 200 GLN cc_start: 0.6801 (tt0) cc_final: 0.6423 (tm-30) REVERT: D 312 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7431 (ttt180) REVERT: D 322 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7710 (mtt-85) REVERT: D 724 MET cc_start: 0.7487 (mtp) cc_final: 0.7238 (mtp) REVERT: D 993 GLU cc_start: 0.4688 (mm-30) cc_final: 0.4379 (mm-30) REVERT: D 1024 THR cc_start: 0.4301 (OUTLIER) cc_final: 0.4056 (p) REVERT: D 1334 GLU cc_start: 0.8230 (tp30) cc_final: 0.7988 (tp30) REVERT: F 100 MET cc_start: 0.7953 (mtm) cc_final: 0.7736 (mtm) REVERT: F 288 MET cc_start: -0.1932 (tpp) cc_final: -0.2211 (tpt) REVERT: H 47 MET cc_start: 0.6479 (tmm) cc_final: 0.6174 (tmm) REVERT: H 95 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8164 (mmt) REVERT: H 209 THR cc_start: 0.6825 (m) cc_final: 0.6432 (p) outliers start: 96 outliers final: 52 residues processed: 343 average time/residue: 0.7388 time to fit residues: 301.4664 Evaluate side-chains 322 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 310 optimal weight: 4.9990 chunk 315 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 382 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 103 ASN B 132 HIS C 628 HIS C 894 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.175063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104900 restraints weight = 40669.053| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.69 r_work: 0.3195 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35908 Z= 0.157 Angle : 0.616 12.184 48979 Z= 0.331 Chirality : 0.045 0.410 5529 Planarity : 0.005 0.060 5981 Dihedral : 15.793 173.554 5746 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.27 % Allowed : 16.34 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.32 (0.12), residues: 4117 helix: -0.27 (0.13), residues: 1576 sheet: -0.01 (0.24), residues: 494 loop : -1.58 (0.12), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 12 TYR 0.018 0.001 TYR F 137 PHE 0.021 0.001 PHE H 183 TRP 0.011 0.001 TRP D1020 HIS 0.005 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (35899) covalent geometry : angle 0.61381 / 0.33 (48967) hydrogen bonds : bond 0.05334 / 3.58 ( 1416) hydrogen bonds : angle 4.60831 / 3.16 ( 3946) metal coordination : bond 0.00463 / 0.30 ( 8) metal coordination : angle 3.45038 / 1.80 ( 12) Misc. bond : bond 0.00212 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 276 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: B 15 ASP cc_start: 0.7802 (m-30) cc_final: 0.7483 (t0) REVERT: B 25 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7144 (mtmm) REVERT: B 226 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: C 60 GLN cc_start: 0.7566 (mt0) cc_final: 0.7045 (mm-40) REVERT: C 371 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7144 (mtp-110) REVERT: C 378 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7634 (ttt-90) REVERT: C 473 ARG cc_start: 0.7130 (mtp-110) cc_final: 0.6904 (ttm-80) REVERT: C 510 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: C 541 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6710 (tp30) REVERT: C 799 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8228 (p0) REVERT: C 859 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7194 (tp30) REVERT: C 899 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6699 (tm-30) REVERT: C 903 ARG cc_start: 0.7625 (mmt90) cc_final: 0.7381 (mmt90) REVERT: C 1041 ASP cc_start: 0.8354 (p0) cc_final: 0.8122 (p0) REVERT: C 1085 MET cc_start: 0.8799 (mmm) cc_final: 0.8558 (mmm) REVERT: C 1135 GLN cc_start: 0.8616 (tp40) cc_final: 0.7812 (mp10) REVERT: D 133 ARG cc_start: 0.7393 (mmm160) cc_final: 0.6676 (mtm110) REVERT: D 155 GLU cc_start: 0.7683 (pm20) cc_final: 0.7434 (pm20) REVERT: D 196 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6906 (tm-30) REVERT: D 200 GLN cc_start: 0.6834 (tt0) cc_final: 0.6500 (tm-30) REVERT: D 322 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7590 (mtt-85) REVERT: D 724 MET cc_start: 0.7451 (mtp) cc_final: 0.7186 (mtp) REVERT: D 802 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7319 (t0) REVERT: D 993 GLU cc_start: 0.4603 (mm-30) cc_final: 0.4296 (mm-30) REVERT: D 1189 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.5762 (ttm) REVERT: D 1334 GLU cc_start: 0.8210 (tp30) cc_final: 0.8009 (tp30) REVERT: F 288 MET cc_start: -0.1940 (tpp) cc_final: -0.2161 (tpt) REVERT: F 555 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: H 47 MET cc_start: 0.6495 (tmm) cc_final: 0.6263 (tmm) REVERT: H 95 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8130 (mmt) REVERT: H 209 THR cc_start: 0.6848 (m) cc_final: 