Starting phenix.real_space_refine on Mon Dec 30 03:23:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w2e_21526/12_2024/6w2e_21526.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2e_21526/12_2024/6w2e_21526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w2e_21526/12_2024/6w2e_21526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2e_21526/12_2024/6w2e_21526.map" model { file = "/net/cci-nas-00/data/ceres_data/6w2e_21526/12_2024/6w2e_21526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2e_21526/12_2024/6w2e_21526.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 353 5.16 5 C 39758 2.51 5 N 10845 2.21 5 O 11569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 236 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62525 Number of models: 1 Model: "" Number of chains: 19 Chain: "J" Number of atoms: 10252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10252 Classifications: {'peptide': 1305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1236} Chain breaks: 2 Chain: "K" Number of atoms: 10832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1381, 10832 Classifications: {'peptide': 1381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 72, 'TRANS': 1308} Chain: "N" Number of atoms: 10683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10683 Classifications: {'peptide': 1362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1290} Chain breaks: 1 Chain: "O" Number of atoms: 10194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1299, 10194 Classifications: {'peptide': 1299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 69, 'TRANS': 1229} Chain breaks: 1 Chain: "v" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2288 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain breaks: 4 Chain: "w" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "x" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "y" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 317 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'TRANS': 36} Chain: "z" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 317 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'TRANS': 36} Chain: "Z" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "a" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "d" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "e" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 649 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 7, 'TRANS': 69} Chain: "f" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1992 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 234} Chain breaks: 2 Chain: "h" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2604 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 313} Chain breaks: 2 Chain: "k" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain: "m" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain: "p" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain: "r" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Time building chain proxies: 26.63, per 1000 atoms: 0.43 Number of scatterers: 62525 At special positions: 0 Unit cell: (238, 240.72, 208.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 353 16.00 O 11569 8.00 N 10845 7.00 C 39758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.21 Conformation dependent library (CDL) restraints added in 6.1 seconds 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15018 Finding SS restraints... Secondary structure from input PDB file: 329 helices and 84 sheets defined 44.3% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.88 Creating SS restraints... Processing helix chain 'J' and resid 24 through 31 Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 135 through 141 Processing helix chain 'J' and resid 147 through 188 removed outlier: 3.603A pdb=" N ILE J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 199 removed outlier: 5.237A pdb=" N THR J 196 " --> pdb=" O PHE J 192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP J 199 " --> pdb=" O GLN J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 226 Processing helix chain 'J' and resid 228 through 237 removed outlier: 4.073A pdb=" N GLU J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN J 235 " --> pdb=" O ASP J 231 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET J 236 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY J 237 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 255 removed outlier: 3.778A pdb=" N TYR J 243 " --> pdb=" O GLY J 239 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL J 255 " --> pdb=" O MET J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 294 Processing helix chain 'J' and resid 384 through 390 removed outlier: 3.859A pdb=" N TYR J 388 " --> pdb=" O LEU J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 433 removed outlier: 3.587A pdb=" N GLN J 433 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 460 removed outlier: 4.419A pdb=" N LYS J 457 " --> pdb=" O GLN J 453 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL J 458 " --> pdb=" O ASN J 454 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU J 459 " --> pdb=" O ALA J 455 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 466 removed outlier: 3.738A pdb=" N HIS J 465 " --> pdb=" O HIS J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 477 removed outlier: 3.712A pdb=" N ALA J 477 " --> pdb=" O SER J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 508 Processing helix chain 'J' and resid 516 through 522 Processing helix chain 'J' and resid 534 through 540 removed outlier: 3.952A pdb=" N LEU J 540 " --> pdb=" O ASP J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 577 through 593 Processing helix chain 'J' and resid 599 through 611 Processing helix chain 'J' and resid 616 through 627 removed outlier: 4.046A pdb=" N TYR J 620 " --> pdb=" O PRO J 616 " (cutoff:3.500A) Processing helix chain 'J' and resid 629 through 636 Processing helix chain 'J' and resid 636 through 651 removed outlier: 3.513A pdb=" N SER J 651 " --> pdb=" O TYR J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 669 removed outlier: 3.643A pdb=" N ILE J 663 " --> pdb=" O SER J 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 676 through 702 removed outlier: 4.150A pdb=" N MET J 682 " --> pdb=" O GLU J 678 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J 686 " --> pdb=" O MET J 682 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR J 687 " --> pdb=" O TYR J 683 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY J 702 " --> pdb=" O MET J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 716 Processing helix chain 'J' and resid 731 through 738 removed outlier: 3.858A pdb=" N HIS J 735 " --> pdb=" O ASP J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 758 through 762 Processing helix chain 'J' and resid 770 through 774 removed outlier: 3.755A pdb=" N ALA J 773 " --> pdb=" O ASP J 770 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA J 774 " --> pdb=" O GLU J 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 770 through 774' Processing helix chain 'J' and resid 775 through 786 removed outlier: 3.796A pdb=" N ARG J 783 " --> pdb=" O LEU J 779 " (cutoff:3.500A) Processing helix chain 'J' and resid 806 through 813 Processing helix chain 'J' and resid 815 through 821 Processing helix chain 'J' and resid 831 through 841 Processing helix chain 'J' and resid 856 through 860 Processing helix chain 'J' and resid 863 through 873 Processing helix chain 'J' and resid 877 through 886 Processing helix chain 'J' and resid 887 through 891 Processing helix chain 'J' and resid 913 through 916 removed outlier: 3.638A pdb=" N ASP J 916 " --> pdb=" O ASN J 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 913 through 916' Processing helix chain 'J' and resid 936 through 942 removed outlier: 4.267A pdb=" N VAL J 940 " --> pdb=" O ARG J 936 " (cutoff:3.500A) Processing helix chain 'J' and resid 956 through 964 Processing helix chain 'J' and resid 964 through 974 Processing helix chain 'J' and resid 998 through 1007 removed outlier: 3.550A pdb=" N GLU J1007 " --> pdb=" O LYS J1003 " (cutoff:3.500A) Processing helix chain 'J' and resid 1011 through 1022 removed outlier: 3.686A pdb=" N HIS J1022 " --> pdb=" O MET J1018 " (cutoff:3.500A) Processing helix chain 'J' and resid 1026 through 1036 removed outlier: 3.839A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1123 through 1128 removed outlier: 4.162A pdb=" N VAL J1127 " --> pdb=" O ASP J1123 " (cutoff:3.500A) Processing helix chain 'J' and resid 1135 through 1147 Processing helix chain 'J' and resid 1192 through 1198 removed outlier: 3.963A pdb=" N PHE J1196 " --> pdb=" O ASP J1192 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS J1198 " --> pdb=" O ALA J1194 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1241 through 1246 removed outlier: 3.710A pdb=" N GLN J1246 " --> pdb=" O PRO J1242 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1256 Processing helix chain 'J' and resid 1271 through 1276 Processing helix chain 'J' and resid 1277 through 1282 Processing helix chain 'J' and resid 1283 through 1285 No H-bonds generated for 'chain 'J' and resid 1283 through 1285' Processing helix chain 'J' and resid 1286 through 1297 removed outlier: 3.561A pdb=" N SER J1295 " --> pdb=" O VAL J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1324 through 1329 removed outlier: 3.536A pdb=" N LEU J1328 " --> pdb=" O PRO J1324 " (cutoff:3.500A) Processing helix chain 'J' and resid 1339 through 1349 removed outlier: 3.689A pdb=" N ILE J1343 " --> pdb=" O SER J1339 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.538A pdb=" N ASP K 44 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG K 46 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 84 through 88 Processing helix chain 'K' and resid 135 through 143 Processing helix chain 'K' and resid 147 through 187 removed outlier: 3.764A pdb=" N GLY K 175 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE K 177 " --> pdb=" O GLU K 173 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS K 187 " --> pdb=" O VAL K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 199 removed outlier: 4.684A pdb=" N THR K 196 " --> pdb=" O PHE K 192 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 203 Processing helix chain 'K' and resid 208 through 227 removed outlier: 4.104A pdb=" N SER K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 236 Processing helix chain 'K' and resid 239 through 255 removed outlier: 3.725A pdb=" N VAL K 255 " --> pdb=" O MET K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 264 removed outlier: 4.112A pdb=" N GLY K 263 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 295 removed outlier: 3.915A pdb=" N GLN K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 324 Processing helix chain 'K' and resid 330 through 339 removed outlier: 3.659A pdb=" N ALA K 336 " --> pdb=" O GLU K 332 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG K 337 " --> pdb=" O HIS K 333 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE K 338 " --> pdb=" O PHE K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 357 Proline residue: K 353 - end of helix removed outlier: 3.911A pdb=" N ALA K 356 " --> pdb=" O LEU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 392 removed outlier: 4.309A pdb=" N TYR K 388 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 460 removed outlier: 3.732A pdb=" N ALA K 455 " --> pdb=" O ASN K 451 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS K 457 " --> pdb=" O GLN K 453 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL K 458 " --> pdb=" O ASN K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 466 removed outlier: 4.000A pdb=" N HIS K 465 " --> pdb=" O HIS K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 477 Processing helix chain 'K' and resid 499 through 508 Processing helix chain 'K' and resid 516 through 524 removed outlier: 3.537A pdb=" N GLY K 523 " --> pdb=" O ALA K 519 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU K 524 " --> pdb=" O LEU K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 531 Processing helix chain 'K' and resid 534 through 540 removed outlier: 3.519A pdb=" N LEU K 538 " --> pdb=" O ASN K 534 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU K 540 " --> pdb=" O ASP K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 567 through 571 Processing helix chain 'K' and resid 577 through 592 Processing helix chain 'K' and resid 599 through 611 removed outlier: 3.597A pdb=" N ILE K 603 " --> pdb=" O ASP K 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 616 through 627 removed outlier: 4.299A pdb=" N TYR K 620 " --> pdb=" O PRO K 616 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 621 " --> pdb=" O ALA K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 636 removed outlier: 3.874A pdb=" N ASN K 636 " --> pdb=" O LYS K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 651 removed outlier: 3.576A pdb=" N SER K 651 " --> pdb=" O TYR K 647 " (cutoff:3.500A) Processing helix chain 'K' and resid 659 through 669 Processing helix chain 'K' and resid 676 through 701 removed outlier: 4.022A pdb=" N MET K 682 " --> pdb=" O GLU K 678 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR K 683 " --> pdb=" O ALA K 679 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA K 701 " --> pdb=" O LEU K 697 " (cutoff:3.500A) Processing helix chain 'K' and resid 711 through 716 Processing helix chain 'K' and resid 731 through 740 removed outlier: 4.180A pdb=" N HIS K 735 " --> pdb=" O ASP K 731 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 762 Processing helix chain 'K' and resid 775 through 786 removed outlier: 3.829A pdb=" N TYR K 780 " --> pdb=" O PHE K 776 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL K 784 " --> pdb=" O TYR K 780 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN K 785 " --> pdb=" O GLY K 781 " (cutoff:3.500A) Processing helix chain 'K' and resid 806 through 815 Processing helix chain 'K' and resid 815 through 821 Processing helix chain 'K' and resid 831 through 840 Processing helix chain 'K' and resid 842 through 847 Processing helix chain 'K' and resid 855 through 860 removed outlier: 4.355A pdb=" N ASN K 859 " --> pdb=" O ASP K 855 " (cutoff:3.500A) Processing helix chain 'K' and resid 863 through 873 removed outlier: 3.738A pdb=" N ASP K 867 " --> pdb=" O GLY K 863 " (cutoff:3.500A) Processing helix chain 'K' and resid 877 through 887 removed outlier: 3.884A pdb=" N ILE K 881 " --> pdb=" O THR K 877 " (cutoff:3.500A) Processing helix chain 'K' and resid 940 through 943 Processing helix chain 'K' and resid 956 through 964 Processing helix chain 'K' and resid 965 through 974 Processing helix chain 'K' and resid 975 through 979 removed outlier: 3.738A pdb=" N ALA K 979 " --> pdb=" O GLN K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 998 through 1008 removed outlier: 3.893A pdb=" N GLY K1002 " --> pdb=" O ARG K 998 " (cutoff:3.500A) Processing helix chain 'K' and resid 1011 through 1021 Processing helix chain 'K' and resid 1026 through 1036 Processing helix chain 'K' and resid 1123 through 1128 removed outlier: 3.515A pdb=" N VAL K1127 " --> pdb=" O ASP K1123 " (cutoff:3.500A) Processing helix chain 'K' and resid 1135 through 1147 Processing helix chain 'K' and resid 1192 through 1198 removed outlier: 3.877A pdb=" N PHE K1196 " --> pdb=" O ASP K1192 " (cutoff:3.500A) Processing helix chain 'K' and resid 1216 through 1226 removed outlier: 3.524A pdb=" N ALA K1220 " --> pdb=" O ASN K1216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K1224 " --> pdb=" O ALA K1220 " (cutoff:3.500A) Processing helix chain 'K' and resid 1241 through 1246 removed outlier: 3.731A pdb=" N SER K1245 " --> pdb=" O ASN K1241 " (cutoff:3.500A) Processing helix chain 'K' and resid 1249 through 1255 Processing helix chain 'K' and resid 1269 through 1276 removed outlier: 4.093A pdb=" N ALA K1273 " --> pdb=" O SER K1269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE K1274 " --> pdb=" O PRO K1270 " (cutoff:3.500A) Processing helix chain 'K' and resid 1276 through 1283 removed outlier: 4.205A pdb=" N ASN K1283 " --> pdb=" O GLU K1279 " (cutoff:3.500A) Processing helix chain 'K' and resid 1286 through 1297 removed outlier: 3.786A pdb=" N ASN K1292 " --> pdb=" O TYR K1288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K1297 " --> pdb=" O GLU K1293 " (cutoff:3.500A) Processing helix chain 'K' and resid 1324 through 1329 Processing helix chain 'K' and resid 1339 through 1349 removed outlier: 3.659A pdb=" N ILE K1343 " --> pdb=" O SER K1339 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 32 Processing helix chain 'N' and resid 41 through 45 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 135 through 141 Processing helix chain 'N' and resid 147 through 187 removed outlier: 4.088A pdb=" N GLY N 168 " --> pdb=" O ALA N 164 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS N 187 " --> pdb=" O VAL N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 199 removed outlier: 4.486A pdb=" N THR N 196 " --> pdb=" O PHE N 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU N 197 " --> pdb=" O ILE N 193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP N 199 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 226 removed outlier: 3.743A pdb=" N ALA N 217 " --> pdb=" O SER N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 237 removed outlier: 4.288A pdb=" N GLU N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN N 235 " --> pdb=" O ASP N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 255 removed outlier: 3.785A pdb=" N VAL N 255 " --> pdb=" O MET N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 295 Processing helix chain 'N' and resid 315 through 324 removed outlier: 3.920A pdb=" N VAL N 319 " --> pdb=" O GLY N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 339 removed outlier: 3.586A pdb=" N ILE N 338 " --> pdb=" O PHE N 334 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 356 Proline residue: N 353 - end of helix removed outlier: 3.600A pdb=" N ALA N 356 " --> pdb=" O LEU N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 390 Processing helix chain 'N' and resid 453 through 459 removed outlier: 3.713A pdb=" N LYS N 457 " --> pdb=" O ASN N 454 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL N 458 " --> pdb=" O ALA N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 477 removed outlier: 3.833A pdb=" N ALA N 477 " --> pdb=" O SER N 473 " (cutoff:3.500A) Processing helix chain 'N' and resid 498 through 508 removed outlier: 3.724A pdb=" N ILE N 502 " --> pdb=" O ASN N 498 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE N 506 " --> pdb=" O ILE N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 516 through 522 removed outlier: 3.833A pdb=" N LEU N 520 " --> pdb=" O THR N 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 525 through 531 Processing helix chain 'N' and resid 534 through 540 removed outlier: 3.566A pdb=" N LEU N 538 " --> pdb=" O ASN N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 567 through 571 Processing helix chain 'N' and resid 572 through 576 Processing helix chain 'N' and resid 577 through 593 removed outlier: 3.581A pdb=" N GLN N 581 " --> pdb=" O PRO N 577 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER N 593 " --> pdb=" O GLU N 589 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 611 Processing helix chain 'N' and resid 616 through 627 removed outlier: 3.502A pdb=" N TYR N 620 " --> pdb=" O PRO N 616 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 627 " --> pdb=" O GLU N 623 " (cutoff:3.500A) Processing helix chain 'N' and resid 629 through 635 Processing helix chain 'N' and resid 636 through 651 removed outlier: 3.522A pdb=" N SER N 651 " --> pdb=" O TYR N 647 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 669 Processing helix chain 'N' and resid 676 through 701 removed outlier: 3.748A pdb=" N SER N 681 " --> pdb=" O LYS N 677 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET N 682 " --> pdb=" O GLU N 678 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR N 683 " --> pdb=" O ALA N 679 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU N 694 " --> pdb=" O LEU N 690 " (cutoff:3.500A) Processing helix chain 'N' and resid 711 through 716 Processing helix chain 'N' and resid 731 through 740 removed outlier: 4.208A pdb=" N HIS N 735 " --> pdb=" O ASP N 731 " (cutoff:3.500A) Processing helix chain 'N' and resid 755 through 757 No H-bonds generated for 'chain 'N' and resid 755 through 757' Processing helix chain 'N' and resid 758 through 762 Processing helix chain 'N' and resid 770 through 774 removed outlier: 3.582A pdb=" N ALA N 773 " --> pdb=" O ASP N 770 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA N 774 " --> pdb=" O GLU N 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 770 through 774' Processing helix chain 'N' and resid 775 through 786 removed outlier: 3.748A pdb=" N TYR N 782 " --> pdb=" O ALA N 778 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG N 783 " --> pdb=" O LEU N 779 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL N 784 " --> pdb=" O TYR N 780 " (cutoff:3.500A) Processing helix chain 'N' and resid 806 through 815 removed outlier: 3.508A pdb=" N LYS N 810 " --> pdb=" O ASP N 806 " (cutoff:3.500A) Processing helix chain 'N' and resid 815 through 821 Processing helix chain 'N' and resid 831 through 841 removed outlier: 3.630A pdb=" N TYR N 841 " --> pdb=" O GLN N 837 " (cutoff:3.500A) Processing helix chain 'N' and resid 842 through 847 removed outlier: 3.501A pdb=" N PHE N 846 " --> pdb=" O ASN N 842 " (cutoff:3.500A) Processing helix chain 'N' and resid 855 through 860 removed outlier: 4.050A pdb=" N ASN N 859 " --> pdb=" O ASP N 855 " (cutoff:3.500A) Processing helix chain 'N' and resid 863 through 872 Processing helix chain 'N' and resid 877 through 887 removed outlier: 3.542A pdb=" N ILE N 881 " --> pdb=" O THR N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 914 through 916 No H-bonds generated for 'chain 'N' and resid 914 through 916' Processing helix chain 'N' and resid 940 through 943 Processing helix chain 'N' and resid 956 through 964 Processing helix chain 'N' and resid 964 through 974 Processing helix chain 'N' and resid 975 through 979 removed outlier: 3.921A pdb=" N ALA N 979 " --> pdb=" O GLN N 976 " (cutoff:3.500A) Processing helix chain 'N' and resid 998 through 1007 removed outlier: 3.694A pdb=" N GLY N1002 " --> pdb=" O ARG N 998 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU N1007 " --> pdb=" O LYS N1003 " (cutoff:3.500A) Processing helix chain 'N' and resid 1011 through 1021 Processing helix chain 'N' and resid 1026 through 1037 removed outlier: 3.702A pdb=" N LEU N1036 " --> pdb=" O ALA N1032 " (cutoff:3.500A) Processing helix chain 'N' and resid 1123 through 1128 Processing helix chain 'N' and resid 1135 through 1147 removed outlier: 3.610A pdb=" N GLY N1147 " --> pdb=" O LYS N1143 " (cutoff:3.500A) Processing helix chain 'N' and resid 1192 through 1196 Processing helix chain 'N' and resid 1216 through 1226 Processing helix chain 'N' and resid 1249 through 1256 Processing helix chain 'N' and resid 1269 through 1276 removed outlier: 4.069A pdb=" N ALA N1273 " --> pdb=" O SER N1269 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE N1274 " --> pdb=" O PRO N1270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN N1276 " --> pdb=" O ARG N1272 " (cutoff:3.500A) Processing helix chain 'N' and resid 1276 through 1283 removed outlier: 3.750A pdb=" N ASN N1283 " --> pdb=" O GLU N1279 " (cutoff:3.500A) Processing helix chain 'N' and resid 1286 through 1297 Processing helix chain 'N' and resid 1324 through 1329 removed outlier: 3.572A pdb=" N LEU N1328 " --> pdb=" O PRO N1324 " (cutoff:3.500A) Processing helix chain 'N' and resid 1339 through 1349 removed outlier: 3.885A pdb=" N ILE N1343 " --> pdb=" O SER N1339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP N1344 " --> pdb=" O ARG N1340 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU N1345 " --> pdb=" O ALA N1341 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET N1347 " --> pdb=" O ILE N1343 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 75 Processing helix chain 'O' and resid 135 through 143 removed outlier: 3.775A pdb=" N ILE O 140 " --> pdb=" O LEU O 136 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS O 142 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 187 removed outlier: 3.713A pdb=" N LYS O 159 " --> pdb=" O VAL O 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS O 187 " --> pdb=" O VAL O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 199 removed outlier: 5.104A pdb=" N THR O 196 " --> pdb=" O PHE O 192 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU O 197 " --> pdb=" O ILE O 193 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP O 199 " --> pdb=" O GLN O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 228 through 237 removed outlier: 3.582A pdb=" N ARG O 232 " --> pdb=" O PHE O 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU O 234 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN O 235 " --> pdb=" O ASP O 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 255 Processing helix chain 'O' and resid 259 through 263 removed outlier: 4.564A pdb=" N GLY O 263 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 294 Processing helix chain 'O' and resid 314 through 325 removed outlier: 3.886A pdb=" N THR O 320 " --> pdb=" O GLU O 316 " (cutoff:3.500A) Processing helix chain 'O' and resid 330 through 339 removed outlier: 3.811A pdb=" N PHE O 334 " --> pdb=" O THR O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 356 Proline residue: O 353 - end of helix removed outlier: 3.879A pdb=" N ALA O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 390 Processing helix chain 'O' and resid 455 through 460 removed outlier: 3.596A pdb=" N LEU O 459 " --> pdb=" O ALA O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 461 through 466 removed outlier: 4.206A pdb=" N HIS O 465 " --> pdb=" O HIS O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 467 through 476 Processing helix chain 'O' and resid 498 through 508 removed outlier: 3.944A pdb=" N ILE O 502 " --> pdb=" O ASN O 498 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 522 Processing helix chain 'O' and resid 525 through 531 Processing helix chain 'O' and resid 537 through 541 Processing helix chain 'O' and resid 567 through 571 Processing helix chain 'O' and resid 577 through 593 Processing helix chain 'O' and resid 599 through 611 removed outlier: 3.621A pdb=" N ILE O 603 " --> pdb=" O ASP O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 617 through 627 removed outlier: 3.735A pdb=" N VAL O 621 " --> pdb=" O ALA O 617 " (cutoff:3.500A) Processing helix chain 'O' and resid 629 through 651 Proline residue: O 638 - end of helix removed outlier: 4.061A pdb=" N LEU O 642 " --> pdb=" O PRO O 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 659 through 670 removed outlier: 3.548A pdb=" N ILE O 663 " --> pdb=" O SER O 659 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 670 " --> pdb=" O ILE O 666 " (cutoff:3.500A) Processing helix chain 'O' and resid 676 through 702 removed outlier: 3.752A pdb=" N MET O 682 " --> pdb=" O GLU O 678 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR O 683 " --> pdb=" O ALA O 679 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY O 702 " --> pdb=" O MET O 698 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 731 through 740 removed outlier: 4.078A pdb=" N HIS O 735 " --> pdb=" O ASP O 731 " (cutoff:3.500A) Processing helix chain 'O' and resid 758 through 762 removed outlier: 4.111A pdb=" N PHE O 762 " --> pdb=" O ALA O 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 758 through 762' Processing helix chain 'O' and resid 768 through 773 Processing helix chain 'O' and resid 775 through 785 removed outlier: 3.891A pdb=" N ARG O 783 " --> pdb=" O LEU O 779 " (cutoff:3.500A) Processing helix chain 'O' and resid 807 through 815 Processing helix chain 'O' and resid 815 through 822 Processing helix chain 'O' and resid 831 through 840 Processing helix chain 'O' and resid 841 through 843 No H-bonds generated for 'chain 'O' and resid 841 through 843' Processing helix chain 'O' and resid 863 through 873 removed outlier: 3.741A pdb=" N SER O 872 " --> pdb=" O LEU O 868 " (cutoff:3.500A) Processing helix chain 'O' and resid 877 through 886 Processing helix chain 'O' and resid 887 through 889 No H-bonds generated for 'chain 'O' and resid 887 through 889' Processing helix chain 'O' and resid 937 through 942 Processing helix chain 'O' and resid 956 through 964 removed outlier: 4.084A pdb=" N THR O 962 " --> pdb=" O ARG O 958 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET O 963 " --> pdb=" O VAL O 959 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS O 964 " --> pdb=" O ALA O 960 " (cutoff:3.500A) Processing helix chain 'O' and resid 964 through 974 removed outlier: 3.532A pdb=" N ASN O 974 " --> pdb=" O PHE O 970 " (cutoff:3.500A) Processing helix chain 'O' and resid 975 through 979 removed outlier: 4.013A pdb=" N ALA O 979 " --> pdb=" O GLN O 976 " (cutoff:3.500A) Processing helix chain 'O' and resid 998 through 1007 removed outlier: 3.633A pdb=" N GLY O1002 " --> pdb=" O ARG O 998 " (cutoff:3.500A) Processing helix chain 'O' and resid 1012 through 1022 removed outlier: 3.668A pdb=" N SER O1016 " --> pdb=" O LEU O1012 " (cutoff:3.500A) Processing helix chain 'O' and resid 1026 through 1037 removed outlier: 3.744A pdb=" N LEU O1036 " --> pdb=" O ALA O1032 " (cutoff:3.500A) Processing helix chain 'O' and resid 1123 through 1128 removed outlier: 3.687A pdb=" N VAL O1127 " --> pdb=" O ASP O1123 " (cutoff:3.500A) Processing helix chain 'O' and resid 1135 through 1146 Processing helix chain 'O' and resid 1193 through 1198 removed outlier: 4.041A pdb=" N LYS O1198 " --> pdb=" O ALA O1194 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1226 Processing helix chain 'O' and resid 1241 through 1246 removed outlier: 3.869A pdb=" N GLN O1246 " --> pdb=" O PRO O1242 " (cutoff:3.500A) Processing helix chain 'O' and resid 1249 through 1256 Processing helix chain 'O' and resid 1271 through 1276 Processing helix chain 'O' and resid 1276 through 1282 Processing helix chain 'O' and resid 1283 through 1285 No H-bonds generated for 'chain 'O' and resid 1283 through 1285' Processing helix chain 'O' and resid 1286 through 1297 removed outlier: 3.780A pdb=" N SER O1295 " --> pdb=" O VAL O1291 " (cutoff:3.500A) Processing helix chain 'O' and resid 1324 through 1329 Processing helix chain 'O' and resid 1339 through 1349 removed outlier: 3.629A pdb=" N ILE O1343 " --> pdb=" O SER O1339 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 11 Processing helix chain 'v' and resid 24 through 32 removed outlier: 3.953A pdb=" N GLU v 30 " --> pdb=" O THR v 26 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU v 31 " --> pdb=" O VAL v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 74 removed outlier: 3.727A pdb=" N HIS v 73 " --> pdb=" O ARG v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 123 Processing helix chain 'v' and resid 332 through 360 removed outlier: 4.276A pdb=" N GLU v 336 " --> pdb=" O LEU v 332 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG v 337 " --> pdb=" O GLY v 333 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU v 338 " --> pdb=" O ALA v 334 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE v 339 " --> pdb=" O PRO v 335 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU v 342 " --> pdb=" O GLU v 338 " (cutoff:3.500A) Processing helix chain 'v' and resid 382 through 396 removed outlier: 3.714A pdb=" N GLU v 388 " --> pdb=" O ASP v 384 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN v 394 " --> pdb=" O PHE v 390 " (cutoff:3.500A) Processing helix chain 'v' and resid 401 through 408 removed outlier: 3.510A pdb=" N LYS v 405 " --> pdb=" O SER v 401 " (cutoff:3.500A) Processing helix chain 'v' and resid 412 through 418 Processing helix chain 'v' and resid 425 through 429 removed outlier: 4.259A pdb=" N GLU v 428 " --> pdb=" O PRO v 425 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU v 429 " --> pdb=" O LEU v 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 425 through 429' Processing helix chain 'v' and resid 455 through 459 Processing helix chain 'v' and resid 490 through 502 Processing helix chain 'w' and resid 36 through 53 Processing helix chain 'w' and resid 60 through 98 removed outlier: 3.886A pdb=" N ARG w 64 " --> pdb=" O VAL w 60 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU w 70 " --> pdb=" O LEU w 66 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP w 71 " --> pdb=" O ARG w 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL w 92 " --> pdb=" O LEU w 88 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA w 93 " --> pdb=" O ASP w 89 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 101 No H-bonds generated for 'chain 'w' and resid 99 through 101' Processing helix chain 'x' and resid 36 through 96 removed outlier: 4.399A pdb=" N GLU x 40 " --> pdb=" O PRO x 36 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU x 41 " --> pdb=" O GLU x 37 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU x 83 " --> pdb=" O ALA x 79 " (cutoff:3.500A) Processing helix chain 'y' and resid 3114 through 3148 removed outlier: 3.795A pdb=" N SER y3120 " --> pdb=" O SER y3116 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG y3121 " --> pdb=" O ARG y3117 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL y3123 " --> pdb=" O LEU y3119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS y3129 " --> pdb=" O GLN y3125 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG y3132 " --> pdb=" O ARG y3128 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER y3133 " --> pdb=" O LYS y3129 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR y3134 " --> pdb=" O LEU y3130 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU y3142 " --> pdb=" O ILE y3138 " (cutoff:3.500A) Processing helix chain 'z' and resid 3114 through 3119 Processing helix chain 'z' and resid 3120 through 3148 removed outlier: 4.230A pdb=" N ARG z3132 " --> pdb=" O ARG z3128 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER z3133 " --> pdb=" O LYS z3129 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR z3134 " --> pdb=" O LEU z3130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR z3148 " --> pdb=" O LEU z3144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 18 Processing helix chain 'Z' and resid 22 through 29 removed outlier: 4.799A pdb=" N LYS Z 26 " --> pdb=" O PRO Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 66 removed outlier: 4.112A pdb=" N PHE Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY Z 66 " --> pdb=" O GLN Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 77 removed outlier: 4.020A pdb=" N ARG Z 77 " --> pdb=" O ALA Z 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 18 removed outlier: 3.531A pdb=" N ASP a 17 " --> pdb=" O ARG a 13 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 29 removed outlier: 4.636A pdb=" N LYS a 26 " --> pdb=" O PRO a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 65 removed outlier: 4.219A pdb=" N PHE a 65 " --> pdb=" O VAL a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 77 removed outlier: 3.789A pdb=" N ARG a 77 " --> pdb=" O ALA a 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 18 removed outlier: 3.528A pdb=" N ASP d 17 " --> pdb=" O ARG d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 28 removed outlier: 4.074A pdb=" N LYS d 26 " --> pdb=" O PRO d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 65 removed outlier: 3.776A pdb=" N PHE d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 76 removed outlier: 3.953A pdb=" N ARG d 72 " --> pdb=" O PRO d 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 36 through 65 removed outlier: 3.867A pdb=" N PHE e 65 " --> pdb=" O VAL e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 75 removed outlier: 3.592A pdb=" N ARG e 72 " --> pdb=" O PRO e 68 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 100 No H-bonds generated for 'chain 'f' and resid 98 through 100' Processing helix chain 'f' and resid 127 through 136 removed outlier: 3.560A pdb=" N ILE f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) Processing helix chain 'f' and resid 151 through 159 removed outlier: 3.501A pdb=" N TYR f 159 " --> pdb=" O ALA f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 169 Processing helix chain 'f' and resid 171 through 179 removed outlier: 3.707A pdb=" N ALA f 177 " --> pdb=" O GLY f 173 " (cutoff:3.500A) Processing helix chain 