0.6518 (p) outliers start: 81 outliers final: 44 residues processed: 332 average time/residue: 0.8005 time to fit residues: 314.9994 Evaluate side-chains 313 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 36 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 339 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 137 ASN B 103 ASN C 628 HIS C 894 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** 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 = 0.4280 r_free = 0.4280 target = 0.174207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103510 restraints weight = 40422.042| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.86 r_work: 0.3164 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35908 Z= 0.198 Angle : 0.643 12.310 48979 Z= 0.342 Chirality : 0.047 0.404 5529 Planarity : 0.005 0.059 5981 Dihedral : 15.786 173.550 5746 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.18 % Allowed : 17.24 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 4117 helix: -0.22 (0.13), residues: 1579 sheet: 0.01 (0.24), residues: 493 loop : -1.53 (0.12), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 12 TYR 0.024 0.002 TYR G 127 PHE 0.016 0.002 PHE C 405 TRP 0.008 0.001 TRP D1020 HIS 0.009 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (35899) covalent geometry : angle 0.64123 / 0.34 (48967) hydrogen bonds : bond 0.05678 / 3.82 ( 1416) hydrogen bonds : angle 4.59541 / 3.15 ( 3946) metal coordination : bond 0.00603 / 0.39 ( 8) metal coordination : angle 3.34201 / 1.77 ( 12) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 271 time to evaluate : 1.345 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: 0.8574 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: B 15 ASP cc_start: 0.7775 (m-30) cc_final: 0.7433 (t0) REVERT: B 25 LYS cc_start: 0.7529 (mtpt) cc_final: 0.7130 (mtmm) REVERT: B 226 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: C 5 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: C 60 GLN cc_start: 0.7576 (mt0) cc_final: 0.7090 (mm-40) REVERT: C 371 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.7108 (mtp-110) REVERT: C 378 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7610 (ttt-90) REVERT: C 473 ARG cc_start: 0.7133 (mtp-110) cc_final: 0.6888 (ttm-80) REVERT: C 510 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: C 541 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6677 (tp30) REVERT: C 859 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7155 (tp30) REVERT: C 899 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6658 (tm-30) REVERT: C 1041 ASP cc_start: 0.8363 (p0) cc_final: 0.8122 (p0) REVERT: C 1085 MET cc_start: 0.8773 (mmm) cc_final: 0.8491 (mmm) REVERT: C 1135 GLN cc_start: 0.8603 (tp40) cc_final: 0.7786 (mp10) REVERT: C 1233 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8109 (mt) REVERT: D 155 GLU cc_start: 0.7630 (pm20) cc_final: 0.7366 (pm20) REVERT: D 196 GLN cc_start: 0.7348 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 200 GLN cc_start: 0.6728 (tt0) cc_final: 0.6396 (tm-30) REVERT: D 312 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7314 (tpt-90) REVERT: D 322 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7573 (mtt-85) REVERT: D 724 MET cc_start: 0.7415 (mtp) cc_final: 0.7156 (mtp) REVERT: D 802 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7338 (t0) REVERT: D 993 GLU cc_start: 0.4686 (mm-30) cc_final: 0.4397 (mm-30) REVERT: D 1189 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.5822 (ttm) REVERT: D 1334 GLU cc_start: 0.8224 (tp30) cc_final: 0.7994 (tp30) REVERT: F 100 MET cc_start: 0.7646 (mtt) cc_final: 0.7184 (mtt) REVERT: F 555 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: H 47 MET cc_start: 0.6463 (tmm) cc_final: 0.6198 (tmm) REVERT: H 64 GLU cc_start: 0.8680 (mp0) cc_final: 0.8402 (pm20) REVERT: H 95 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8149 (mmt) REVERT: H 209 THR cc_start: 0.6850 (m) cc_final: 0.6507 (p) outliers start: 78 outliers final: 52 residues processed: 325 average time/residue: 0.7744 time to fit residues: 298.5036 Evaluate side-chains 319 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 5 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1151 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 78 optimal weight: 0.1980 chunk 243 optimal weight: 10.0000 chunk 391 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 414 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 247 optimal weight: 0.0980 chunk 189 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 137 ASN B 103 ASN C 20 GLN C 628 HIS ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.174234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103367 restraints weight = 40419.147| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.91 r_work: 0.3163 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35908 Z= 0.200 Angle : 0.644 13.029 48979 Z= 0.343 Chirality : 0.047 0.397 5529 Planarity : 0.005 0.069 5981 Dihedral : 15.766 173.550 5746 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.43 % Allowed : 17.58 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.19 (0.13), residues: 4117 helix: -0.15 (0.13), residues: 1575 sheet: 0.02 (0.23), residues: 500 loop : -1.50 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D 133 TYR 0.021 0.001 TYR F 137 PHE 0.016 0.002 PHE C 405 TRP 0.010 0.001 TRP D1020 HIS 0.010 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (35899) covalent geometry : angle 0.64229 / 0.34 (48967) hydrogen bonds : bond 0.05652 / 3.80 ( 1416) hydrogen bonds : angle 4.58976 / 3.14 ( 3946) metal coordination : bond 0.00597 / 0.38 ( 8) metal coordination : angle 3.32038 / 1.75 ( 12) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 264 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: B 15 ASP cc_start: 0.7778 (m-30) cc_final: 0.7451 (t0) REVERT: B 25 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7164 (mtmm) REVERT: B 226 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 60 GLN cc_start: 0.7538 (mt0) cc_final: 0.7071 (mm-40) REVERT: C 371 ARG cc_start: 0.7367 (mtt-85) cc_final: 0.7087 (mtp-110) REVERT: C 378 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7609 (ttt-90) REVERT: C 473 ARG cc_start: 0.7038 (mtp-110) cc_final: 0.6783 (ttm-80) REVERT: C 510 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: C 541 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6607 (tp30) REVERT: C 899 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6419 (tm-30) REVERT: C 1041 ASP cc_start: 0.8277 (p0) cc_final: 0.8016 (p0) REVERT: C 1085 MET cc_start: 0.8681 (mmm) cc_final: 0.8425 (mmm) REVERT: C 1135 GLN cc_start: 0.8561 (tp40) cc_final: 0.7803 (mp10) REVERT: C 1233 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8018 (mt) REVERT: D 133 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6564 (mtm-85) REVERT: D 155 GLU cc_start: 0.7589 (pm20) cc_final: 0.7335 (pm20) REVERT: D 196 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7007 (tm-30) REVERT: D 200 GLN cc_start: 0.6770 (tt0) cc_final: 0.6424 (tm-30) REVERT: D 322 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7511 (mtt-85) REVERT: D 569 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8124 (mp) REVERT: D 724 MET cc_start: 0.7401 (mtp) cc_final: 0.7113 (mtp) REVERT: D 802 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7120 (t0) REVERT: D 993 GLU cc_start: 0.4666 (mm-30) cc_final: 0.4373 (mm-30) REVERT: D 1189 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5802 (ttm) REVERT: D 1334 GLU cc_start: 0.8006 (tp30) cc_final: 0.7778 (tp30) REVERT: F 555 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: H 47 MET cc_start: 0.6322 (tmm) cc_final: 0.5974 (tmm) REVERT: H 64 GLU cc_start: 0.8641 (mp0) cc_final: 0.8415 (pm20) REVERT: H 95 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8118 (mmt) REVERT: H 209 THR cc_start: 0.6726 (m) cc_final: 0.6404 (p) outliers start: 87 outliers final: 56 residues processed: 324 average time/residue: 0.7832 time to fit residues: 301.8450 Evaluate side-chains 319 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1151 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 211 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 150 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 319 optimal weight: 40.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 137 ASN B 18 GLN C 628 HIS ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.175219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.105099 restraints weight = 40638.215| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.76 r_work: 0.3187 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35908 Z= 0.152 Angle : 0.608 11.981 48979 Z= 0.324 Chirality : 0.045 0.388 5529 Planarity : 0.004 0.059 5981 Dihedral : 15.678 173.339 5746 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.24 % Allowed : 18.14 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.00 (0.13), residues: 4117 helix: 0.01 (0.13), residues: 1576 sheet: 0.22 (0.24), residues: 481 loop : -1.42 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 133 TYR 0.016 0.001 TYR F 137 PHE 0.015 0.001 PHE C 405 TRP 0.009 0.001 TRP D1020 HIS 0.009 