'f' and resid 180 through 184 Processing helix chain 'f' and resid 285 through 297 removed outlier: 3.943A pdb=" N MET f 290 " --> pdb=" O HIS f 286 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN f 291 " --> pdb=" O CYS f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 297 through 303 Processing helix chain 'f' and resid 312 through 317 removed outlier: 3.514A pdb=" N GLU f 315 " --> pdb=" O HIS f 312 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR f 317 " --> pdb=" O GLU f 314 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 20 removed outlier: 3.845A pdb=" N ARG h 15 " --> pdb=" O ARG h 11 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY h 18 " --> pdb=" O ARG h 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 44 removed outlier: 3.963A pdb=" N LEU h 42 " --> pdb=" O ASP h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 61 Processing helix chain 'h' and resid 127 through 136 Processing helix chain 'h' and resid 150 through 159 Processing helix chain 'h' and resid 162 through 167 Processing helix chain 'h' and resid 171 through 179 removed outlier: 3.931A pdb=" N ALA h 177 " --> pdb=" O GLY h 173 " (cutoff:3.500A) Processing helix chain 'h' and resid 180 through 185 removed outlier: 4.142A pdb=" N PHE h 184 " --> pdb=" O ARG h 180 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE h 185 " --> pdb=" O PHE h 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 180 through 185' Processing helix chain 'h' and resid 233 through 237 removed outlier: 3.846A pdb=" N LEU h 237 " --> pdb=" O LEU h 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 233 through 237' Processing helix chain 'h' and resid 285 through 306 removed outlier: 3.530A pdb=" N ASN h 291 " --> pdb=" O CYS h 287 " (cutoff:3.500A) Proline residue: h 299 - end of helix Processing helix chain 'h' and resid 312 through 317 removed outlier: 3.772A pdb=" N LEU h 316 " --> pdb=" O ILE h 313 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR h 317 " --> pdb=" O GLU h 314 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 24 removed outlier: 3.605A pdb=" N LYS k 20 " --> pdb=" O ASP k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 44 Processing helix chain 'k' and resid 45 through 48 Processing helix chain 'k' and resid 56 through 67 Processing helix chain 'k' and resid 117 through 121 removed outlier: 3.721A pdb=" N ALA k 121 " --> pdb=" O GLY k 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 117 through 121' Processing helix chain 'k' and resid 140 through 161 removed outlier: 4.209A pdb=" N ARG k 158 " --> pdb=" O ASN k 154 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET k 161 " --> pdb=" O SER k 157 " (cutoff:3.500A) Processing helix chain 'k' and resid 164 through 172 removed outlier: 3.540A pdb=" N ASP k 168 " --> pdb=" O PRO k 164 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU k 170 " --> pdb=" O ASN k 166 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL k 172 " --> pdb=" O ASP k 168 " (cutoff:3.500A) Processing helix chain 'k' and resid 197 through 215 removed outlier: 3.687A pdb=" N LEU k 201 " --> pdb=" O LEU k 197 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU k 215 " --> pdb=" O ILE k 211 " (cutoff:3.500A) Processing helix chain 'k' and resid 218 through 231 removed outlier: 4.110A pdb=" N ARG k 229 " --> pdb=" O ARG k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 234 through 239 removed outlier: 4.290A pdb=" N LEU k 238 " --> pdb=" O LEU k 235 " (cutoff:3.500A) Processing helix chain 'k' and resid 244 through 251 removed outlier: 3.890A pdb=" N ALA k 248 " --> pdb=" O PRO k 244 " (cutoff:3.500A) Processing helix chain 'k' and resid 256 through 272 removed outlier: 3.560A pdb=" N ASP k 260 " --> pdb=" O SER k 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER k 262 " --> pdb=" O ALA k 258 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN k 272 " --> pdb=" O MET k 268 " (cutoff:3.500A) Processing helix chain 'k' and resid 273 through 279 removed outlier: 3.525A pdb=" N LEU k 277 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 24 Processing helix chain 'm' and resid 56 through 67 removed outlier: 3.989A pdb=" N SER m 65 " --> pdb=" O TYR m 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 161 Processing helix chain 'm' and resid 165 through 173 Processing helix chain 'm' and resid 197 through 213 removed outlier: 3.570A pdb=" N TYR m 208 " --> pdb=" O ASN m 204 " (cutoff:3.500A) Processing helix chain 'm' and resid 217 through 231 removed outlier: 4.053A pdb=" N MET m 221 " --> pdb=" O PRO m 217 " (cutoff:3.500A) Processing helix chain 'm' and resid 244 through 252 removed outlier: 4.430A pdb=" N ALA m 248 " --> pdb=" O PRO m 244 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG m 249 " --> pdb=" O ASP m 245 " (cutoff:3.500A) Processing helix chain 'm' and resid 256 through 279 removed outlier: 3.956A pdb=" N GLN m 272 " --> pdb=" O MET m 268 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER m 273 " --> pdb=" O THR m 269 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN m 279 " --> pdb=" O ALA m 275 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 24 removed outlier: 3.517A pdb=" N ARG p 24 " --> pdb=" O LYS p 20 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 67 removed outlier: 3.762A pdb=" N MET p 60 " --> pdb=" O ASP p 56 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP p 66 " --> pdb=" O ASN p 62 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 121 Processing helix chain 'p' and resid 140 through 163 Processing helix chain 'p' and resid 168 through 177 removed outlier: 3.698A pdb=" N HIS p 175 " --> pdb=" O ASP p 171 " (cutoff:3.500A) Processing helix chain 'p' and resid 203 through 228 removed outlier: 3.673A pdb=" N LEU p 207 " --> pdb=" O ASP p 203 " (cutoff:3.500A) Proline residue: p 217 - end of helix removed outlier: 3.649A pdb=" N ARG p 222 " --> pdb=" O ARG p 218 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE p 228 " --> pdb=" O VAL p 224 " (cutoff:3.500A) Processing helix chain 'p' and resid 234 through 241 removed outlier: 3.592A pdb=" N LEU p 238 " --> pdb=" O ASP p 234 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU p 241 " --> pdb=" O ASN p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 244 through 249 Processing helix chain 'p' and resid 256 through 279 removed outlier: 3.894A pdb=" N LEU p 261 " --> pdb=" O VAL p 257 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER p 276 " --> pdb=" O GLN p 272 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU p 277 " --> pdb=" O SER p 273 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE p 278 " --> pdb=" O LEU p 274 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN p 279 " --> pdb=" O ALA p 275 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 23 removed outlier: 3.666A pdb=" N ALA r 19 " --> pdb=" O THR r 15 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 43 removed outlier: 3.555A pdb=" N GLY r 42 " --> pdb=" O ASN r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 67 Processing helix chain 'r' and resid 117 through 121 Processing helix chain 'r' and resid 140 through 163 removed outlier: 3.731A pdb=" N LEU r 147 " --> pdb=" O ALA r 143 " (cutoff:3.500A) Processing helix chain 'r' and resid 164 through 167 removed outlier: 3.937A pdb=" N ALA r 167 " --> pdb=" O PRO r 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 164 through 167' Processing helix chain 'r' and resid 168 through 177 Processing helix chain 'r' and resid 204 through 228 Proline residue: r 217 - end of helix removed outlier: 3.754A pdb=" N MET r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG r 222 " --> pdb=" O ARG r 218 " (cutoff:3.500A) Processing helix chain 'r' and resid 233 through 240 removed outlier: 4.184A pdb=" N ASN r 237 " --> pdb=" O HIS r 233 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU r 238 " --> pdb=" O ASP r 234 " (cutoff:3.500A) Processing helix chain 'r' and resid 241 through 243 No H-bonds generated for 'chain 'r' and resid 241 through 243' Processing helix chain 'r' and resid 244 through 249 removed outlier: 3.657A pdb=" N ALA r 248 " --> pdb=" O PRO r 244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG r 249 " --> pdb=" O ASP r 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 244 through 249' Processing helix chain 'r' and resid 256 through 278 Processing sheet with id=AA1, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AA2, first strand: chain 'J' and resid 57 through 60 removed outlier: 6.699A pdb=" N GLY J 57 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ARG K 96 " --> pdb=" O GLY J 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR J 59 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER K 98 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG K 114 " --> pdb=" O VAL K 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 77 through 78 removed outlier: 6.843A pdb=" N VAL J 78 " --> pdb=" O MET J1067 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE J1069 " --> pdb=" O VAL J 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 77 through 78 removed outlier: 6.843A pdb=" N VAL J 78 " --> pdb=" O MET J1067 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE J1069 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA J1083 " --> pdb=" O ALA J1079 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA J1079 " --> pdb=" O ALA J1083 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR J1085 " --> pdb=" O ARG J1077 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG J1077 " --> pdb=" O THR J1085 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 94 through 99 removed outlier: 4.520A pdb=" N ARG J 114 " --> pdb=" O VAL J 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 371 through 374 removed outlier: 4.757A pdb=" N VAL J 276 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA J 380 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY J 278 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLU J 382 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE J 280 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 1183 through 1187 removed outlier: 7.366A pdb=" N GLU J1051 " --> pdb=" O ALA J1112 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA J1112 " --> pdb=" O GLU J1051 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU J1053 " --> pdb=" O VAL J1110 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL J1110 " --> pdb=" O LEU J1053 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU J1055 " --> pdb=" O ALA J1108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 1103 through 1112 removed outlier: 6.663A pdb=" N GLU J1055 " --> pdb=" O ALA J1108 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL J1110 " --> pdb=" O LEU J1053 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU J1053 " --> pdb=" O VAL J1110 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA J1112 " --> pdb=" O GLU J1051 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU J1051 " --> pdb=" O ALA J1112 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N PHE J1332 " --> pdb=" O GLN J 402 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER J 404 " --> pdb=" O PHE J1332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 1332 through 1333 removed outlier: 9.540A pdb=" N PHE J1332 " --> pdb=" O GLN J 402 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER J 404 " --> pdb=" O PHE J1332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 371 through 374 removed outlier: 4.757A pdb=" N VAL J 276 " --> pdb=" O ALA J 378 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA J 380 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY J 278 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLU J 382 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE J 280 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 438 through 441 Processing sheet with id=AB3, first strand: chain 'J' and resid 546 through 549 Processing sheet with id=AB4, first strand: chain 'J' and resid 727 through 728 Processing sheet with id=AB5, first strand: chain 'J' and resid 763 through 765 Processing sheet with id=AB6, first strand: chain 'J' and resid 928 through 930 Processing sheet with id=AB7, first strand: chain 'J' and resid 1336 through 1337 removed outlier: 3.743A pdb=" N SER J1336 " --> pdb=" O ILE J1363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 1373 through 1375 Processing sheet with id=AB9, first strand: chain 'K' and resid 123 through 134 removed outlier: 3.770A pdb=" N LEU K 133 " --> pdb=" O VAL K1084 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K1084 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR K 80 " --> pdb=" O MET K1067 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K1069 " --> pdb=" O THR K 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 123 through 134 removed outlier: 3.770A pdb=" N LEU K 133 " --> pdb=" O VAL K1084 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K1084 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 268 through 269 Processing sheet with id=AC3, first strand: chain 'K' and resid 371 through 374 removed outlier: 6.839A pdb=" N ALA K 378 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY K 278 " --> pdb=" O ALA K 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 1103 through 1113 removed outlier: 6.873A pdb=" N GLU K1055 " --> pdb=" O ALA K1108 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL K1110 " --> pdb=" O LEU K1053 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU K1053 " --> pdb=" O VAL K1110 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA K1112 " --> pdb=" O GLU K1051 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU K1051 " --> pdb=" O ALA K1112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 438 through 441 Processing sheet with id=AC6, first strand: chain 'K' and resid 546 through 550 Processing sheet with id=AC7, first strand: chain 'K' and resid 727 through 728 Processing sheet with id=AC8, first strand: chain 'K' and resid 763 through 765 removed outlier: 3.521A pdb=" N LEU K 796 " --> pdb=" O GLU K 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 928 through 930 Processing sheet with id=AD1, first strand: chain 'K' and resid 1336 through 1337 Processing sheet with id=AD2, first strand: chain 'O' and resid 114 through 121 removed outlier: 4.428A pdb=" N ARG O 114 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE N 52 " --> pdb=" O THR O 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY O 91 " --> pdb=" O PHE N 52 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL N 54 " --> pdb=" O GLY O 91 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE O 93 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU N 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N PHE O 95 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N VAL N 58 " --> pdb=" O PHE O 95 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ILE O 97 " --> pdb=" O VAL N 58 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N THR N 60 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N VAL O 99 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU N 53 " --> pdb=" O VAL O 327 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 123 through 134 removed outlier: 9.653A pdb=" N ALA N 309 " --> pdb=" O CYS N 77 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN N 79 " --> pdb=" O ALA N 309 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE N 311 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU N 81 " --> pdb=" O PHE N 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 123 through 134 Processing sheet with id=AD5, first strand: chain 'N' and resid 92 through 99 removed outlier: 3.861A pdb=" N ARG N 114 " --> pdb=" O VAL N 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 268 through 269 Processing sheet with id=AD7, first strand: chain 'N' and resid 371 through 374 removed outlier: 7.057A pdb=" N ALA N 380 " --> pdb=" O GLY N 277 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL N 279 " --> pdb=" O ALA N 380 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU N 382 " --> pdb=" O VAL N 279 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE N 281 " --> pdb=" O GLU N 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 1103 through 1113 removed outlier: 7.144A pdb=" N SER N1103 " --> pdb=" O SER N1061 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N SER N1061 " --> pdb=" O SER N1103 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N MET N1105 " --> pdb=" O PHE N1059 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE N1059 " --> pdb=" O MET N1105 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE N1057 " --> pdb=" O PRO N1107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG N1109 " --> pdb=" O GLU N1055 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU N1055 " --> pdb=" O ARG N1109 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N1053 " --> pdb=" O ALA N1111 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE N1113 " --> pdb=" O GLU N1051 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU N1051 " --> pdb=" O ILE N1113 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N PHE N1332 " --> pdb=" O GLN N 402 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER N 404 " --> pdb=" O PHE N1332 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 425 through 426 removed outlier: 3.618A pdb=" N LYS N 425 " --> pdb=" O THR O 419 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 438 through 441 Processing sheet with id=AE2, first strand: chain 'N' and resid 546 through 550 Processing sheet with id=AE3, first strand: chain 'N' and resid 727 through 728 Processing sheet with id=AE4, first strand: chain 'N' and resid 763 through 765 Processing sheet with id=AE5, first strand: chain 'N' and resid 928 through 930 removed outlier: 3.657A pdb=" N LEU N 928 " --> pdb=" O LEU N 828 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 123 through 134 removed outlier: 9.481A pdb=" N ALA O 309 " --> pdb=" O CYS O 77 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN O 79 " --> pdb=" O ALA O 309 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE O 311 " --> pdb=" O ASN O 79 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU O 81 " --> pdb=" O PHE O 311 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 123 through 134 removed outlier: 3.730A pdb=" N