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (35899) covalent geometry : angle 0.60569 / 0.32 (48967) hydrogen bonds : bond 0.05020 / 3.37 ( 1416) hydrogen bonds : angle 4.46645 / 3.05 ( 3946) metal coordination : bond 0.00457 / 0.29 ( 8) metal coordination : angle 3.18515 / 1.65 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 268 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: B 15 ASP cc_start: 0.7727 (m-30) cc_final: 0.7380 (t0) REVERT: B 25 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7130 (mtmm) REVERT: B 54 CYS cc_start: 0.7699 (p) cc_final: 0.6806 (m) REVERT: B 226 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: C 60 GLN cc_start: 0.7572 (mt0) cc_final: 0.7071 (mm-40) REVERT: C 371 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.7086 (mtp-110) REVERT: C 378 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7600 (ttt-90) REVERT: C 473 ARG cc_start: 0.7084 (mtp-110) cc_final: 0.6860 (ttm-80) REVERT: C 510 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: C 541 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6415 (tp30) REVERT: C 899 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6584 (tm-30) REVERT: C 1041 ASP cc_start: 0.8369 (p0) cc_final: 0.8113 (p0) REVERT: C 1085 MET cc_start: 0.8805 (mmm) cc_final: 0.8562 (mmm) REVERT: C 1135 GLN cc_start: 0.8550 (tp40) cc_final: 0.7791 (mp10) REVERT: C 1233 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8063 (mt) REVERT: D 133 ARG cc_start: 0.7269 (mmm160) cc_final: 0.6590 (mtm-85) REVERT: D 155 GLU cc_start: 0.7597 (pm20) cc_final: 0.7321 (pm20) REVERT: D 196 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6973 (tm-30) REVERT: D 200 GLN cc_start: 0.6754 (tt0) cc_final: 0.6352 (tm-30) REVERT: D 312 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7379 (tpt-90) REVERT: D 322 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7560 (mtt-85) REVERT: D 569 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8260 (mp) REVERT: D 724 MET cc_start: 0.7417 (mtp) cc_final: 0.7151 (mtp) REVERT: D 802 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7325 (t0) REVERT: D 993 GLU cc_start: 0.4748 (mm-30) cc_final: 0.4467 (mm-30) REVERT: D 1189 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.5880 (ttm) REVERT: D 1334 GLU cc_start: 0.8059 (tp30) cc_final: 0.7841 (tp30) REVERT: F 100 MET cc_start: 0.7543 (mtt) cc_final: 0.7204 (mtt) REVERT: F 288 MET cc_start: -0.1894 (tpp) cc_final: -0.2194 (tpt) REVERT: F 555 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: F 561 MET cc_start: 0.7339 (mmm) cc_final: 0.7085 (mmm) REVERT: G 259 MET cc_start: 0.8499 (tpp) cc_final: 0.8295 (mpp) REVERT: H 47 MET cc_start: 0.6391 (tmm) cc_final: 0.6013 (tmm) REVERT: H 95 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8131 (mmt) REVERT: H 209 THR cc_start: 0.6832 (m) cc_final: 0.6508 (p) REVERT: H 213 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7013 (tptt) outliers start: 80 outliers final: 55 residues processed: 323 average time/residue: 0.8076 time to fit residues: 307.9997 Evaluate side-chains 322 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 859 GLU Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1151 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 546 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 213 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 365 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 137 ASN B 103 ASN C 20 GLN C 628 HIS ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.174546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109274 restraints weight = 41017.985| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.44 r_work: 0.3167 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35908 Z= 0.215 Angle : 0.658 12.397 48979 Z= 0.348 Chirality : 0.047 0.384 5529 Planarity : 0.005 0.060 5981 Dihedral : 15.708 173.341 5746 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.16 % Allowed : 18.53 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -1.11 (0.13), residues: 4117 helix: -0.11 (0.13), residues: 1584 sheet: 0.06 (0.23), residues: 500 loop : -1.44 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 133 TYR 0.022 0.002 TYR G 127 PHE 0.017 0.002 PHE C 514 TRP 0.010 0.001 TRP D1020 HIS 0.008 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.21 (35899) covalent geometry : angle 0.65582 / 0.35 (48967) hydrogen bonds : bond 0.05677 / 3.82 ( 1416) hydrogen bonds : angle 4.54594 / 3.11 ( 3946) metal coordination : bond 0.00653 / 0.41 ( 8) metal coordination : angle 3.28606 / 1.75 ( 12) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 260 