GLU O1078 " --> pdb=" O THR O1085 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU O1087 " --> pdb=" O ARG O1076 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG O1076 " --> pdb=" O GLU O1087 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS O1089 " --> pdb=" O VAL O1074 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL O1074 " --> pdb=" O HIS O1089 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 268 through 269 Processing sheet with id=AE9, first strand: chain 'O' and resid 370 through 374 removed outlier: 4.051A pdb=" N ALA O 370 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY O 278 " --> pdb=" O ALA O 380 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU O 382 " --> pdb=" O GLY O 278 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE O 280 " --> pdb=" O GLU O 382 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 1183 through 1187 removed outlier: 7.834A pdb=" N GLU O1051 " --> pdb=" O ALA O1112 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA O1112 " --> pdb=" O GLU O1051 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU O1053 " --> pdb=" O VAL O1110 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL O1110 " --> pdb=" O LEU O1053 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU O1055 " --> pdb=" O ALA O1108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 1103 through 1113 removed outlier: 7.092A pdb=" N GLU O1055 " --> pdb=" O ALA O1108 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL O1110 " --> pdb=" O LEU O1053 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU O1053 " --> pdb=" O VAL O1110 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA O1112 " --> pdb=" O GLU O1051 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU O1051 " --> pdb=" O ALA O1112 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N PHE O1332 " --> pdb=" O GLN O 402 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER O 404 " --> pdb=" O PHE O1332 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 1332 through 1333 removed outlier: 9.267A pdb=" N PHE O1332 " --> pdb=" O GLN O 402 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER O 404 " --> pdb=" O PHE O1332 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 370 through 374 removed outlier: 4.051A pdb=" N ALA O 370 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY O 278 " --> pdb=" O ALA O 380 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU O 382 " --> pdb=" O GLY O 278 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE O 280 " --> pdb=" O GLU O 382 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 438 through 441 Processing sheet with id=AF6, first strand: chain 'O' and resid 546 through 550 Processing sheet with id=AF7, first strand: chain 'O' and resid 727 through 728 removed outlier: 3.519A pdb=" N ALA O 728 " --> pdb=" O LEU O 924 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 763 through 765 Processing sheet with id=AF9, first strand: chain 'O' and resid 928 through 930 Processing sheet with id=AG1, first strand: chain 'O' and resid 1336 through 1337 Processing sheet with id=AG2, first strand: chain 'O' and resid 1373 through 1375 Processing sheet with id=AG3, first strand: chain 'v' and resid 21 through 22 Processing sheet with id=AG4, first strand: chain 'v' and resid 58 through 59 Processing sheet with id=AG5, first strand: chain 'v' and resid 63 through 65 Processing sheet with id=AG6, first strand: chain 'v' and resid 433 through 438 removed outlier: 5.577A pdb=" N TRP v 434 " --> pdb=" O SER v 423 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER v 423 " --> pdb=" O TRP v 434 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU v 419 " --> pdb=" O ILE v 438 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS v 424 " --> pdb=" O VAL v 463 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL v 463 " --> pdb=" O HIS v 424 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 89 through 96 removed outlier: 7.002A pdb=" N VAL f 89 " --> pdb=" O VAL f 207 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY f 91 " --> pdb=" O THR f 205 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY f 209 " --> pdb=" O SER f 355 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER f 355 " --> pdb=" O GLY f 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR f 354 " --> pdb=" O THR f 326 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU f 324 " --> pdb=" O ASN f 356 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY f 319 " --> pdb=" O TYR f 270 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR f 270 " --> pdb=" O GLY f 319 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL f 321 " --> pdb=" O LEU f 268 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU f 268 " --> pdb=" O VAL f 321 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N CYS f 323 " --> pdb=" O VAL f 266 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL f 266 " --> pdb=" O CYS f 323 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY f 325 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN f 281 " --> pdb=" O VAL f 231 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 125 through 126 removed outlier: 3.614A pdb=" N GLY f 189 " --> pdb=" O LEU f 110 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLN f 112 " --> pdb=" O PRO f 187 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N GLY f 189 " --> pdb=" O HIS f 208 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N HIS f 208 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU f 191 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL f 206 " --> pdb=" O LEU f 191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY f 209 " --> pdb=" O SER f 355 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER f 355 " --> pdb=" O GLY f 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR f 354 " --> pdb=" O THR f 326 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU f 324 " --> pdb=" O ASN f 356 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY f 319 " --> pdb=" O ILE f 363 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 223 through 226 removed outlier: 4.375A pdb=" N LEU f 345 " --> pdb=" O PHE f 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU f 349 " --> pdb=" O ARG f 334 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 89 through 96 removed outlier: 5.375A pdb=" N VAL h 206 " --> pdb=" O LEU h 191 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU h 191 " --> pdb=" O VAL h 206 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 110 through 112 removed outlier: 6.390A pdb=" N LEU h 110 " --> pdb=" O VAL h 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 209 through 210 Processing sheet with id=AH4, first strand: chain 'h' and resid 223 through 226 Processing sheet with id=AH5, first strand: chain 'h' and resid 230 through 232 removed outlier: 3.979A pdb=" N GLN h 281 " --> pdb=" O VAL h 231 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY h 325 " --> pdb=" O LEU h 264 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL h 266 " --> pdb=" O CYS h 323 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N CYS h 323 " --> pdb=" O VAL h 266 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU h 268 " --> pdb=" O VAL h 321 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL h 321 " --> pdb=" O LEU h 268 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TYR h 270 " --> pdb=" O GLY h 319 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY h 319 " --> pdb=" O TYR h 270 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'k' and resid 28 through 30 removed outlier: 6.598A pdb=" N ILE k 81 " --> pdb=" O ASP k 73 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL k 75 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER k 79 " --> pdb=" O VAL k 75 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL k 6 " --> pdb=" O GLN k 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'k' and resid 91 through 94 removed outlier: 4.254A pdb=" N TYR k 91 " --> pdb=" O CYS k 298 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS k 298 " --> pdb=" O TYR k 91 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR k 297 " --> pdb=" O ALA k 287 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'k' and resid 122 through 125 Processing sheet with id=AH9, first strand: chain 'k' and resid 178 through 181 Processing sheet with id=AI1, first strand: chain 'm' and resid 28 through 31 removed outlier: 3.665A pdb=" N THR m 68 " --> pdb=" O LEU m 31 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE m 81 " --> pdb=" O ASP m 73 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL m 75 " --> pdb=" O SER m 79 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER m 79 " --> pdb=" O VAL m 75 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'm' and resid 91 through 94 removed outlier: 3.919A pdb=" N ALA m 288 " --> pdb=" O THR m 297 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP m 299 " --> pdb=" O THR m 286 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR m 286 " --> pdb=" O TRP m 299 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'm' and resid 122 through 125 Processing sheet with id=AI4, first strand: chain 'm' and resid 178 through 181 Processing sheet with id=AI5, first strand: chain 'p' and resid 4 through 8 removed outlier: 6.863A pdb=" N SER p 79 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL p 75 " --> pdb=" O SER p 79 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE p 81 " --> pdb=" O ASP p 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR p 68 " --> pdb=" O LEU p 31 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'p' and resid 91 through 93 removed outlier: 6.413A pdb=" N THR p 295 " --> pdb=" O TYR p 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR p 289 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR p 297 " --> pdb=" O ALA p 287 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'p' and resid 122 through 125 Processing sheet with id=AI8, first strand: chain 'p' and resid 178 through 181 Processing sheet with id=AI9, first strand: chain 'r' and resid 28 through 31 removed outlier: 3.864A pdb=" N THR r 68 " --> pdb=" O LEU r 31 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE r 81 " --> pdb=" O ASP r 73 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL r 6 " --> pdb=" O GLN r 38 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 91 through 94 removed outlier: 3.740A pdb=" N ALA r 288 " --> pdb=" O THR r 297 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'r' and resid 122 through 125 Processing sheet with id=AJ3, first strand: chain 'r' and resid 178 through 181 2688 hydrogen bonds defined for protein. 7596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 36.43 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18795 1.34 - 1.46: 12205 1.46 - 1.58: 32365 1.58 - 1.70: 2 1.70 - 1.82: 599 Bond restraints: 63966 Sorted by residual: bond pdb=" CA TYR N 841 " pdb=" C TYR N 841 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.80e-02 3.09e+03 2.05e+01 bond pdb=" C PHE d 18 " pdb=" N PRO d 19 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.22e-02 6.72e+03 1.24e+01 bond pdb=" CA ARG K1150 " pdb=" CB ARG K1150 " ideal model delta sigma weight residual 1.527 1.613 -0.086 2.48e-02 1.63e+03 1.21e+01 bond pdb=" N PRO K 726 " pdb=" CA PRO K 726 " ideal model delta sigma weight residual 1.471 1.431 0.040 1.29e-02 6.01e+03 9.81e+00 bond pdb=" C ALA m 163 " pdb=" N PRO m 164 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.26e-02 6.30e+03 9.64e+00 ... (remaining 63961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.80: 86651 5.80 - 11.59: 275 11.59 - 17.39: 4 17.39 - 23.19: 1 23.19 - 28.98: 1 Bond angle restraints: 86932 Sorted by residual: angle pdb=" C SER f 161 " pdb=" N PRO f 162 " pdb=" CA PRO f 162 " ideal model delta sigma weight residual 119.84 90.86 28.98 1.25e+00 6.40e-01 5.38e+02 angle pdb=" C PHE a 18 " pdb=" N PRO a 19 " pdb=" CA PRO a 19 " ideal model delta sigma weight residual 119.84 99.25 20.59 1.25e+00 6.40e-01 2.71e+02 angle pdb=" N ARG N 483 " pdb=" CA ARG N 483 " pdb=" C ARG N 483 " ideal model delta sigma weight residual 111.07 120.82 -9.75 1.07e+00 8.73e-01 8.31e+01 angle pdb=" C VAL K1264 " pdb=" N PRO K1265 " pdb=" CA PRO K1265 " ideal model delta sigma weight residual 119.84 130.68 -10.84 1.25e+00 6.40e-01 7.52e+01 angle pdb=" C ALA K 911 " pdb=" N PRO K 912 " pdb=" CA PRO K 912 " ideal model delta sigma weight residual 119.84 129.78 -9.94 1.25e+00 6.40e-01 6.32e+01 ... (remaining 86927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 36749 17.34 - 34.69: 1428 34.69 - 52.03: 230 52.03 - 69.38: 29 69.38 - 86.72: 28 Dihedral angle restraints: 38464 sinusoidal: 15224 harmonic: 23240 Sorted by residual: dihedral pdb=" CA TYR K1161 " pdb=" C TYR K1161 " pdb=" N LEU K1162 " pdb=" CA LEU K1162 " ideal model delta harmonic sigma weight residual 180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA SER J1245 " pdb=" C SER J1245 " pdb=" N GLN J1246 " pdb=" CA GLN J1246 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLN k 162 " pdb=" C GLN k 162 " pdb=" N ALA k 163 " pdb=" CA ALA k 163 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 38461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 8736 0.093 - 0.187: 987 0.187 - 0.280: 59 0.280 - 0.374: 11 0.374 - 0.467: 2 Chirality restraints: 9795 Sorted by residual: chirality pdb=" CA ARG N 484 " pdb=" N ARG N 484 " pdb=" C ARG N 484 " pdb=" CB ARG N 484 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CB THR N 922 " pdb=" CA THR N 922 " pdb=" OG1 THR N 922 " pdb=" CG2 THR N 922 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA ASN N 672 " pdb=" N ASN N 672 " pdb=" C ASN N 672 " pdb=" CB ASN N 672 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 9792 not shown) Planarity restraints: 11336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE a 18 " 0.107 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO a 19 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO a 19 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO a 19 " 0.104 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER f 161 " 0.099 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO f 162 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO f 162 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO f 162 " 0.100 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE f 216 " -0.055 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO f 217 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO f 217 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO f 217 " -0.048 5.00e-02 4.00e+02 ... (remaining 11333 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 34 2.27 - 2.93: 24927 2.93 - 3.59: 88616 3.59 - 4.24: 135793 4.24 - 4.90: 228245 Nonbonded interactions: 477615 Sorted by model distance: nonbonded pdb=" NH2 ARG O 483 " pdb=" OD2 ASP O 553 " model vdw 1.618 3.120 nonbonded pdb=" O VAL r 77 " pdb=" OD1 ASP r 78 " model vdw 1.729 3.040 nonbonded pdb=" O GLY K 803 " pdb=" CD2 HIS K 804 " model vdw 1.862 3.260 nonbonded pdb=" O PRO O1010 " pdb=" O SER O1011 " model vdw 1.922 3.040 nonbonded pdb=" OD1 ASP K1252 " pdb=" ND2 ASN K1256 " model vdw 1.923 3.120 ... (remaining 477610 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 'J' and (resid 62 through 1148 or resid 1170 through 1381)) selection = (chain 'K' and (resid 62 through 307 or resid 364 through 1148 or resid 1170 thr \ ough 1381)) selection = (chain 'N' and (resid 62 through 307 or resid 364 through 1148 or resid 1170 thr \ ough 1381)) selection = (chain 'O' and (resid 62 through 307 or resid 364 through 1381)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'k' selection = chain 'm' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 1.820 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 120.310 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.460 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: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 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 : 0.006 0.093 63966 Z= 0.397 Angle : 1.038 28.981 86932 Z= 0.582 Chirality : 0.059 0.467 9795 Planarity : 0.008 0.163 11336 Dihedral : 10.302 86.722 23446 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.50 % Favored : 95.06 % Rotamer: Outliers : 0.68 % Allowed : 2.54 % Favored : 96.78 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.08), residues: 7881 helix: -1.68 (0.08), residues: 2878 sheet: -0.09 (0.15), residues: 1117 loop : -1.90 (0.09), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K1243 HIS 0.024 0.002 HIS O 469 PHE 0.056 0.003 PHE O 240 TYR 0.030 0.003 TYR N 680 ARG 0.018 0.001 ARG v 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2693 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 2647 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 PHE cc_start: 0.4761 (p90) cc_final: 0.4418 (p90) REVERT: J 121 ASN cc_start: 0.5435 (m110) cc_final: 0.5049 (m-40) REVERT: J 746 ILE cc_start: 0.5685 (mm) cc_final: 0.5000 (mm) REVERT: J 813 TYR cc_start: 0.5231 (m-80) cc_final: 0.4663 (m-80) REVERT: J 1119 ILE cc_start: 0.6926 (mm) cc_final: 0.6671 (mm) REVERT: J 1259 TYR cc_start: 0.5829 (p90) cc_final: 0.5602 (p90) REVERT: J 1335 LEU cc_start: 0.8258 (mt) cc_final: 0.7858 (mt) REVERT: K 39 LEU cc_start: 0.8263 (pp) cc_final: 0.7923 (pp) REVERT: K 147 THR cc_start: 0.6393 (p) cc_final: 0.6093 (t) REVERT: K 174 ARG cc_start: 0.6199 (mmt90) cc_final: 0.4688 (ptt180) REVERT: K 202 PHE cc_start: 0.6033 (m-80) cc_final: 0.5804 (m-80) REVERT: K 248 LEU cc_start: 0.7336 (mt) cc_final: 0.7093 (mt) REVERT: K 368 SER cc_start: 0.7923 (t) cc_final: 0.7565 (p) REVERT: K 426 MET cc_start: 0.5617 (mtt) cc_final: 0.4579 (mmt) REVERT: K 452 LEU cc_start: 0.7162 (tp) cc_final: 0.6817 (tp) REVERT: K 658 ASN cc_start: 0.6183 (m-40) cc_final: 0.5779 (t0) REVERT: K 813 TYR cc_start: 0.5238 (m-10) cc_final: 0.4689 (m-10) REVERT: K 882 ARG cc_start: 0.5303 (mtt180) cc_final: 0.5096 (mtt180) REVERT: K 902 VAL cc_start: 0.7990 (t) cc_final: 0.7741 (t) REVERT: K 1210 VAL cc_start: 0.8030 (t) cc_final: 0.7722 (t) REVERT: K 1224 ILE cc_start: 0.8056 (mm) cc_final: 0.7499 (mm) REVERT: K 1225 TYR cc_start: 0.4604 (m-80) cc_final: 0.4061 (m-80) REVERT: K 1287 LEU cc_start: 0.7052 (pp) cc_final: 0.6773 (pt) REVERT: K 1347 MET cc_start: 0.5499 (mmm) cc_final: 0.4904 (mmm) REVERT: N 46 ARG cc_start: 0.6534 (ptt-90) cc_final: 0.5611 (mmt180) REVERT: N 54 VAL cc_start: 0.6482 (p) cc_final: 0.6220 (p) REVERT: N 68 PHE cc_start: 0.7724 (t80) cc_final: 0.7510 (t80) REVERT: N 141 LEU cc_start: 0.5832 (tt) cc_final: 0.5497 (tt) REVERT: N 236 MET cc_start: 0.7024 (mmm) cc_final: 0.6711 (tpp) REVERT: N 411 LEU cc_start: 0.7051 (mp) cc_final: 0.6629 (mp) REVERT: N 426 MET cc_start: 0.6202 (mtt) cc_final: 0.5861 (mmm) REVERT: N 515 VAL cc_start: 0.6894 (t) cc_final: 0.6426 (m) REVERT: N 546 TYR cc_start: 0.6769 (m-80) cc_final: 0.6457 (m-80) REVERT: N 644 ILE cc_start: 0.7695 (mt) cc_final: 0.7436 (mm) REVERT: N 647 TYR cc_start: 0.7450 (t80) cc_final: 0.7089 (t80) REVERT: N 807 VAL cc_start: 0.7982 (t) cc_final: 0.7677 (t) REVERT: N 869 LEU cc_start: 0.7347 (mt) cc_final: 0.7132 (tp) REVERT: N 1001 MET cc_start: 0.6641 (mmm) cc_final: 0.5944 (mmt) REVERT: N 1050 ASP cc_start: 0.6518 (m-30) cc_final: 0.6031 (m-30) REVERT: N 1174 LEU cc_start: 0.6829 (pp) cc_final: 0.6525 (pp) REVERT: N 1309 VAL cc_start: 0.8409 (m) cc_final: 0.8148 (t) REVERT: O 102 ILE cc_start: 0.8644 (mt) cc_final: 0.8346 (mm) REVERT: O 169 VAL cc_start: 0.8130 (m) cc_final: 0.7918 (p) REVERT: O 248 LEU cc_start: 0.5837 (mt) cc_final: 0.5296 (mt) REVERT: O 389 ASN cc_start: 0.6931 (m-40) cc_final: 0.6639 (m-40) REVERT: O 560 HIS cc_start: 0.3386 (m-70) cc_final: 0.2990 (m-70) REVERT: O 619 PHE cc_start: 0.5809 (m-10) cc_final: 0.5520 (m-80) REVERT: O 654 LEU cc_start: 0.7985 (pp) cc_final: 0.7458 (mm) REVERT: O 756 THR cc_start: 0.4041 (p) cc_final: 0.3791 (p) REVERT: O 772 MET cc_start: 0.5565 (mmm) cc_final: 0.5071 (mmp) REVERT: O 882 ARG cc_start: 0.4496 (mtt180) cc_final: 0.4290 (mtp180) REVERT: O 889 MET cc_start: 0.4831 (mpm) cc_final: 0.4496 (tpp) REVERT: O 928 LEU cc_start: 0.8124 (pp) cc_final: 0.7654 (pp) REVERT: O 972 MET cc_start: 0.7788 (mmp) cc_final: 0.7526 (mmm) REVERT: O 1038 ILE cc_start: 0.7757 (mt) cc_final: 0.7199 (mt) REVERT: O 1059 PHE cc_start: 0.8125 (t80) cc_final: 0.7810 (t80) REVERT: O 1193 VAL cc_start: 0.5694 (t) cc_final: 0.4671 (m) REVERT: v 15 THR cc_start: 0.6718 (p) cc_final: 0.6157 (t) REVERT: v 363 THR cc_start: 0.5136 (p) cc_final: 0.4792 (p) REVERT: v 489 LEU cc_start: 0.7308 (mt) cc_final: 0.6998 (mt) REVERT: a 10 LEU cc_start: 0.6366 (mt) cc_final: 0.5999 (mt) REVERT: d 44 GLN cc_start: 0.6925 (tt0) cc_final: 0.6426 (tm-30) REVERT: f 356 ASN cc_start: 0.6776 (t0) cc_final: 0.6369 (t0) REVERT: h 2 LYS cc_start: 0.5048 (ptpp) cc_final: 0.4752 (ptpt) REVERT: h 114 LYS cc_start: 0.7202 (mptt) cc_final: 0.6521 (pttt) REVERT: h 123 ASP cc_start: 0.4709 (p0) cc_final: 0.4397 (p0) REVERT: h 154 MET cc_start: 0.6935 (tpt) cc_final: 0.6731 (tpt) REVERT: h 201 ASN cc_start: 0.6248 (m-40) cc_final: 0.6016 (m110) REVERT: h 327 PHE cc_start: 0.6553 (t80) cc_final: 0.6317 (t80) REVERT: k 83 THR cc_start: 0.6334 (t) cc_final: 0.6043 (t) REVERT: m 81 ILE cc_start: 0.5119 (mt) cc_final: 0.4729 (mp) REVERT: m 82 LEU cc_start: 0.6908 (mp) cc_final: 0.6548 (mp) REVERT: m 86 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6288 (t) REVERT: m 136 MET cc_start: 0.3118 (tpt) cc_final: 0.2878 (tpt) REVERT: m 181 TYR cc_start: 0.6879 (m-10) cc_final: 0.6588 (m-10) REVERT: p 228 ILE cc_start: 0.6850 (mt) cc_final: 0.6583 (mt) REVERT: p 251 ASP cc_start: 0.6024 (m-30) cc_final: 0.5538 (m-30) REVERT: r 2 ASP cc_start: 0.5793 (t0) cc_final: 0.4615 (p0) REVERT: r 43 LEU cc_start: 0.6963 (pp) cc_final: 0.6653 (tp) REVERT: r 87 PRO cc_start: 0.8037 (Cg_exo) cc_final: 0.7736 (Cg_endo) REVERT: r 140 THR cc_start: 0.7955 (m) cc_final: 0.7603 (m) outliers start: 46 outliers final: 13 residues processed: 2675 average time/residue: 0.6368 time to fit residues: 2813.7183 Evaluate side-chains 1482 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1468 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 30.0000 chunk 592 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 316 optimal weight: 8.9990 chunk 612 optimal weight: 30.0000 chunk 237 optimal weight: 30.0000 chunk 372 optimal weight: 9.9990 chunk 456 optimal weight: 8.9990 chunk 710 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 126 HIS J 289 GLN J 389 ASN J 444 ASN J 531 HIS J 596 HIS J 627 HIS J 636 ASN J 669 HIS J 795 HIS J 804 HIS J 824 HIS ** J 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 859 ASN J 921 GLN J 926 ASN ** J1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1176 HIS J1178 GLN J1261 GLN J1360 HIS K 317 ASN K 377 HIS ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 570 ASN ** K 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 750 ASN ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1022 HIS K1357 HIS N 123 HIS ** N 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 385 GLN N 531 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 570 ASN N 587 GLN N 596 HIS ** N 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 672 ASN N 761 GLN ** N 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 804 HIS N 913 ASN N 926 ASN ** N 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 964 HIS N 974 ASN ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1033 GLN ** N1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1246 GLN N1283 ASN ** N1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1323 GLN N1353 HIS O 79 ASN O 178 ASN O 222 HIS ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS O 385 GLN O 415 ASN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 469 HIS ** O 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 607 GLN O 658 ASN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS O1135 ASN ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1216 ASN ** O1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 7 ASN v 73 HIS v 93 ASN ** v 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z3114 GLN a 11 GLN d 32 GLN e 62 GLN f 115 GLN h 13 GLN h 208 HIS k 120 HIS k 128 ASN k 230 HIS ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 HIS p 89 GLN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 162 GLN p 185 HIS p 230 HIS r 154 ASN r 233 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 63966 Z= 0.376 Angle : 0.859 15.535 86932 Z= 0.450 Chirality : 0.049 0.267 9795 Planarity : 0.007 0.096 11336 Dihedral : 6.173 67.225 8722 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.95 % Favored : 94.86 % Rotamer: Outliers : 0.35 % Allowed : 5.11 % Favored : 94.53 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.09), residues: 7881 helix: -0.70 (0.09), residues: 2978 sheet: -0.27 (0.15), residues: 1101 loop : -1.68 (0.09), residues: 3802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP x 54 HIS 0.023 0.002 HIS K 564 PHE 0.052 0.003 PHE J 990 TYR 0.054 0.003 TYR O 403 ARG 0.039 0.001 ARG J 985 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1920 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1896 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 191 MET cc_start: 0.7886 (mmm) cc_final: 0.6737 (mmm) REVERT: J 208 SER cc_start: 0.6730 (p) cc_final: 0.6459 (m) REVERT: J 210 THR cc_start: 0.8031 (p) cc_final: 0.7546 (p) REVERT: J 401 MET cc_start: 0.6850 (mtt) cc_final: 0.6506 (mtp) REVERT: J 426 MET cc_start: 0.7216 (tpp) cc_final: 0.6989 (tpp) REVERT: J 575 LEU cc_start: 0.7053 (tp) cc_final: 0.6701 (tp) REVERT: J 990 PHE cc_start: 0.6176 (t80) cc_final: 0.5224 (t80) REVERT: J 1010 PRO cc_start: 0.7323 (Cg_exo) cc_final: 0.7123 (Cg_endo) REVERT: J 1018 MET cc_start: 0.5655 (tpp) cc_final: 0.5292 (tpp) REVERT: J 1259 TYR cc_start: 0.6834 (p90) cc_final: 0.6436 (p90) REVERT: K 129 THR cc_start: 0.8086 (p) cc_final: 0.7740 (p) REVERT: K 426 MET cc_start: 0.7260 (mtt) cc_final: 0.6209 (mmt) REVERT: K 457 LYS cc_start: 0.7066 (mttt) cc_final: 0.6737 (mtpp) REVERT: K 543 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5833 (t-170) REVERT: K 694 GLU cc_start: 0.6239 (pt0) cc_final: 0.5708 (pt0) REVERT: K 880 MET cc_start: 0.5830 (ptp) cc_final: 0.5255 (mtt) REVERT: K 998 ARG cc_start: 0.6249 (mmt90) cc_final: 0.5179 (mmt90) REVERT: K 1183 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7606 (mt-10) REVERT: K 1347 MET cc_start: 0.6086 (mmm) cc_final: 0.5136 (mmm) REVERT: K 1357 HIS cc_start: 0.7191 (t70) cc_final: 0.6756 (t-90) REVERT: N 214 ASP cc_start: 0.6862 (t70) cc_final: 0.6533 (t70) REVERT: N 431 THR cc_start: 0.8596 (p) cc_final: 0.8358 (t) REVERT: N 500 LEU cc_start: 0.7071 (mt) cc_final: 0.6432 (mt) REVERT: N 515 VAL cc_start: 0.7074 (t) cc_final: 0.6786 (m) REVERT: N 581 GLN cc_start: 0.8320 (tp40) cc_final: 0.7403 (mt0) REVERT: N 619 PHE cc_start: 0.6865 (m-10) cc_final: 0.6607 (m-10) REVERT: N 647 TYR cc_start: 0.7611 (t80) cc_final: 0.6955 (t80) REVERT: N 653 ARG cc_start: 0.5197 (mpt180) cc_final: 0.4916 (mmt-90) REVERT: N 807 VAL cc_start: 0.8475 (t) cc_final: 0.8251 (t) REVERT: N 809 GLU cc_start: 0.6669 (mp0) cc_final: 0.6336 (mp0) REVERT: N 1021 MET cc_start: 0.6758 (mtt) cc_final: 0.6329 (mtt) REVERT: N 1196 PHE cc_start: 0.6710 (m-10) cc_final: 0.5986 (m-10) REVERT: O 226 HIS cc_start: 0.7305 (m90) cc_final: 0.7011 (m90) REVERT: O 385 GLN cc_start: 0.6055 (mt0) cc_final: 0.5675 (mm-40) REVERT: O 395 TYR cc_start: 0.7905 (t80) cc_final: 0.6414 (t80) REVERT: O 517 ASP cc_start: 0.6778 (p0) cc_final: 0.5952 (p0) REVERT: O 587 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7889 (tt0) REVERT: O 684 ARG cc_start: 0.6049 (ttm170) cc_final: 0.5735 (tpp80) REVERT: O 772 MET cc_start: 0.5271 (mmm) cc_final: 0.4906 (mmp) REVERT: O 1067 MET cc_start: 0.7847 (tpp) cc_final: 0.7599 (tpt) REVERT: v 489 LEU cc_start: 0.8183 (mt) cc_final: 0.7935 (mt) REVERT: f 135 MET cc_start: 0.5650 (mtm) cc_final: 0.5311 (mtm) REVERT: f 151 LEU cc_start: 0.4033 (tt) cc_final: 0.3352 (tt) REVERT: f 193 GLU cc_start: 0.6009 (pt0) cc_final: 0.4944 (pt0) REVERT: f 261 ASP cc_start: 0.6518 (m-30) cc_final: 0.6131 (m-30) REVERT: f 278 THR cc_start: 0.5495 (p) cc_final: 0.5042 (p) REVERT: h 123 ASP cc_start: 0.6056 (p0) cc_final: 0.5798 (p0) REVERT: h 154 MET cc_start: 0.8501 (tpt) cc_final: 0.8020 (tpt) REVERT: h 221 VAL cc_start: 0.8612 (t) cc_final: 0.8080 (p) REVERT: h 233 LEU cc_start: 0.7864 (tp) cc_final: 0.7629 (tp) REVERT: h 349 GLU cc_start: 0.6353 (mp0) cc_final: 0.6064 (mp0) REVERT: k 73 ASP cc_start: 0.8253 (m-30) cc_final: 0.7735 (m-30) REVERT: k 283 ARG cc_start: 0.6379 (ppt170) cc_final: 0.6088 (ppt170) REVERT: m 17 GLU cc_start: 0.4548 (pt0) cc_final: 0.4103 (pt0) REVERT: m 41 GLN cc_start: 0.7586 (pm20) cc_final: 0.6696 (tt0) REVERT: m 152 LEU cc_start: 0.6935 (mt) cc_final: 0.6291 (tt) REVERT: m 261 LEU cc_start: 0.8079 (tt) cc_final: 0.7772 (tt) REVERT: p 81 ILE cc_start: 0.5901 (mp) cc_final: 0.5273 (mp) REVERT: p 152 LEU cc_start: 0.7809 (tt) cc_final: 0.7309 (tt) REVERT: p 161 MET cc_start: 0.4948 (ptm) cc_final: 0.4466 (ttp) REVERT: p 168 ASP cc_start: 0.6985 (t0) cc_final: 0.6369 (t0) REVERT: p 172 VAL cc_start: 0.8313 (t) cc_final: 0.8058 (t) REVERT: p 187 GLU cc_start: 0.6570 (tp30) cc_final: 0.6035 (pt0) REVERT: r 43 LEU cc_start: 0.7345 (pp) cc_final: 0.7083 (tp) REVERT: r 109 LEU cc_start: 0.7132 (mp) cc_final: 0.6932 (mp) REVERT: r 169 MET cc_start: 0.7533 (mmp) cc_final: 0.7331 (mmm) outliers start: 24 outliers final: 6 residues processed: 1911 average time/residue: 0.6240 time to fit residues: 2021.0855 Evaluate side-chains 1314 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1307 time to evaluate : 5.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 591 optimal weight: 6.9990 chunk 483 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 711 optimal weight: 0.0060 chunk 768 optimal weight: 5.9990 chunk 633 optimal weight: 20.0000 chunk 705 optimal weight: 30.0000 chunk 242 optimal weight: 0.9990 chunk 570 optimal weight: 5.9990 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 187 HIS J 444 ASN ** J 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 750 ASN ** J1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1216 ASN K 289 GLN K 333 HIS K 496 HIS K 607 GLN K 627 HIS ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1056 ASN K1246 GLN K1261 GLN N 222 HIS N 300 ASN ** N 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 496 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 824 HIS N 913 ASN ** N 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 997 HIS N1022 HIS ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1178 GLN O 79 ASN O 222 HIS O 285 ASN O 445 ASN O 472 ASN O 531 HIS O 596 HIS O 607 GLN O 824 HIS ** O 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 977 GLN O 984 ASN ** O 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1022 HIS ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1178 GLN O1217 GLN O1284 ASN ** O1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 GLN v 73 HIS v 360 GLN v 424 HIS d 28 GLN d 32 GLN m 35 HIS ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 233 HIS p 95 ASN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 173 HIS r 38 GLN r 154 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 63966 Z= 0.215 Angle : 0.691 12.479 86932 Z= 0.353 Chirality : 0.045 0.252 9795 Planarity : 0.006 0.093 11336 Dihedral : 5.593 61.950 8722 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.09), residues: 7881 helix: -0.19 (0.09), residues: 2981 sheet: -0.04 (0.15), residues: 1037 loop : -1.57 (0.09), residues: 3863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP v 403 HIS 0.018 0.001 HIS K 951 PHE 0.033 0.002 PHE J 776 TYR 0.026 0.002 TYR k 61 ARG 0.010 0.001 ARG O 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1803 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1799 time to evaluate : 6.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 153 GLU cc_start: 0.5658 (mm-30) cc_final: 0.5377 (tp30) REVERT: J 208 SER cc_start: 0.7047 (p) cc_final: 0.6779 (m) REVERT: J 210 THR cc_start: 0.8022 (p) cc_final: 0.7652 (p) REVERT: J 426 MET cc_start: 0.7027 (tpp) cc_final: 0.6717 (tpp) REVERT: J 669 HIS cc_start: 0.4044 (m-70) cc_final: 0.3833 (m-70) REVERT: J 951 HIS cc_start: 0.6363 (t-90) cc_final: 0.5956 (t70) REVERT: J 990 PHE cc_start: 0.6705 (t80) cc_final: 0.6446 (t80) REVERT: J 1010 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7494 (Cg_endo) REVERT: J 1028 MET cc_start: 0.6613 (pmm) cc_final: 0.6119 (pmm) REVERT: J 1179 GLN cc_start: 0.7907 (pp30) cc_final: 0.7495 (pp30) REVERT: J 1259 TYR cc_start: 0.6673 (p90) cc_final: 0.6383 (p90) REVERT: J 1264 VAL cc_start: 0.8638 (t) cc_final: 0.8309 (m) REVERT: K 88 MET cc_start: 0.7381 (ttp) cc_final: 0.7164 (ttm) REVERT: K 426 MET cc_start: 0.7480 (mtt) cc_final: 0.7062 (mmt) REVERT: K 457 LYS cc_start: 0.7095 (mttt) cc_final: 0.6530 (mtpp) REVERT: K 502 ILE cc_start: 0.8099 (mt) cc_final: 0.7779 (mm) REVERT: K 587 GLN cc_start: 0.6789 (mt0) cc_final: 0.6520 (mt0) REVERT: K 612 ASP cc_start: 0.8056 (t0) cc_final: 0.7791 (t0) REVERT: K 880 MET cc_start: 0.5855 (ptp) cc_final: 0.5231 (mtt) REVERT: K 889 MET cc_start: 0.7270 (mtm) cc_final: 0.7046 (mtm) REVERT: K 1021 MET cc_start: 0.5399 (mtp) cc_final: 0.5000 (mtp) REVERT: K 1225 TYR cc_start: 0.5156 (m-80) cc_final: 0.4924 (m-80) REVERT: K 1271 CYS cc_start: 0.7675 (m) cc_final: 0.7269 (m) REVERT: K 1347 MET cc_start: 0.5655 (mmm) cc_final: 0.5281 (mmm) REVERT: N 426 MET cc_start: 0.6813 (mtt) cc_final: 0.6322 (mmm) REVERT: N 515 VAL cc_start: 0.7023 (t) cc_final: 0.6785 (m) REVERT: N 581 GLN cc_start: 0.8311 (tp40) cc_final: 0.7392 (mt0) REVERT: N 647 TYR cc_start: 0.7534 (t80) cc_final: 0.6758 (t80) REVERT: N 807 VAL cc_start: 0.8395 (t) cc_final: 0.8145 (t) REVERT: N 809 GLU cc_start: 0.6383 (mp0) cc_final: 0.6059 (mp0) REVERT: N 812 PHE cc_start: 0.8125 (t80) cc_final: 0.7881 (t80) REVERT: N 972 MET cc_start: 0.4664 (ttm) cc_final: 0.4350 (ttp) REVERT: N 1021 MET cc_start: 0.7482 (mtt) cc_final: 0.6605 (mtt) REVERT: N 1045 THR cc_start: 0.7151 (p) cc_final: 0.6950 (p) REVERT: O 294 LEU cc_start: 0.6458 (mt) cc_final: 0.6039 (mt) REVERT: O 344 LYS cc_start: 0.4198 (tptt) cc_final: 0.3957 (tppt) REVERT: O 395 TYR cc_start: 0.7771 (t80) cc_final: 0.7234 (t80) REVERT: O 517 ASP cc_start: 0.6354 (p0) cc_final: 0.5706 (p0) REVERT: O 587 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7835 (tt0) REVERT: O 607 GLN cc_start: 0.6587 (tp40) cc_final: 0.6372 (tp-100) REVERT: O 639 LEU cc_start: 0.7620 (mp) cc_final: 0.7251 (mt) REVERT: O 693 LEU cc_start: 0.8678 (mp) cc_final: 0.8394 (mp) REVERT: O 772 MET cc_start: 0.5844 (mmm) cc_final: 0.5252 (mmp) REVERT: O 1021 MET cc_start: 0.5053 (ttm) cc_final: 0.3826 (ttm) REVERT: O 1067 MET cc_start: 0.7653 (tpp) cc_final: 0.7194 (tpt) REVERT: O 1105 MET cc_start: 0.6388 (ttp) cc_final: 0.6146 (ttp) REVERT: O 1141 TYR cc_start: 0.6753 (t80) cc_final: 0.6207 (t80) REVERT: O 1200 ASN cc_start: 0.7630 (p0) cc_final: 0.7406 (p0) REVERT: O 1290 MET cc_start: 0.6389 (mmt) cc_final: 0.6173 (tpp) REVERT: O 1364 GLU cc_start: 0.6423 (tm-30) cc_final: 0.5700 (tm-30) REVERT: v 32 CYS cc_start: 0.4590 (t) cc_final: 0.4175 (m) REVERT: v 388 GLU cc_start: 0.6279 (tp30) cc_final: 0.5750 (tp30) REVERT: v 427 TYR cc_start: 0.6155 (m-80) cc_final: 0.5399 (m-80) REVERT: v 489 LEU cc_start: 0.8130 (mt) cc_final: 0.7880 (mp) REVERT: w 47 GLU cc_start: 0.5668 (mm-30) cc_final: 0.5401 (mm-30) REVERT: a 41 ARG cc_start: 0.6013 (ttp80) cc_final: 0.5509 (ttp80) REVERT: d 72 ARG cc_start: 0.5960 (mmp-170) cc_final: 0.5284 (mmp80) REVERT: f 154 MET cc_start: 0.4701 (tmm) cc_final: 0.4156 (ttm) REVERT: f 193 GLU cc_start: 0.5790 (pt0) cc_final: 0.4872 (pt0) REVERT: f 261 ASP cc_start: 0.6617 (m-30) cc_final: 0.6177 (m-30) REVERT: h 154 MET cc_start: 0.8458 (tpt) cc_final: 0.8086 (tpt) REVERT: h 161 SER cc_start: 0.8065 (t) cc_final: 0.7854 (p) REVERT: h 221 VAL cc_start: 0.8743 (t) cc_final: 0.8125 (p) REVERT: h 272 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7544 (tp30) REVERT: h 333 TRP cc_start: 0.6311 (p90) cc_final: 0.5837 (p90) REVERT: h 349 GLU cc_start: 0.5914 (mp0) cc_final: 0.5404 (mp0) REVERT: k 247 ILE cc_start: 0.8045 (mt) cc_final: 0.7650 (mp) REVERT: k 283 ARG cc_start: 0.6398 (ppt170) cc_final: 0.6158 (ppt170) REVERT: m 136 MET cc_start: 0.4515 (tpt) cc_final: 0.4173 (tpt) REVERT: m 152 LEU cc_start: 0.7312 (mt) cc_final: 0.6342 (tt) REVERT: m 255 LEU cc_start: 0.8068 (mt) cc_final: 0.7502 (mp) REVERT: m 265 ARG cc_start: 0.7216 (ptp-110) cc_final: 0.6908 (ttp-110) REVERT: m 270 TYR cc_start: 0.7255 (m-80) cc_final: 0.6710 (m-80) REVERT: p 152 LEU cc_start: 0.7019 (tt) cc_final: 0.6696 (tt) REVERT: p 172 VAL cc_start: 0.8235 (t) cc_final: 0.7835 (t) REVERT: p 173 HIS cc_start: 0.5365 (m-70) cc_final: 0.4973 (m170) REVERT: p 187 GLU cc_start: 0.6801 (tp30) cc_final: 0.6243 (pt0) REVERT: r 64 LEU cc_start: 0.8197 (mt) cc_final: 0.7747 (mm) REVERT: r 103 TRP cc_start: 0.7618 (m100) cc_final: 0.7186 (m100) REVERT: r 109 LEU cc_start: 0.6669 (mp) cc_final: 0.6428 (mp) outliers start: 4 outliers final: 1 residues processed: 1801 average time/residue: 0.5937 time to fit residues: 1803.5137 Evaluate side-chains 1312 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1311 time to evaluate : 5.