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: B 15 ASP cc_start: 0.7804 (m-30) cc_final: 0.7445 (t0) REVERT: B 25 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7072 (mtmm) REVERT: B 54 CYS cc_start: 0.7681 (p) cc_final: 0.6769 (m) REVERT: B 226 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: C 60 GLN cc_start: 0.7566 (mt0) cc_final: 0.7142 (mm-40) REVERT: C 371 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7105 (mtp-110) REVERT: C 378 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7606 (ttt-90) REVERT: C 473 ARG cc_start: 0.7111 (mtp-110) cc_final: 0.6866 (ttm-80) REVERT: C 510 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: C 541 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6370 (tp30) REVERT: C 899 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6579 (tm-30) REVERT: C 1041 ASP cc_start: 0.8362 (p0) cc_final: 0.8103 (p0) REVERT: C 1085 MET cc_start: 0.8751 (mmm) cc_final: 0.8464 (mmm) REVERT: C 1135 GLN cc_start: 0.8527 (tp40) cc_final: 0.7914 (mt0) REVERT: C 1233 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8099 (mt) REVERT: D 133 ARG cc_start: 0.7281 (mmm160) cc_final: 0.6607 (mtm-85) REVERT: D 155 GLU cc_start: 0.7596 (pm20) cc_final: 0.7322 (pm20) REVERT: D 196 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7013 (tm-30) REVERT: D 200 GLN cc_start: 0.6764 (tt0) cc_final: 0.6338 (tm-30) REVERT: D 312 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7415 (tpt-90) REVERT: D 322 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7554 (mtt-85) REVERT: D 569 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8214 (mp) REVERT: D 680 ASN cc_start: 0.6278 (m-40) cc_final: 0.5682 (t160) REVERT: D 724 MET cc_start: 0.7390 (mtp) cc_final: 0.7131 (mtp) REVERT: D 802 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7329 (t0) REVERT: D 993 GLU cc_start: 0.4828 (mm-30) cc_final: 0.4500 (mm-30) REVERT: D 1189 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5887 (ttm) REVERT: D 1334 GLU cc_start: 0.8168 (tp30) cc_final: 0.7939 (tp30) REVERT: F 100 MET cc_start: 0.7473 (mtt) cc_final: 0.7103 (mtt) REVERT: F 288 MET cc_start: -0.1788 (tpp) cc_final: -0.2065 (tpt) REVERT: F 555 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: F 561 MET cc_start: 0.7292 (mmm) cc_final: 0.7037 (mmm) REVERT: G 227 MET cc_start: 0.7155 (mmt) cc_final: 0.6953 (mpm) REVERT: H 47 MET cc_start: 0.6448 (tmm) cc_final: 0.6188 (tmm) REVERT: H 95 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8124 (mmt) REVERT: H 209 THR cc_start: 0.6854 (m) cc_final: 0.6536 (p) REVERT: H 213 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6999 (tptt) outliers start: 77 outliers final: 60 residues processed: 317 average time/residue: 0.7974 time to fit residues: 299.7066 Evaluate side-chains 325 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 859 GLU Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1151 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 546 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 GLU Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 213 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 237 optimal weight: 1.9990 chunk 416 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 210 optimal weight: 0.0870 chunk 23 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 385 optimal weight: 30.0000 chunk 164 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 137 ASN B 18 GLN C 628 HIS ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.176234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110937 restraints weight = 41235.110| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.37 r_work: 0.3196 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35908 Z= 0.138 Angle : 0.609 12.849 48979 Z= 0.324 Chirality : 0.045 0.377 5529 Planarity : 0.004 0.059 5981 Dihedral : 15.627 173.051 5746 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.07 % Allowed : 18.64 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -0.88 (0.13), residues: 4117 helix: 0.12 (0.13), residues: 1573 sheet: 0.21 (0.24), residues: 469 loop : -1.33 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 133 TYR 0.014 0.001 TYR D 631 PHE 0.015 0.001 PHE C 405 TRP 0.007 0.001 TRP D1020 HIS 0.008 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (35899) covalent geometry : angle 0.60716 / 0.32 (48967) hydrogen bonds : bond 0.04794 / 3.22 ( 1416) hydrogen bonds : angle 4.41328 / 3.01 ( 3946) metal coordination : bond 0.00404 / 0.26 ( 8) metal coordination : angle 3.12592 / 1.60 ( 12) Misc. bond : bond 0.00048 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8234 Ramachandran restraints generated. 