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 9.9990 chunk 534 optimal weight: 9.9990 chunk 369 optimal weight: 0.0470 chunk 78 optimal weight: 40.0000 chunk 339 optimal weight: 7.9990 chunk 477 optimal weight: 10.0000 chunk 713 optimal weight: 0.6980 chunk 755 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 676 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 overall best weight: 4.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 24 ASN ** J 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 833 GLN J 859 ASN J 921 GLN ** J1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1216 ASN ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1261 GLN ** N 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 788 HIS ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS O 285 ASN ** O 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 627 HIS O 713 GLN O 788 HIS ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 997 HIS ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1310 GLN ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 GLN v 360 GLN d 28 GLN h 13 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 201 ASN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 230 HIS r 154 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 63966 Z= 0.249 Angle : 0.696 14.345 86932 Z= 0.355 Chirality : 0.045 0.239 9795 Planarity : 0.006 0.096 11336 Dihedral : 5.423 55.388 8722 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.09), residues: 7881 helix: 0.03 (0.09), residues: 2952 sheet: -0.10 (0.15), residues: 1081 loop : -1.53 (0.09), residues: 3848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP v 403 HIS 0.008 0.001 HIS K 543 PHE 0.031 0.002 PHE m 278 TYR 0.024 0.002 TYR N 687 ARG 0.027 0.001 ARG d 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1689 time to evaluate : 6.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 50 ILE cc_start: 0.8271 (mt) cc_final: 0.7986 (pt) REVERT: J 88 MET cc_start: 0.5162 (mtt) cc_final: 0.4865 (mtt) REVERT: J 153 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5700 (tp30) REVERT: J 173 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6238 (mm-30) REVERT: J 180 VAL cc_start: 0.8426 (t) cc_final: 0.8124 (p) REVERT: J 191 MET cc_start: 0.7950 (mmm) cc_final: 0.7747 (mmm) REVERT: J 515 VAL cc_start: 0.8304 (t) cc_final: 0.8032 (t) REVERT: J 590 THR cc_start: 0.8471 (p) cc_final: 0.8199 (t) REVERT: J 723 LEU cc_start: 0.8421 (tp) cc_final: 0.8014 (tt) REVERT: J 742 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6840 (mtm180) REVERT: J 884 LEU cc_start: 0.8989 (tp) cc_final: 0.8704 (tp) REVERT: J 951 HIS cc_start: 0.6502 (t-90) cc_final: 0.6211 (t70) REVERT: J 1028 MET cc_start: 0.7190 (pmm) cc_final: 0.6836 (pmm) REVERT: J 1088 VAL cc_start: 0.8001 (t) cc_final: 0.7771 (m) REVERT: J 1117 MET cc_start: 0.6834 (mmt) cc_final: 0.6250 (mmp) REVERT: J 1179 GLN cc_start: 0.8237 (pp30) cc_final: 0.7898 (pp30) REVERT: J 1259 TYR cc_start: 0.6904 (p90) cc_final: 0.6633 (p90) REVERT: J 1264 VAL cc_start: 0.8791 (t) cc_final: 0.8512 (m) REVERT: K 79 ASN cc_start: 0.7335 (m-40) cc_final: 0.7094 (m-40) REVERT: K 88 MET cc_start: 0.8012 (ttp) cc_final: 0.7705 (ttm) REVERT: K 191 MET cc_start: 0.5874 (tmm) cc_final: 0.5668 (tpp) REVERT: K 457 LYS cc_start: 0.7191 (mttt) cc_final: 0.6706 (mtpp) REVERT: K 502 ILE cc_start: 0.8118 (mt) cc_final: 0.7904 (mm) REVERT: K 587 GLN cc_start: 0.7209 (mt0) cc_final: 0.6723 (mt0) REVERT: K 706 VAL cc_start: 0.6595 (p) cc_final: 0.6299 (p) REVERT: K 708 ASP cc_start: 0.5222 (t0) cc_final: 0.4993 (t0) REVERT: K 880 MET cc_start: 0.6590 (ptp) cc_final: 0.5898 (mtt) REVERT: K 1080 ARG cc_start: 0.5633 (ttt-90) cc_final: 0.1063 (tpm170) REVERT: K 1154 LEU cc_start: 0.8115 (pp) cc_final: 0.7656 (pp) REVERT: K 1225 TYR cc_start: 0.5670 (m-80) cc_final: 0.5411 (m-80) REVERT: K 1308 GLU cc_start: 0.7070 (tt0) cc_final: 0.6709 (tt0) REVERT: N 63 ILE cc_start: 0.8588 (mp) cc_final: 0.8117 (mt) REVERT: N 83 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7761 (mmmt) REVERT: N 193 ILE cc_start: 0.7594 (mp) cc_final: 0.7309 (mp) REVERT: N 214 ASP cc_start: 0.6694 (t70) cc_final: 0.5984 (t70) REVERT: N 215 LEU cc_start: 0.7421 (tp) cc_final: 0.6815 (tp) REVERT: N 320 THR cc_start: 0.6493 (p) cc_final: 0.6241 (p) REVERT: N 581 GLN cc_start: 0.8236 (tp40) cc_final: 0.7503 (mt0) REVERT: N 647 TYR cc_start: 0.7608 (t80) cc_final: 0.6723 (t80) REVERT: N 662 MET cc_start: 0.7620 (mtt) cc_final: 0.7362 (mtt) REVERT: N 752 VAL cc_start: 0.8509 (p) cc_final: 0.8134 (p) REVERT: N 799 TYR cc_start: 0.6811 (t80) cc_final: 0.6563 (t80) REVERT: N 807 VAL cc_start: 0.8363 (t) cc_final: 0.8052 (t) REVERT: N 902 VAL cc_start: 0.6095 (t) cc_final: 0.5817 (t) REVERT: N 972 MET cc_start: 0.4396 (ttm) cc_final: 0.3960 (ttp) REVERT: N 998 ARG cc_start: 0.7695 (mmt-90) cc_final: 0.7339 (mmt-90) REVERT: N 1190 THR cc_start: 0.9087 (p) cc_final: 0.8631 (m) REVERT: N 1196 PHE cc_start: 0.7023 (m-10) cc_final: 0.6354 (m-10) REVERT: O 236 MET cc_start: 0.5011 (ptp) cc_final: 0.4325 (mmm) REVERT: O 294 LEU cc_start: 0.6638 (mt) cc_final: 0.6421 (mt) REVERT: O 517 ASP cc_start: 0.6394 (p0) cc_final: 0.5795 (p0) REVERT: O 587 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8053 (tt0) REVERT: O 607 GLN cc_start: 0.6883 (tp40) cc_final: 0.6493 (tp-100) REVERT: O 639 LEU cc_start: 0.7830 (mp) cc_final: 0.7587 (mt) REVERT: O 772 MET cc_start: 0.5781 (mmm) cc_final: 0.5302 (mmp) REVERT: O 838 THR cc_start: 0.8086 (p) cc_final: 0.7841 (t) REVERT: O 889 MET cc_start: 0.4323 (tpt) cc_final: 0.4122 (tpp) REVERT: O 1001 MET cc_start: 0.7845 (tpp) cc_final: 0.7520 (mmm) REVERT: O 1021 MET cc_start: 0.5078 (ttm) cc_final: 0.3716 (ttm) REVERT: O 1044 MET cc_start: 0.6592 (ptp) cc_final: 0.6336 (ptp) REVERT: O 1119 ILE cc_start: 0.5853 (mm) cc_final: 0.5393 (mm) REVERT: O 1200 ASN cc_start: 0.7994 (p0) cc_final: 0.7709 (p0) REVERT: v 32 CYS cc_start: 0.5091 (t) cc_final: 0.4771 (m) REVERT: v 359 MET cc_start: 0.6366 (mtp) cc_final: 0.5750 (mtt) REVERT: v 388 GLU cc_start: 0.6894 (tp30) cc_final: 0.5758 (tp30) REVERT: v 427 TYR cc_start: 0.6235 (m-80) cc_final: 0.5118 (m-80) REVERT: v 489 LEU cc_start: 0.8116 (mt) cc_final: 0.7877 (mp) REVERT: w 101 MET cc_start: 0.3182 (mtm) cc_final: 0.2813 (mtt) REVERT: Z 52 THR cc_start: 0.6352 (p) cc_final: 0.6103 (p) REVERT: f 135 MET cc_start: 0.5643 (mtm) cc_final: 0.5402 (mtm) REVERT: f 154 MET cc_start: 0.5117 (tmm) cc_final: 0.4832 (tmm) REVERT: f 202 LYS cc_start: 0.5153 (mmtm) cc_final: 0.4836 (mmtm) REVERT: f 261 ASP cc_start: 0.6717 (m-30) cc_final: 0.6279 (m-30) REVERT: f 350 ILE cc_start: 0.6171 (pt) cc_final: 0.5923 (pt) REVERT: h 154 MET cc_start: 0.8584 (tpt) cc_final: 0.8284 (tpt) REVERT: k 112 MET cc_start: 0.6200 (mtp) cc_final: 0.5932 (mtp) REVERT: k 235 LEU cc_start: 0.5352 (pt) cc_final: 0.4831 (pp) REVERT: m 24 ARG cc_start: 0.6150 (mmt180) cc_final: 0.5811 (mmm-85) REVERT: m 78 ASP cc_start: 0.5515 (p0) cc_final: 0.5143 (p0) REVERT: m 152 LEU cc_start: 0.7366 (mt) cc_final: 0.6598 (tt) REVERT: m 255 LEU cc_start: 0.8030 (mt) cc_final: 0.7806 (mp) REVERT: m 270 TYR cc_start: 0.7284 (m-80) cc_final: 0.6704 (m-80) REVERT: p 81 ILE cc_start: 0.6959 (tt) cc_final: 0.6718 (tt) REVERT: p 119 GLU cc_start: 0.6762 (pm20) cc_final: 0.6441 (tm-30) REVERT: p 187 GLU cc_start: 0.6587 (tp30) cc_final: 0.6291 (tt0) REVERT: r 20 LYS cc_start: 0.8153 (mttt) cc_final: 0.7940 (mttt) REVERT: r 37 THR cc_start: 0.5988 (m) cc_final: 0.5669 (m) REVERT: r 64 LEU cc_start: 0.8247 (mt) cc_final: 0.7827 (mm) REVERT: r 103 TRP cc_start: 0.7755 (m100) cc_final: 0.7444 (m100) REVERT: r 286 THR cc_start: 0.5101 (t) cc_final: 0.4685 (t) outliers start: 3 outliers final: 0 residues processed: 1690 average time/residue: 0.5919 time to fit residues: 1698.4182 Evaluate side-chains 1278 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1278 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 20.0000 chunk 429 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 562 optimal weight: 6.9990 chunk 311 optimal weight: 30.0000 chunk 645 optimal weight: 1.9990 chunk 522 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 385 optimal weight: 9.9990 chunk 678 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 GLN J 833 GLN J1090 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 833 GLN ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1283 ASN N 178 ASN N 222 HIS N 300 ASN ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 722 ASN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 HIS ** O 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1284 ASN O1310 GLN ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 GLN d 28 GLN h 201 ASN k 23 GLN ** m 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 154 ASN ** r 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 63966 Z= 0.223 Angle : 0.677 14.375 86932 Z= 0.343 Chirality : 0.044 0.223 9795 Planarity : 0.005 0.096 11336 Dihedral : 5.271 51.730 8722 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.43 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 7881 helix: 0.10 (0.09), residues: 2974 sheet: -0.15 (0.15), residues: 1107 loop : -1.51 (0.10), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP x 54 HIS 0.011 0.001 HIS N 560 PHE 0.035 0.002 PHE K 665 TYR 0.026 0.002 TYR k 61 ARG 0.019 0.001 ARG p 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1662 time to evaluate : 5.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 50 ILE cc_start: 0.8316 (mt) cc_final: 0.8079 (pt) REVERT: J 88 MET cc_start: 0.5483 (mtt) cc_final: 0.5159 (mtt) REVERT: J 131 MET cc_start: 0.8010 (ptp) cc_final: 0.7789 (ptt) REVERT: J 153 GLU cc_start: 0.5904 (mm-30) cc_final: 0.5650 (tp30) REVERT: J 173 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6361 (mm-30) REVERT: J 191 MET cc_start: 0.8213 (mmm) cc_final: 0.7928 (mmm) REVERT: J 208 SER cc_start: 0.7308 (p) cc_final: 0.7099 (m) REVERT: J 210 THR cc_start: 0.8557 (p) cc_final: 0.8133 (p) REVERT: J 590 THR cc_start: 0.8563 (p) cc_final: 0.8338 (t) REVERT: J 723 LEU cc_start: 0.8317 (tp) cc_final: 0.8055 (tt) REVERT: J 742 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6655 (mtm180) REVERT: J 884 LEU cc_start: 0.8775 (tp) cc_final: 0.8370 (tp) REVERT: J 951 HIS cc_start: 0.6992 (t-90) cc_final: 0.6560 (t70) REVERT: J 990 PHE cc_start: 0.6929 (t80) cc_final: 0.6471 (t80) REVERT: J 1028 MET cc_start: 0.7489 (pmm) cc_final: 0.7210 (pmm) REVERT: J 1055 GLU cc_start: 0.5993 (mt-10) cc_final: 0.5677 (mt-10) REVERT: J 1117 MET cc_start: 0.6818 (mmt) cc_final: 0.6350 (mmp) REVERT: J 1179 GLN cc_start: 0.8269 (pp30) cc_final: 0.7945 (pp30) REVERT: J 1259 TYR cc_start: 0.5932 (p90) cc_final: 0.5674 (p90) REVERT: J 1264 VAL cc_start: 0.8711 (t) cc_final: 0.8479 (m) REVERT: K 88 MET cc_start: 0.8238 (ttp) cc_final: 0.8007 (ttm) REVERT: K 180 VAL cc_start: 0.8593 (t) cc_final: 0.8338 (p) REVERT: K 457 LYS cc_start: 0.7244 (mttt) cc_final: 0.6803 (mtpp) REVERT: K 502 ILE cc_start: 0.8027 (mt) cc_final: 0.7818 (mm) REVERT: K 587 GLN cc_start: 0.7357 (mt0) cc_final: 0.6938 (mt0) REVERT: K 972 MET cc_start: 0.6761 (mmt) cc_final: 0.6472 (mmm) REVERT: K 1080 ARG cc_start: 0.5684 (ttt-90) cc_final: 0.1124 (tpm170) REVERT: K 1165 MET cc_start: 0.5160 (mtt) cc_final: 0.4920 (tpp) REVERT: K 1308 GLU cc_start: 0.7068 (tt0) cc_final: 0.6617 (tt0) REVERT: K 1328 LEU cc_start: 0.7189 (mt) cc_final: 0.6936 (mt) REVERT: N 141 LEU cc_start: 0.5385 (pp) cc_final: 0.5179 (pp) REVERT: N 176 LEU cc_start: 0.8182 (mm) cc_final: 0.7881 (mm) REVERT: N 219 PHE cc_start: 0.7317 (m-80) cc_final: 0.7075 (m-80) REVERT: N 307 SER cc_start: 0.8961 (t) cc_final: 0.8643 (p) REVERT: N 372 ILE cc_start: 0.8594 (mm) cc_final: 0.8245 (mt) REVERT: N 382 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7389 (mm-30) REVERT: N 581 GLN cc_start: 0.8224 (tp40) cc_final: 0.7606 (mt0) REVERT: N 643 CYS cc_start: 0.7114 (m) cc_final: 0.6897 (m) REVERT: N 647 TYR cc_start: 0.7644 (t80) cc_final: 0.6970 (t80) REVERT: N 649 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6865 (mm-30) REVERT: N 662 MET cc_start: 0.7764 (mtt) cc_final: 0.7456 (mtt) REVERT: N 807 VAL cc_start: 0.8468 (t) cc_final: 0.8141 (t) REVERT: N 952 MET cc_start: 0.7157 (tpt) cc_final: 0.6943 (tpt) REVERT: N 972 MET cc_start: 0.4415 (ttm) cc_final: 0.3975 (ttp) REVERT: N 1033 GLN cc_start: 0.8764 (tt0) cc_final: 0.8213 (tt0) REVERT: N 1123 ASP cc_start: 0.7444 (m-30) cc_final: 0.6640 (t0) REVERT: N 1190 THR cc_start: 0.9022 (p) cc_final: 0.8571 (m) REVERT: N 1196 PHE cc_start: 0.6984 (m-10) cc_final: 0.6411 (m-10) REVERT: O 294 LEU cc_start: 0.6685 (mt) cc_final: 0.6464 (mt) REVERT: O 344 LYS cc_start: 0.4524 (tptt) cc_final: 0.4100 (tppt) REVERT: O 517 ASP cc_start: 0.6352 (p0) cc_final: 0.5704 (p0) REVERT: O 553 ASP cc_start: 0.6336 (p0) cc_final: 0.6031 (p0) REVERT: O 563 VAL cc_start: 0.7336 (t) cc_final: 0.7062 (t) REVERT: O 587 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8042 (tt0) REVERT: O 607 GLN cc_start: 0.6883 (tp40) cc_final: 0.6368 (tp-100) REVERT: O 639 LEU cc_start: 0.8049 (mp) cc_final: 0.7678 (mt) REVERT: O 772 MET cc_start: 0.5884 (mmm) cc_final: 0.5405 (mmp) REVERT: O 889 MET cc_start: 0.4059 (tpt) cc_final: 0.3701 (tpp) REVERT: O 1044 MET cc_start: 0.6652 (ptp) cc_final: 0.6308 (ptp) REVERT: O 1119 ILE cc_start: 0.6085 (mm) cc_final: 0.5612 (mm) REVERT: O 1200 ASN cc_start: 0.8196 (p0) cc_final: 0.7851 (p0) REVERT: O 1290 MET cc_start: 0.6956 (mmt) cc_final: 0.6581 (mmt) REVERT: O 1369 VAL cc_start: 0.6056 (p) cc_final: 0.5775 (p) REVERT: O 1370 ARG cc_start: 0.6691 (mmt180) cc_final: 0.6318 (mmt180) REVERT: v 32 CYS cc_start: 0.5398 (t) cc_final: 0.4779 (m) REVERT: v 359 MET cc_start: 0.6283 (mtp) cc_final: 0.5698 (mtt) REVERT: v 379 ILE cc_start: 0.4970 (tt) cc_final: 0.4757 (tt) REVERT: y 3148 TYR cc_start: 0.5838 (m-80) cc_final: 0.5372 (m-80) REVERT: Z 52 THR cc_start: 0.6581 (p) cc_final: 0.6274 (p) REVERT: a 41 ARG cc_start: 0.6308 (ttp80) cc_final: 0.5921 (ttp80) REVERT: f 135 MET cc_start: 0.5688 (mtm) cc_final: 0.4809 (mtp) REVERT: f 154 MET cc_start: 0.5154 (tmm) cc_final: 0.4902 (ttm) REVERT: f 193 GLU cc_start: 0.5492 (pt0) cc_final: 0.4118 (pt0) REVERT: f 261 ASP cc_start: 0.6756 (m-30) cc_final: 0.6423 (m-30) REVERT: h 154 MET cc_start: 0.8496 (tpt) cc_final: 0.8175 (tpt) REVERT: k 235 LEU cc_start: 0.5196 (pt) cc_final: 0.4842 (pp) REVERT: k 268 MET cc_start: 0.6526 (ttp) cc_final: 0.6249 (ttm) REVERT: m 17 GLU cc_start: 0.4241 (pt0) cc_final: 0.4033 (mt-10) REVERT: m 24 ARG cc_start: 0.6048 (mmt180) cc_final: 0.5848 (mmm-85) REVERT: m 78 ASP cc_start: 0.5996 (p0) cc_final: 0.5742 (p0) REVERT: m 152 LEU cc_start: 0.7446 (mt) cc_final: 0.6655 (tt) REVERT: m 232 HIS cc_start: 0.6474 (m90) cc_final: 0.6143 (m-70) REVERT: m 270 TYR cc_start: 0.7342 (m-80) cc_final: 0.6934 (m-80) REVERT: p 15 THR cc_start: 0.6352 (p) cc_final: 0.5848 (t) REVERT: p 119 GLU cc_start: 0.7214 (pm20) cc_final: 0.6655 (tp30) REVERT: p 145 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5633 (mt-10) REVERT: p 172 VAL cc_start: 0.8328 (t) cc_final: 0.8095 (t) REVERT: r 25 ILE cc_start: 0.5125 (tt) cc_final: 0.4900 (mm) REVERT: r 37 THR cc_start: 0.6132 (m) cc_final: 0.5807 (m) REVERT: r 64 LEU cc_start: 0.8445 (mt) cc_final: 0.8045 (mm) REVERT: r 240 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7896 (tm-30) REVERT: r 286 THR cc_start: 0.5342 (t) cc_final: 0.5051 (t) outliers start: 0 outliers final: 0 residues processed: 1662 average time/residue: 0.5757 time to fit residues: 1632.3004 Evaluate side-chains 1283 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1283 time to evaluate : 5.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 9.9990 chunk 680 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 443 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 756 optimal weight: 7.9990 chunk 628 optimal weight: 20.0000 chunk 350 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 397 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 587 GLN J 833 GLN J 921 GLN K 531 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN ** K 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS N 178 ASN N 222 HIS ** N 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 491 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 722 ASN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1149 GLN N1227 HIS O 79 ASN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 HIS O 285 ASN ** O 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 ASN O 761 GLN ** O 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 909 GLN ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS O1122 GLN ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1301 HIS O1329 GLN O1353 HIS O1377 ASN ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN d 54 GLN h 13 GLN h 201 ASN h 312 HIS k 23 GLN ** k 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 41 GLN m 148 GLN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 GLN r 148 GLN r 154 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 63966 Z= 0.289 Angle : 0.742 14.121 86932 Z= 0.381 Chirality : 0.046 0.252 9795 Planarity : 0.006 0.099 11336 Dihedral : 5.466 47.303 8722 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.15 % Favored : 93.73 % Rotamer: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 7881 helix: 0.02 (0.09), residues: 2973 sheet: -0.15 (0.15), residues: 1090 loop : -1.55 (0.10), residues: 3818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP x 54 HIS 0.011 0.001 HIS K 964 PHE 0.033 0.002 PHE m 278 TYR 0.036 0.002 TYR z3148 ARG 0.019 0.001 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1702 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1699 time to evaluate : 5.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 88 MET cc_start: 0.5652 (mtt) cc_final: 0.5400 (mtt) REVERT: J 131 MET cc_start: 0.8645 (ptp) cc_final: 0.8440 (ptt) REVERT: J 153 GLU cc_start: 0.5566 (mm-30) cc_final: 0.5314 (tp30) REVERT: J 173 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6481 (mm-30) REVERT: J 517 ASP cc_start: 0.7776 (p0) cc_final: 0.7445 (p0) REVERT: J 635 MET cc_start: 0.6849 (mtm) cc_final: 0.6541 (mtp) REVERT: J 723 LEU cc_start: 0.8547 (tp) cc_final: 0.8104 (tt) REVERT: J 889 MET cc_start: 0.6572 (ttt) cc_final: 0.6205 (ttt) REVERT: J 951 HIS cc_start: 0.6887 (t-90) cc_final: 0.6661 (t70) REVERT: J 952 MET cc_start: 0.8367 (mtp) cc_final: 0.8089 (mtp) REVERT: J 1028 MET cc_start: 0.7484 (pmm) cc_final: 0.7097 (pmm) REVERT: J 1117 MET cc_start: 0.7369 (mmt) cc_final: 0.6939 (mmm) REVERT: J 1119 ILE cc_start: 0.7843 (mm) cc_final: 0.7536 (mm) REVERT: J 1259 TYR cc_start: 0.6186 (p90) cc_final: 0.5891 (p90) REVERT: K 180 VAL cc_start: 0.8882 (t) cc_final: 0.8667 (p) REVERT: K 415 ASN cc_start: 0.8026 (p0) cc_final: 0.7760 (p0) REVERT: K 543 HIS cc_start: 0.7636 (t-90) cc_final: 0.6488 (t-90) REVERT: K 587 GLN cc_start: 0.7613 (mt0) cc_final: 0.7027 (mt0) REVERT: K 880 MET cc_start: 0.6749 (ptp) cc_final: 0.6049 (mtt) REVERT: K 1021 MET cc_start: 0.6109 (mtp) cc_final: 0.5347 (ttm) REVERT: K 1076 ARG cc_start: 0.6532 (ptm160) cc_final: 0.5005 (mtt90) REVERT: K 1080 ARG cc_start: 0.5954 (ttt-90) cc_final: 0.1409 (tpm170) REVERT: K 1297 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7383 (tpp-160) REVERT: K 1308 GLU cc_start: 0.7138 (tt0) cc_final: 0.6852 (tt0) REVERT: N 83 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8450 (mtpt) REVERT: N 176 LEU cc_start: 0.8411 (mm) cc_final: 0.8035 (mm) REVERT: N 193 ILE cc_start: 0.7619 (mp) cc_final: 0.7402 (mp) REVERT: N 205 ARG cc_start: 0.5956 (mmt180) cc_final: 0.5364 (ptm160) REVERT: N 215 LEU cc_start: 0.7931 (tp) cc_final: 0.7713 (tp) REVERT: N 219 PHE cc_start: 0.7843 (m-80) cc_final: 0.7596 (m-80) REVERT: N 320 THR cc_start: 0.6424 (p) cc_final: 0.6201 (p) REVERT: N 372 ILE cc_start: 0.8722 (mm) cc_final: 0.8445 (mt) REVERT: N 382 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7614 (mm-30) REVERT: N 581 GLN cc_start: 0.8264 (tp40) cc_final: 0.7602 (mt0) REVERT: N 584 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7610 (tmm-80) REVERT: N 647 TYR cc_start: 0.7849 (t80) cc_final: 0.7085 (t80) REVERT: N 662 MET cc_start: 0.7879 (mtt) cc_final: 0.7428 (mtt) REVERT: N 807 VAL cc_start: 0.8846 (t) cc_final: 0.8521 (t) REVERT: N 972 MET cc_start: 0.4650 (ttm) cc_final: 0.4179 (ttp) REVERT: N 977 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7616 (mm-40) REVERT: N 1021 MET cc_start: 0.7479 (mtt) cc_final: 0.6177 (mtt) REVERT: N 1033 GLN cc_start: 0.8754 (tt0) cc_final: 0.8086 (tt0) REVERT: N 1145 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8296 (mmmt) REVERT: N 1190 THR cc_start: 0.9203 (p) cc_final: 0.8610 (m) REVERT: N 1196 PHE cc_start: 0.7285 (m-10) cc_final: 0.6643 (m-10) REVERT: N 1218 GLU cc_start: 0.7097 (tp30) cc_final: 0.6885 (tm-30) REVERT: N 1327 PHE cc_start: 0.7902 (t80) cc_final: 0.7529 (t80) REVERT: O 281 ILE cc_start: 0.8489 (tp) cc_final: 0.8118 (mp) REVERT: O 294 LEU cc_start: 0.7143 (mt) cc_final: 0.6823 (mt) REVERT: O 517 ASP cc_start: 0.5936 (p0) cc_final: 0.5404 (p0) REVERT: O 553 ASP cc_start: 0.6065 (p0) cc_final: 0.5684 (p0) REVERT: O 587 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8206 (tt0) REVERT: O 607 GLN cc_start: 0.6982 (tp40) cc_final: 0.6513 (tp-100) REVERT: O 739 VAL cc_start: 0.8051 (t) cc_final: 0.7704 (t) REVERT: O 772 MET cc_start: 0.6130 (mmm) cc_final: 0.5683 (mmp) REVERT: O 838 THR cc_start: 0.8291 (p) cc_final: 0.8079 (t) REVERT: O 889 MET cc_start: 0.4370 (tpt) cc_final: 0.4169 (tpp) REVERT: O 1099 LEU cc_start: 0.8587 (mm) cc_final: 0.8382 (mt) REVERT: O 1119 ILE cc_start: 0.6260 (mm) cc_final: 0.5722 (mm) REVERT: O 1290 MET cc_start: 0.7564 (mmt) cc_final: 0.6913 (mmt) REVERT: O 1364 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7197 (tm-30) REVERT: O 1370 ARG cc_start: 0.7337 (mmt180) cc_final: 0.7124 (mmt180) REVERT: O 1373 LEU cc_start: 0.9034 (mm) cc_final: 0.8483 (mm) REVERT: v 32 CYS cc_start: 0.5532 (t) cc_final: 0.4904 (m) REVERT: y 3148 TYR cc_start: 0.5896 (m-80) cc_final: 0.5220 (m-80) REVERT: Z 34 ASN cc_start: 0.7533 (p0) cc_final: 0.7333 (p0) REVERT: Z 52 THR cc_start: 0.6762 (p) cc_final: 0.6371 (p) REVERT: Z 60 TYR cc_start: 0.6592 (t80) cc_final: 0.6351 (t80) REVERT: f 135 MET cc_start: 0.6339 (mtm) cc_final: 0.5778 (mtp) REVERT: f 192 VAL cc_start: 0.7582 (t) cc_final: 0.7370 (t) REVERT: f 193 GLU cc_start: 0.5921 (pt0) cc_final: 0.5558 (pt0) REVERT: f 202 LYS cc_start: 0.6073 (mmtm) cc_final: 0.5739 (mptt) REVERT: f 261 ASP cc_start: 0.7006 (m-30) cc_final: 0.6667 (m-30) REVERT: h 92 ASP cc_start: 0.7633 (p0) cc_final: 0.7249 (p0) REVERT: h 154 MET cc_start: 0.8193 (tpt) cc_final: 0.7931 (tpp) REVERT: k 11 SER cc_start: 0.5362 (p) cc_final: 0.5156 (m) REVERT: k 118 ARG cc_start: 0.6437 (tpt90) cc_final: 0.6112 (tpt90) REVERT: k 138 LEU cc_start: 0.7956 (mt) cc_final: 0.7756 (mt) REVERT: k 235 LEU cc_start: 0.5406 (pt) cc_final: 0.5076 (pp) REVERT: k 268 MET cc_start: 0.5985 (ttp) cc_final: 0.5243 (ttp) REVERT: m 78 ASP cc_start: 0.6477 (p0) cc_final: 0.6238 (p0) REVERT: m 112 MET cc_start: 0.7100 (ptp) cc_final: 0.6800 (ptp) REVERT: m 152 LEU cc_start: 0.7563 (mt) cc_final: 0.6708 (tt) REVERT: m 270 TYR cc_start: 0.7601 (m-80) cc_final: 0.7086 (m-80) REVERT: p 15 THR cc_start: 0.6491 (p) cc_final: 0.6157 (t) REVERT: p 17 GLU cc_start: 0.6751 (pm20) cc_final: 0.6346 (pm20) REVERT: p 119 GLU cc_start: 0.7574 (pm20) cc_final: 0.6756 (tp30) REVERT: p 173 HIS cc_start: 0.6498 (m170) cc_final: 0.6151 (m170) REVERT: p 211 ILE cc_start: 0.8058 (mt) cc_final: 0.7670 (mm) REVERT: p 278 PHE cc_start: 0.8161 (m-10) cc_final: 0.7249 (m-80) REVERT: r 6 VAL cc_start: 0.8174 (t) cc_final: 0.7928 (m) REVERT: r 25 ILE cc_start: 0.6037 (tt) cc_final: 0.5820 (mm) REVERT: r 35 HIS cc_start: 0.5690 (m-70) cc_final: 0.5367 (m170) REVERT: r 64 LEU cc_start: 0.8582 (mt) cc_final: 0.8233 (mm) outliers start: 3 outliers final: 1 residues processed: 1702 average time/residue: 0.5748 time to fit residues: 1665.6601 Evaluate side-chains 1275 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1274 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 431 optimal weight: 0.0770 chunk 552 optimal weight: 7.9990 chunk 428 optimal weight: 20.0000 chunk 636 optimal weight: 10.0000 chunk 422 optimal weight: 8.9990 chunk 753 optimal weight: 8.9990 chunk 471 optimal weight: 5.9990 chunk 459 optimal weight: 8.9990 chunk 347 optimal weight: 40.0000 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 833 GLN J1022 HIS J1178 GLN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 722 ASN K 745 GLN ** K 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN K 833 GLN K 974 ASN N 9 ASN N 121 ASN N 222 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN N 722 ASN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 ASN ** O 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 842 ASN O1033 GLN O1090 HIS ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1284 ASN O1310 GLN ** v 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN d 54 GLN f 182 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 201 ASN ** k 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 204 ASN ** p 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 232 HIS r 23 GLN ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 154 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 63966 Z= 0.253 Angle : 0.716 16.281 86932 Z= 0.363 Chirality : 0.046 0.273 9795 Planarity : 0.006 0.100 11336 Dihedral : 5.448 44.298 8722 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.89 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.09), residues: 7881 helix: 0.03 (0.09), residues: 2975 sheet: -0.13 (0.15), residues: 1053 loop : -1.54 (0.10), residues: 3853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP x 54 HIS 0.013 0.001 HIS O1022 PHE 0.025 0.002 PHE N 619 TYR 0.055 0.002 TYR k 270 ARG 0.015 0.001 ARG h 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1671 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1671 time to evaluate : 5.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 88 MET cc_start: 0.5349 (mtt) cc_final: 0.4939 (mtt) REVERT: J 97 ILE cc_start: 0.6718 (tp) cc_final: 0.6412 (pt) REVERT: J 153 GLU cc_start: 0.5651 (mm-30) cc_final: 0.5436 (tp30) REVERT: J 173 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6997 (mm-30) REVERT: J 191 MET cc_start: 0.8306 (mmm) cc_final: 0.7797 (tpt) REVERT: J 769 MET cc_start: 0.6121 (tpp) cc_final: 0.5623 (tpp) REVERT: J 1028 MET cc_start: 0.7441 (pmm) cc_final: 0.6704 (mpp) REVERT: J 1050 ASP cc_start: 0.7498 (m-30) cc_final: 0.7224 (m-30) REVERT: J 1119 ILE cc_start: 0.7993 (mm) cc_final: 0.7696 (mm) REVERT: J 1223 LEU cc_start: 0.8490 (mt) cc_final: 0.8137 (mt) REVERT: J 1259 TYR cc_start: 0.6185 (p90) cc_final: 0.5673 (p90) REVERT: K 21 LEU cc_start: 0.8014 (mm) cc_final: 0.7503 (tt) REVERT: K 76 SER cc_start: 0.7987 (m) cc_final: 0.7665 (m) REVERT: K 191 MET cc_start: 0.5406 (tpt) cc_final: 0.5149 (tpp) REVERT: K 587 GLN cc_start: 0.7712 (mt0) cc_final: 0.7099 (mt0) REVERT: K 639 LEU cc_start: 0.7607 (tt) cc_final: 0.6599 (tp) REVERT: K 666 ILE cc_start: 0.7246 (mt) cc_final: 0.6986 (mm) REVERT: K 772 MET cc_start: 0.5139 (mpp) cc_final: 0.4927 (mpp) REVERT: K 807 VAL cc_start: 0.8842 (t) cc_final: 0.8527 (t) REVERT: K 978 ARG cc_start: 0.6999 (mpt-90) cc_final: 0.6675 (mmm160) REVERT: K 1018 MET cc_start: 0.7264 (tmm) cc_final: 0.6998 (tmm) REVERT: K 1076 ARG cc_start: 0.6498 (ptm160) cc_final: 0.5060 (mtt90) REVERT: K 1080 ARG cc_start: 0.6052 (ttt-90) cc_final: 0.1894 (tpm170) REVERT: K 1139 ASN cc_start: 0.7718 (t0) cc_final: 0.7483 (t0) REVERT: N 83 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8626 (mtpt) REVERT: N 205 ARG cc_start: 0.6193 (mmt180) cc_final: 0.5461 (ptm160) REVERT: N 219 PHE cc_start: 0.7657 (m-80) cc_final: 0.7382 (m-80) REVERT: N 320 THR cc_start: 0.6462 (p) cc_final: 0.6174 (p) REVERT: N 367 ILE cc_start: 0.6062 (mm) cc_final: 0.5392 (mm) REVERT: N 372 ILE cc_start: 0.8591 (mm) cc_final: 0.8368 (mt) REVERT: N 382 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7706 (mm-30) REVERT: N 402 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7678 (tm-30) REVERT: N 581 GLN cc_start: 0.8244 (tp40) cc_final: 0.7673 (mt0) REVERT: N 619 PHE cc_start: 0.7591 (m-10) cc_final: 0.7088 (m-80) REVERT: N 807 VAL cc_start: 0.8994 (t) cc_final: 0.8517 (t) REVERT: N 972 MET cc_start: 0.4694 (ttm) cc_final: 0.4247 (ttp) REVERT: N 977 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7663 (mm-40) REVERT: N 998 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.8263 (mmt-90) REVERT: N 1058 LEU cc_start: 0.9082 (tp) cc_final: 0.8655 (tp) REVERT: N 1113 ILE cc_start: 0.8733 (mp) cc_final: 0.8477 (mt) REVERT: N 1123 ASP cc_start: 0.7528 (m-30) cc_final: 0.7302 (m-30) REVERT: N 1190 THR cc_start: 0.9202 (p) cc_final: 0.8553 (m) REVERT: N 1327 PHE cc_start: 0.7873 (t80) cc_final: 0.7492 (t80) REVERT: O 251 MET cc_start: 0.7918 (tpp) cc_final: 0.7067 (tpp) REVERT: O 281 ILE cc_start: 0.8677 (tp) cc_final: 0.8430 (pt) REVERT: O 355 VAL cc_start: 0.8481 (t) cc_final: 0.8250 (p) REVERT: O 386 LYS cc_start: 0.8431 (tmtt) cc_final: 0.8108 (tptm) REVERT: O 517 ASP cc_start: 0.6173 (p0) cc_final: 0.5890 (p0) REVERT: O 553 ASP cc_start: 0.6053 (p0) cc_final: 0.5546 (p0) REVERT: O 587 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8241 (tt0) REVERT: O 739 VAL cc_start: 0.8126 (t) cc_final: 0.7793 (t) REVERT: O 772 MET cc_start: 0.6055 (mmm) cc_final: 0.5639 (mmp) REVERT: O 838 THR cc_start: 0.8379 (p) cc_final: 0.8135 (t) REVERT: O 889 MET cc_start: 0.4341 (tpt) cc_final: 0.3875 (tpp) REVERT: O 1099 LEU cc_start: 0.8622 (mm) cc_final: 0.8301 (mt) REVERT: O 1119 ILE cc_start: 0.6271 (mm) cc_final: 0.5882 (mm) REVERT: O 1290 MET cc_start: 0.7599 (mmt) cc_final: 0.6873 (mmp) REVERT: O 1364 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7580 (tm-30) REVERT: v 28 MET cc_start: 0.6735 (mmt) cc_final: 0.6509 (tpp) REVERT: v 32 CYS cc_start: 0.5948 (t) cc_final: 0.5185 (m) REVERT: v 388 GLU cc_start: 0.6777 (tp30) cc_final: 0.6413 (tp30) REVERT: v 475 LEU cc_start: 0.8920 (tp) cc_final: 0.8378 (tp) REVERT: x 65 LEU cc_start: 0.6149 (mt) cc_final: 0.5732 (mt) REVERT: y 3148 TYR cc_start: 0.5765 (m-80) cc_final: 0.5269 (m-80) REVERT: Z 21 SER cc_start: 0.6746 (t) cc_final: 0.6292 (p) REVERT: Z 34 ASN cc_start: 0.7837 (p0) cc_final: 0.7264 (p0) REVERT: a 48 LEU cc_start: 0.8222 (pp) cc_final: 0.7887 (pp) REVERT: a 51 LEU cc_start: 0.8411 (pp) cc_final: 0.8023 (tt) REVERT: e 72 ARG cc_start: 0.5571 (mtm180) cc_final: 0.4961 (mtm180) REVERT: f 135 MET cc_start: 0.6368 (mtm) cc_final: 0.5658 (mtp) REVERT: f 193 GLU cc_start: 0.5879 (pt0) cc_final: 0.5654 (pt0) REVERT: f 202 LYS cc_start: 0.5959 (mmtm) cc_final: 0.5604 (mptt) REVERT: f 261 ASP cc_start: 0.7032 (m-30) cc_final: 0.6778 (m-30) REVERT: h 154 MET cc_start: 0.8067 (tpt) cc_final: 0.7857 (tpp) REVERT: h 277 PHE cc_start: 0.6984 (m-80) cc_final: 0.6730 (m-10) REVERT: h 295 ILE cc_start: 0.8411 (tt) cc_final: 0.8190 (tt) REVERT: k 18 ILE cc_start: 0.7576 (tt) cc_final: 0.7369 (tt) REVERT: k 235 LEU cc_start: 0.5795 (pt) cc_final: 0.5409 (pp) REVERT: k 264 MET cc_start: 0.6726 (ppp) cc_final: 0.6129 (tmm) REVERT: k 268 MET cc_start: 0.6577 (ttp) cc_final: 0.4284 (ttp) REVERT: m 152 LEU cc_start: 0.7619 (mt) cc_final: 0.6866 (tt) REVERT: m 261 LEU cc_start: 0.8724 (pp) cc_final: 0.8506 (pp) REVERT: m 268 MET cc_start: 0.7234 (tpt) cc_final: 0.6826 (tpp) REVERT: m 270 TYR cc_start: 0.7436 (m-80) cc_final: 0.7078 (m-80) REVERT: m 274 LEU cc_start: 0.8384 (mm) cc_final: 0.8011 (mm) REVERT: p 119 GLU cc_start: 0.7498 (pm20) cc_final: 0.7216 (tp30) REVERT: p 145 GLU cc_start: 0.6151 (mt-10) cc_final: 0.5780 (mt-10) REVERT: p 173 HIS cc_start: 0.6634 (m170) cc_final: 0.6066 (m170) REVERT: p 211 ILE cc_start: 0.8140 (mt) cc_final: 0.7750 (mm) REVERT: r 6 VAL cc_start: 0.8209 (t) cc_final: 0.7976 (m) REVERT: r 35 HIS cc_start: 0.6120 (m-70) cc_final: 0.5681 (m170) REVERT: r 140 THR cc_start: 0.8120 (m) cc_final: 0.7871 (p) REVERT: r 240 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7925 (tm-30) REVERT: r 242 MET cc_start: 0.8314 (mmm) cc_final: 0.7967 (mpp) outliers start: 0 outliers final: 0 residues processed: 1671 average time/residue: 0.6134 time to fit residues: 1745.6799 Evaluate side-chains 1290 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1290 time to evaluate : 5.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 8.9990 chunk 300 optimal weight: 5.9990 chunk 450 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 479 optimal weight: 1.9990 chunk 513 optimal weight: 30.0000 chunk 372 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 592 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 824 HIS J 833 GLN J 921 GLN J1022 HIS K 722 ASN ** K 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 ASN h 13 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 104 HIS ** k 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 128 ASN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 237 ASN r 23 GLN r 128 ASN ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 154 ASN r 272 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.9045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 63966 Z= 0.229 Angle : 0.705 14.069 86932 Z= 0.358 Chirality : 0.045 0.251 9795 Planarity : 0.006 0.115 11336 Dihedral : 5.318 41.524 8722 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 0.01 % Allowed : 1.31 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.09), residues: 7881 helix: 0.06 (0.09), residues: 2970 sheet: -0.15 (0.15), residues: 1058 loop : -1.48 (0.10), residues: 3853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP x 54 HIS 0.012 0.001 HIS v 96 PHE 0.026 0.002 PHE z3146 TYR 0.023 0.002 TYR k 61 ARG 0.023 0.001 ARG Z 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1633 time to evaluate : 5.