4117 Oldfield, 0 Emsley, 4117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: B 15 ASP cc_start: 0.7731 (m-30) cc_final: 0.7384 (t0) REVERT: B 25 LYS cc_start: 0.7504 (mtpt) cc_final: 0.7225 (ttmt) REVERT: B 54 CYS cc_start: 0.7671 (p) cc_final: 0.6788 (m) REVERT: B 226 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: C 60 GLN cc_start: 0.7543 (mt0) cc_final: 0.7085 (mm-40) REVERT: C 371 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.7066 (mtp-110) REVERT: C 378 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7599 (ttt-90) REVERT: C 510 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: C 541 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6478 (tp30) REVERT: C 899 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6545 (tm-30) REVERT: C 1041 ASP cc_start: 0.8347 (p0) cc_final: 0.8096 (p0) REVERT: C 1085 MET cc_start: 0.8770 (mmm) cc_final: 0.8525 (mmm) REVERT: C 1135 GLN cc_start: 0.8530 (tp40) cc_final: 0.7791 (mp10) REVERT: C 1233 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8023 (mt) REVERT: D 133 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6577 (mtm-85) REVERT: D 155 GLU cc_start: 0.7579 (pm20) cc_final: 0.7298 (pm20) REVERT: D 196 GLN cc_start: 0.7378 (tm-30) cc_final: 0.6990 (tm-30) REVERT: D 200 GLN cc_start: 0.6764 (tt0) cc_final: 0.6337 (tm-30) REVERT: D 312 ARG cc_start: 0.8117 (ttt180) cc_final: 0.7575 (tpt-90) REVERT: D 322 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7471 (mtt-85) REVERT: D 569 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8215 (mp) REVERT: D 680 ASN cc_start: 0.6286 (m-40) cc_final: 0.6071 (m-40) REVERT: D 715 LYS cc_start: 0.7830 (mttp) cc_final: 0.7507 (mtpm) REVERT: D 802 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7271 (t0) REVERT: D 993 GLU cc_start: 0.4796 (mm-30) cc_final: 0.4497 (mm-30) REVERT: D 1189 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.5931 (ttm) REVERT: D 1334 GLU cc_start: 0.7974 (tp30) cc_final: 0.7752 (tp30) REVERT: F 288 MET cc_start: -0.1819 (tpp) cc_final: -0.2098 (tpt) REVERT: F 555 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: F 561 MET cc_start: 0.7302 (mmm) cc_final: 0.7045 (mmm) REVERT: G 259 MET cc_start: 0.8486 (tpp) cc_final: 0.8275 (mpp) REVERT: H 47 MET cc_start: 0.6359 (tmm) cc_final: 0.6092 (tmm) REVERT: H 95 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8100 (mmt) REVERT: H 209 THR cc_start: 0.6846 (m) cc_final: 0.6491 (p) REVERT: H 213 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7043 (tptt) outliers start: 74 outliers final: 54 residues processed: 315 average time/residue: 0.8044 time to fit residues: 298.5125 Evaluate side-chains 322 residues out of total 3573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 1012 GLU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1151 LYS Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 546 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 GLU Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 213 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 195 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 393 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 137 ASN C 20 GLN C 628 HIS C 799 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 736 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.174941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109523 restraints weight = 41055.066| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.87 r_work: 0.3148 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35908 Z= 0.197 Angle : 0.655 15.080 48979 Z= 0.345 Chirality : 0.047 0.375 5529 Planarity : 0.005 0.059 5981 Dihedral : 15.645 173.157 5746 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.16 % Allowed : 18.53 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.19 % 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: -0.96 (0.13), residues: 4117 helix: 0.06 (0.13), residues: 1569 sheet: 0.07 (0.24), residues: 499 loop : -1.35 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 12 TYR 0.019 0.001 TYR D 631 PHE 0.016 0.002 PHE C 514 TRP 0.009 0.001 TRP D1020 HIS 0.007 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (35899) covalent geometry : angle 0.65293 / 0.35 (48967) hydrogen bonds : bond 0.05442 / 3.66 ( 1416) hydrogen bonds : angle 4.47213 / 3.06 ( 3946) metal coordination : bond 0.00588 / 0.37 ( 8) metal coordination : angle 3.16587 / 1.69 ( 12) Misc. bond : bond 0.00027 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25751.86 seconds wall clock time: 434 minutes 59.87 seconds (26099.87 seconds total)