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 173 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7037 (mm-30) REVERT: J 179 THR cc_start: 0.8697 (p) cc_final: 0.8496 (p) REVERT: J 186 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7278 (ttm-80) REVERT: J 387 MET cc_start: 0.8062 (tmm) cc_final: 0.7640 (tmm) REVERT: J 596 HIS cc_start: 0.7698 (m-70) cc_final: 0.7358 (m170) REVERT: J 615 TYR cc_start: 0.6236 (t80) cc_final: 0.5894 (t80) REVERT: J 620 TYR cc_start: 0.7358 (m-80) cc_final: 0.6960 (m-80) REVERT: J 1117 MET cc_start: 0.7558 (mmm) cc_final: 0.6810 (mmm) REVERT: J 1119 ILE cc_start: 0.7998 (mm) cc_final: 0.7784 (mm) REVERT: J 1184 ILE cc_start: 0.8994 (tp) cc_final: 0.8734 (tp) REVERT: J 1190 THR cc_start: 0.9286 (p) cc_final: 0.9010 (m) REVERT: J 1223 LEU cc_start: 0.8475 (mt) cc_final: 0.8258 (mt) REVERT: J 1254 MET cc_start: 0.7510 (ttp) cc_final: 0.7306 (ptm) REVERT: J 1259 TYR cc_start: 0.6257 (p90) cc_final: 0.5909 (p90) REVERT: J 1339 SER cc_start: 0.9306 (p) cc_final: 0.9035 (t) REVERT: K 21 LEU cc_start: 0.8003 (mm) cc_final: 0.7465 (tt) REVERT: K 112 LYS cc_start: 0.7714 (mmtt) cc_final: 0.6737 (pttt) REVERT: K 159 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7238 (mmtt) REVERT: K 587 GLN cc_start: 0.7694 (mt0) cc_final: 0.7126 (mt0) REVERT: K 639 LEU cc_start: 0.8902 (tt) cc_final: 0.7903 (tt) REVERT: K 978 ARG cc_start: 0.7096 (mpt-90) cc_final: 0.6780 (tpp80) REVERT: K 1080 ARG cc_start: 0.5926 (ttt-90) cc_final: 0.1564 (tpm170) REVERT: K 1205 ARG cc_start: 0.8960 (mtp85) cc_final: 0.8500 (ttm-80) REVERT: K 1225 TYR cc_start: 0.6132 (m-80) cc_final: 0.5886 (m-80) REVERT: N 176 LEU cc_start: 0.8413 (mm) cc_final: 0.8061 (mm) REVERT: N 205 ARG cc_start: 0.6460 (mmt180) cc_final: 0.5155 (ttt180) REVERT: N 320 THR cc_start: 0.6366 (p) cc_final: 0.6093 (p) REVERT: N 372 ILE cc_start: 0.8584 (mm) cc_final: 0.8383 (mt) REVERT: N 402 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7682 (tm-30) REVERT: N 581 GLN cc_start: 0.8087 (tp40) cc_final: 0.7663 (mt0) REVERT: N 619 PHE cc_start: 0.7519 (m-10) cc_final: 0.7036 (m-80) REVERT: N 643 CYS cc_start: 0.7165 (m) cc_final: 0.6705 (m) REVERT: N 649 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6279 (tp30) REVERT: N 816 PHE cc_start: 0.7328 (t80) cc_final: 0.6824 (t80) REVERT: N 972 MET cc_start: 0.4565 (ttm) cc_final: 0.4117 (ttp) REVERT: N 977 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7605 (mm-40) REVERT: N 998 ARG cc_start: 0.8457 (mmt-90) cc_final: 0.8233 (mmt-90) REVERT: N 1021 MET cc_start: 0.7165 (mtt) cc_final: 0.6286 (mtt) REVERT: N 1058 LEU cc_start: 0.9124 (tp) cc_final: 0.8551 (tp) REVERT: N 1113 ILE cc_start: 0.8703 (mp) cc_final: 0.8417 (mt) REVERT: N 1123 ASP cc_start: 0.7302 (m-30) cc_final: 0.7057 (m-30) REVERT: N 1190 THR cc_start: 0.9182 (p) cc_final: 0.8497 (m) REVERT: O 251 MET cc_start: 0.7832 (tpp) cc_final: 0.7112 (tpp) REVERT: O 281 ILE cc_start: 0.8760 (tp) cc_final: 0.8331 (mp) REVERT: O 355 VAL cc_start: 0.8580 (t) cc_final: 0.8374 (p) REVERT: O 458 VAL cc_start: 0.8183 (p) cc_final: 0.7954 (p) REVERT: O 517 ASP cc_start: 0.6159 (p0) cc_final: 0.5764 (p0) REVERT: O 553 ASP cc_start: 0.5960 (p0) cc_final: 0.5574 (p0) REVERT: O 662 MET cc_start: 0.7264 (ttt) cc_final: 0.7047 (ttt) REVERT: O 739 VAL cc_start: 0.8187 (t) cc_final: 0.7926 (t) REVERT: O 763 ILE cc_start: 0.6409 (pt) cc_final: 0.6186 (pt) REVERT: O 772 MET cc_start: 0.6221 (mmm) cc_final: 0.5460 (mmm) REVERT: O 838 THR cc_start: 0.8382 (p) cc_final: 0.8126 (t) REVERT: O 889 MET cc_start: 0.4442 (tpt) cc_final: 0.3808 (tpp) REVERT: O 1067 MET cc_start: 0.8352 (tpp) cc_final: 0.7732 (tpt) REVERT: O 1099 LEU cc_start: 0.8680 (mm) cc_final: 0.8256 (mt) REVERT: O 1119 ILE cc_start: 0.6300 (mm) cc_final: 0.5851 (mm) REVERT: O 1184 ILE cc_start: 0.9021 (pt) cc_final: 0.8740 (pt) REVERT: O 1290 MET cc_start: 0.7676 (mmt) cc_final: 0.7152 (mmp) REVERT: O 1364 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7542 (tm-30) REVERT: O 1373 LEU cc_start: 0.9065 (mm) cc_final: 0.8601 (mm) REVERT: v 32 CYS cc_start: 0.5956 (t) cc_final: 0.5506 (m) REVERT: v 359 MET cc_start: 0.6838 (mtt) cc_final: 0.6554 (mtt) REVERT: v 388 GLU cc_start: 0.6753 (tp30) cc_final: 0.6466 (tp30) REVERT: v 475 LEU cc_start: 0.8964 (tp) cc_final: 0.8446 (tp) REVERT: x 65 LEU cc_start: 0.6032 (mt) cc_final: 0.5757 (mt) REVERT: y 3148 TYR cc_start: 0.5693 (m-80) cc_final: 0.5336 (m-80) REVERT: Z 21 SER cc_start: 0.6633 (t) cc_final: 0.6290 (p) REVERT: Z 34 ASN cc_start: 0.7653 (p0) cc_final: 0.7431 (p0) REVERT: a 41 ARG cc_start: 0.5856 (ttp80) cc_final: 0.5368 (ttp80) REVERT: a 51 LEU cc_start: 0.8390 (pp) cc_final: 0.8002 (tt) REVERT: d 24 LEU cc_start: 0.7996 (mt) cc_final: 0.7677 (mt) REVERT: d 72 ARG cc_start: 0.6103 (mtt90) cc_final: 0.5858 (mtm180) REVERT: e 72 ARG cc_start: 0.5777 (mtm180) cc_final: 0.5267 (mtm180) REVERT: f 135 MET cc_start: 0.6272 (mtm) cc_final: 0.5978 (mtp) REVERT: f 183 ASN cc_start: 0.7910 (m110) cc_final: 0.7688 (t0) REVERT: f 192 VAL cc_start: 0.7708 (t) cc_final: 0.7357 (t) REVERT: f 193 GLU cc_start: 0.5949 (pt0) cc_final: 0.4932 (pt0) REVERT: f 261 ASP cc_start: 0.7210 (m-30) cc_final: 0.6970 (m-30) REVERT: h 154 MET cc_start: 0.8169 (tpt) cc_final: 0.7958 (tpp) REVERT: h 295 ILE cc_start: 0.8457 (tt) cc_final: 0.8166 (tt) REVERT: k 112 MET cc_start: 0.7380 (mtp) cc_final: 0.7148 (mtp) REVERT: k 138 LEU cc_start: 0.7832 (mt) cc_final: 0.7487 (mt) REVERT: k 235 LEU cc_start: 0.5719 (pt) cc_final: 0.5418 (pp) REVERT: k 264 MET cc_start: 0.6783 (ppp) cc_final: 0.5354 (tmm) REVERT: k 283 ARG cc_start: 0.5612 (ppt170) cc_final: 0.4677 (tmm160) REVERT: m 207 LEU cc_start: 0.8723 (mt) cc_final: 0.8203 (mm) REVERT: m 211 ILE cc_start: 0.7892 (mm) cc_final: 0.7523 (mm) REVERT: m 267 MET cc_start: 0.7931 (ttp) cc_final: 0.7547 (ttp) REVERT: m 270 TYR cc_start: 0.7476 (m-80) cc_final: 0.7222 (m-80) REVERT: m 274 LEU cc_start: 0.8342 (mm) cc_final: 0.8124 (mm) REVERT: p 119 GLU cc_start: 0.7497 (pm20) cc_final: 0.7189 (tp30) REVERT: p 211 ILE cc_start: 0.8298 (mt) cc_final: 0.7831 (mm) REVERT: r 6 VAL cc_start: 0.8229 (t) cc_final: 0.8022 (m) REVERT: r 35 HIS cc_start: 0.6155 (m-70) cc_final: 0.5782 (m170) REVERT: r 119 GLU cc_start: 0.7997 (pm20) cc_final: 0.6841 (pm20) REVERT: r 138 LEU cc_start: 0.8763 (tp) cc_final: 0.8540 (tp) REVERT: r 140 THR cc_start: 0.8055 (m) cc_final: 0.7744 (p) REVERT: r 240 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8038 (tm-30) REVERT: r 242 MET cc_start: 0.8226 (mmm) cc_final: 0.7659 (tpp) outliers start: 1 outliers final: 0 residues processed: 1633 average time/residue: 0.5860 time to fit residues: 1629.9033 Evaluate side-chains 1282 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1282 time to evaluate : 5.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 0.0770 chunk 722 optimal weight: 20.0000 chunk 658 optimal weight: 8.9990 chunk 702 optimal weight: 2.9990 chunk 721 optimal weight: 8.9990 chunk 422 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 551 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 634 optimal weight: 5.9990 chunk 664 optimal weight: 7.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 788 HIS J1022 HIS K 289 GLN K 722 ASN ** K 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN K 833 GLN ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS N 222 HIS ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1283 ASN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 HIS O 333 HIS ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 581 GLN O 587 GLN O 627 HIS O 695 GLN O 761 GLN ** O 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 HIS f 201 ASN ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 128 ASN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 23 GLN ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 272 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.9313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 63966 Z= 0.205 Angle : 0.707 14.136 86932 Z= 0.356 Chirality : 0.045 0.230 9795 Planarity : 0.006 0.102 11336 Dihedral : 5.214 38.454 8722 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.99 % Rotamer: Outliers : 0.04 % Allowed : 0.71 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.09), residues: 7881 helix: 0.11 (0.09), residues: 2958 sheet: -0.10 (0.15), residues: 1058 loop : -1.44 (0.10), residues: 3865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP x 54 HIS 0.013 0.001 HIS N 560 PHE 0.054 0.002 PHE K 665 TYR 0.032 0.002 TYR O 841 ARG 0.015 0.001 ARG K 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1635 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1632 time to evaluate : 5.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.6016 (tp) cc_final: 0.5212 (pt) REVERT: J 173 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7076 (mm-30) REVERT: J 179 THR cc_start: 0.8754 (p) cc_final: 0.8477 (p) REVERT: J 210 THR cc_start: 0.9015 (p) cc_final: 0.8804 (p) REVERT: J 387 MET cc_start: 0.8114 (tmm) cc_final: 0.7786 (tmm) REVERT: J 596 HIS cc_start: 0.7733 (m-70) cc_final: 0.7344 (m170) REVERT: J 615 TYR cc_start: 0.6267 (t80) cc_final: 0.6022 (t80) REVERT: J 620 TYR cc_start: 0.7472 (m-80) cc_final: 0.6956 (m-80) REVERT: J 1028 MET cc_start: 0.7655 (pmm) cc_final: 0.7272 (pmm) REVERT: J 1117 MET cc_start: 0.7431 (mmm) cc_final: 0.6932 (mmm) REVERT: J 1119 ILE cc_start: 0.8028 (mm) cc_final: 0.7785 (mm) REVERT: J 1190 THR cc_start: 0.9287 (p) cc_final: 0.9078 (m) REVERT: J 1259 TYR cc_start: 0.6306 (p90) cc_final: 0.6020 (p90) REVERT: J 1339 SER cc_start: 0.9272 (p) cc_final: 0.9019 (t) REVERT: K 21 LEU cc_start: 0.7958 (mm) cc_final: 0.7433 (tt) REVERT: K 112 LYS cc_start: 0.7661 (mmtt) cc_final: 0.6687 (pttt) REVERT: K 159 LYS cc_start: 0.7567 (mmtt) cc_final: 0.7137 (mmtt) REVERT: K 543 HIS cc_start: 0.7954 (t-90) cc_final: 0.6374 (t-90) REVERT: K 557 ARG cc_start: 0.6040 (mmp80) cc_final: 0.5189 (mmm-85) REVERT: K 587 GLN cc_start: 0.7682 (mt0) cc_final: 0.7143 (mt0) REVERT: K 663 ILE cc_start: 0.7503 (mm) cc_final: 0.7169 (mm) REVERT: K 772 MET cc_start: 0.5272 (mpp) cc_final: 0.5038 (mpp) REVERT: K 813 TYR cc_start: 0.6805 (m-10) cc_final: 0.6259 (m-10) REVERT: K 978 ARG cc_start: 0.7165 (mpt-90) cc_final: 0.6618 (tpp-160) REVERT: K 1080 ARG cc_start: 0.5879 (ttt-90) cc_final: 0.1435 (tpm170) REVERT: K 1139 ASN cc_start: 0.7552 (t0) cc_final: 0.7343 (t0) REVERT: K 1205 ARG cc_start: 0.8961 (mtp85) cc_final: 0.8529 (ttm-80) REVERT: K 1308 GLU cc_start: 0.7341 (tt0) cc_final: 0.7066 (tt0) REVERT: N 159 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7720 (ptmt) REVERT: N 176 LEU cc_start: 0.8490 (mm) cc_final: 0.8234 (mm) REVERT: N 205 ARG cc_start: 0.6504 (mmt180) cc_final: 0.5163 (ttt180) REVERT: N 367 ILE cc_start: 0.5718 (mm) cc_final: 0.5217 (mm) REVERT: N 372 ILE cc_start: 0.8545 (mm) cc_final: 0.8337 (mt) REVERT: N 402 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7906 (tm-30) REVERT: N 426 MET cc_start: 0.7603 (mmt) cc_final: 0.7357 (mmt) REVERT: N 581 GLN cc_start: 0.8087 (tp40) cc_final: 0.7700 (mt0) REVERT: N 619 PHE cc_start: 0.7482 (m-10) cc_final: 0.7024 (m-80) REVERT: N 643 CYS cc_start: 0.6847 (m) cc_final: 0.6585 (m) REVERT: N 649 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6375 (tp30) REVERT: N 769 MET cc_start: 0.7002 (tmm) cc_final: 0.6792 (tmm) REVERT: N 807 VAL cc_start: 0.8939 (t) cc_final: 0.8735 (t) REVERT: N 816 PHE cc_start: 0.7201 (t80) cc_final: 0.6980 (t80) REVERT: N 972 MET cc_start: 0.4987 (ttm) cc_final: 0.4637 (ttp) REVERT: N 977 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7374 (mm-40) REVERT: N 1021 MET cc_start: 0.7291 (mtt) cc_final: 0.6296 (mtt) REVERT: N 1058 LEU cc_start: 0.9091 (tp) cc_final: 0.8623 (tp) REVERT: N 1113 ILE cc_start: 0.8630 (mp) cc_final: 0.8327 (mt) REVERT: N 1123 ASP cc_start: 0.7198 (m-30) cc_final: 0.6912 (m-30) REVERT: N 1190 THR cc_start: 0.9161 (p) cc_final: 0.8493 (m) REVERT: N 1290 MET cc_start: 0.6944 (tpp) cc_final: 0.6740 (tpp) REVERT: O 251 MET cc_start: 0.7696 (tpp) cc_final: 0.7117 (tpp) REVERT: O 281 ILE cc_start: 0.8633 (tp) cc_final: 0.8256 (mp) REVERT: O 344 LYS cc_start: 0.4621 (tptt) cc_final: 0.3676 (tmtt) REVERT: O 517 ASP cc_start: 0.6109 (p0) cc_final: 0.5821 (p0) REVERT: O 553 ASP cc_start: 0.5963 (p0) cc_final: 0.5549 (p0) REVERT: O 739 VAL cc_start: 0.8248 (t) cc_final: 0.7986 (t) REVERT: O 772 MET cc_start: 0.6185 (mmm) cc_final: 0.5571 (mmm) REVERT: O 838 THR cc_start: 0.8462 (p) cc_final: 0.8258 (t) REVERT: O 889 MET cc_start: 0.4230 (tpt) cc_final: 0.3713 (tpp) REVERT: O 1021 MET cc_start: 0.7628 (mtt) cc_final: 0.6975 (mtt) REVERT: O 1028 MET cc_start: 0.8075 (mmm) cc_final: 0.6938 (mmt) REVERT: O 1067 MET cc_start: 0.8584 (tpp) cc_final: 0.7932 (tpt) REVERT: O 1099 LEU cc_start: 0.8629 (mm) cc_final: 0.8273 (mt) REVERT: O 1119 ILE cc_start: 0.6381 (mm) cc_final: 0.5915 (mm) REVERT: O 1200 ASN cc_start: 0.8487 (p0) cc_final: 0.8077 (p0) REVERT: O 1290 MET cc_start: 0.7628 (mmt) cc_final: 0.7143 (mmp) REVERT: O 1373 LEU cc_start: 0.8990 (mm) cc_final: 0.8546 (mm) REVERT: v 28 MET cc_start: 0.6755 (tpp) cc_final: 0.6353 (tpp) REVERT: v 32 CYS cc_start: 0.6301 (t) cc_final: 0.5396 (m) REVERT: v 388 GLU cc_start: 0.6627 (tp30) cc_final: 0.6331 (tp30) REVERT: v 462 CYS cc_start: 0.6854 (m) cc_final: 0.6622 (m) REVERT: v 475 LEU cc_start: 0.8890 (tp) cc_final: 0.8472 (tp) REVERT: x 62 LYS cc_start: 0.7497 (mmmt) cc_final: 0.6864 (mtpt) REVERT: x 65 LEU cc_start: 0.5933 (mt) cc_final: 0.5646 (mt) REVERT: y 3148 TYR cc_start: 0.5455 (m-80) cc_final: 0.5029 (m-80) REVERT: Z 34 ASN cc_start: 0.7433 (p0) cc_final: 0.6873 (p0) REVERT: Z 52 THR cc_start: 0.6730 (p) cc_final: 0.6502 (p) REVERT: a 41 ARG cc_start: 0.5786 (ttp80) cc_final: 0.5189 (ttp80) REVERT: e 72 ARG cc_start: 0.5666 (mtm180) cc_final: 0.5178 (mtm180) REVERT: f 135 MET cc_start: 0.6223 (mtm) cc_final: 0.5947 (mtp) REVERT: f 192 VAL cc_start: 0.7398 (t) cc_final: 0.7111 (t) REVERT: f 193 GLU cc_start: 0.6052 (pt0) cc_final: 0.4985 (pt0) REVERT: f 261 ASP cc_start: 0.7147 (m-30) cc_final: 0.6913 (m-30) REVERT: h 295 ILE cc_start: 0.8547 (tt) cc_final: 0.8232 (tt) REVERT: k 235 LEU cc_start: 0.5833 (pt) cc_final: 0.5536 (pp) REVERT: k 264 MET cc_start: 0.6354 (ppp) cc_final: 0.4904 (tmm) REVERT: k 283 ARG cc_start: 0.5471 (ppt170) cc_final: 0.4698 (tmm160) REVERT: m 267 MET cc_start: 0.7507 (ttp) cc_final: 0.7126 (ttm) REVERT: p 119 GLU cc_start: 0.7521 (pm20) cc_final: 0.7313 (tp30) REVERT: p 161 MET cc_start: 0.5561 (ptm) cc_final: 0.4749 (ttt) REVERT: p 173 HIS cc_start: 0.6836 (m170) cc_final: 0.6447 (m170) REVERT: p 211 ILE cc_start: 0.8352 (mt) cc_final: 0.8109 (mm) REVERT: r 6 VAL cc_start: 0.8192 (t) cc_final: 0.7946 (m) REVERT: r 35 HIS cc_start: 0.6235 (m-70) cc_final: 0.5779 (m170) REVERT: r 120 HIS cc_start: 0.4826 (m-70) cc_final: 0.4529 (m-70) REVERT: r 138 LEU cc_start: 0.8720 (tp) cc_final: 0.8384 (tp) REVERT: r 140 THR cc_start: 0.7994 (m) cc_final: 0.7674 (p) REVERT: r 240 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8031 (tm-30) REVERT: r 242 MET cc_start: 0.8102 (mmm) cc_final: 0.7596 (tpp) outliers start: 3 outliers final: 0 residues processed: 1634 average time/residue: 0.5763 time to fit residues: 1607.3092 Evaluate side-chains 1294 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1294 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 5.9990 chunk 461 optimal weight: 6.9990 chunk 742 optimal weight: 2.9990 chunk 453 optimal weight: 7.9990 chunk 352 optimal weight: 20.0000 chunk 516 optimal weight: 20.0000 chunk 779 optimal weight: 5.9990 chunk 717 optimal weight: 10.0000 chunk 620 optimal weight: 0.0370 chunk 64 optimal weight: 5.9990 chunk 479 optimal weight: 0.0270 overall best weight: 3.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 788 HIS J 921 GLN ** J 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1022 HIS K 289 GLN K 722 ASN ** K 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 HIS ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 695 GLN O 822 ASN ** O 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1033 GLN ** O1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 464 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 62 ASN ** k 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 128 ASN m 230 HIS ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 23 GLN ** r 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 272 GLN r 291 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.9556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 63966 Z= 0.210 Angle : 0.715 16.054 86932 Z= 0.360 Chirality : 0.045 0.229 9795 Planarity : 0.006 0.108 11336 Dihedral : 5.199 35.773 8722 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 0.07 % Allowed : 0.38 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.09), residues: 7881 helix: 0.11 (0.09), residues: 2964 sheet: -0.09 (0.15), residues: 1051 loop : -1.45 (0.10), residues: 3866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP v 43 HIS 0.010 0.001 HIS v 96 PHE 0.043 0.002 PHE N 219 TYR 0.036 0.002 TYR N 535 ARG 0.010 0.001 ARG p 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15762 Ramachandran restraints generated. 7881 Oldfield, 0 Emsley, 7881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1599 time to evaluate : 5.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 85 LEU cc_start: 0.6791 (tp) cc_final: 0.6322 (pt) REVERT: J 179 THR cc_start: 0.8664 (p) cc_final: 0.8399 (p) REVERT: J 191 MET cc_start: 0.8251 (mmm) cc_final: 0.7970 (tpt) REVERT: J 387 MET cc_start: 0.8131 (tmm) cc_final: 0.7780 (tmm) REVERT: J 596 HIS cc_start: 0.7791 (m-70) cc_final: 0.7363 (m170) REVERT: J 615 TYR cc_start: 0.6239 (t80) cc_final: 0.5896 (t80) REVERT: J 620 TYR cc_start: 0.7329 (m-80) cc_final: 0.6867 (m-80) REVERT: J 646 THR cc_start: 0.8339 (p) cc_final: 0.7882 (t) REVERT: J 1028 MET cc_start: 0.7703 (pmm) cc_final: 0.7494 (pmm) REVERT: J 1044 MET cc_start: 0.7585 (tpp) cc_final: 0.7275 (tpp) REVERT: J 1067 MET cc_start: 0.6439 (tpt) cc_final: 0.5951 (tpp) REVERT: J 1117 MET cc_start: 0.7586 (mmm) cc_final: 0.6529 (mmm) REVERT: J 1119 ILE cc_start: 0.8069 (mm) cc_final: 0.7765 (mm) REVERT: J 1184 ILE cc_start: 0.8861 (tp) cc_final: 0.8657 (tp) REVERT: J 1190 THR cc_start: 0.9330 (p) cc_final: 0.9089 (m) REVERT: J 1223 LEU cc_start: 0.8607 (mt) cc_final: 0.8375 (mt) REVERT: J 1259 TYR cc_start: 0.6331 (p90) cc_final: 0.6019 (p90) REVERT: J 1339 SER cc_start: 0.9271 (p) cc_final: 0.8991 (t) REVERT: K 21 LEU cc_start: 0.7975 (mm) cc_final: 0.7396 (tt) REVERT: K 82 PHE cc_start: 0.7208 (t80) cc_final: 0.6434 (t80) REVERT: K 112 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6792 (pttt) REVERT: K 159 LYS cc_start: 0.7596 (mmtt) cc_final: 0.7129 (mmtt) REVERT: K 218 MET cc_start: 0.8305 (ptp) cc_final: 0.7693 (mtm) REVERT: K 398 ASN cc_start: 0.8269 (t0) cc_final: 0.8033 (t0) REVERT: K 543 HIS cc_start: 0.7926 (t-90) cc_final: 0.6606 (t-90) REVERT: K 587 GLN cc_start: 0.7710 (mt0) cc_final: 0.7349 (mt0) REVERT: K 663 ILE cc_start: 0.7646 (mm) cc_final: 0.7321 (mm) REVERT: K 813 TYR cc_start: 0.6638 (m-10) cc_final: 0.6389 (m-80) REVERT: K 941 THR cc_start: 0.6911 (m) cc_final: 0.6643 (m) REVERT: K 1080 ARG cc_start: 0.5583 (ttt-90) cc_final: 0.1273 (tpm170) REVERT: K 1205 ARG cc_start: 0.8990 (mtp85) cc_final: 0.8562 (ttm-80) REVERT: N 159 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7734 (ptmt) REVERT: N 205 ARG cc_start: 0.6542 (mmt180) cc_final: 0.5081 (ttt180) REVERT: N 215 LEU cc_start: 0.8247 (tp) cc_final: 0.7891 (tp) REVERT: N 320 THR cc_start: 0.6523 (p) cc_final: 0.6215 (p) REVERT: N 372 ILE cc_start: 0.8568 (mm) cc_final: 0.8252 (mt) REVERT: N 426 MET cc_start: 0.7727 (mmt) cc_final: 0.7517 (mmt) REVERT: N 581 GLN cc_start: 0.7852 (tp40) cc_final: 0.7579 (mt0) REVERT: N 619 PHE cc_start: 0.7412 (m-10) cc_final: 0.7103 (m-80) REVERT: N 643 CYS cc_start: 0.6913 (m) cc_final: 0.6587 (m) REVERT: N 649 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6531 (tp30) REVERT: N 662 MET cc_start: 0.7905 (mtt) cc_final: 0.7616 (mtt) REVERT: N 816 PHE cc_start: 0.7189 (t80) cc_final: 0.6823 (t80) REVERT: N 972 MET cc_start: 0.4855 (ttm) cc_final: 0.4526 (ttp) REVERT: N 977 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7364 (mm-40) REVERT: N 1021 MET cc_start: 0.7136 (mtt) cc_final: 0.6299 (mtt) REVERT: N 1058 LEU cc_start: 0.9067 (tp) cc_final: 0.8488 (tp) REVERT: N 1113 ILE cc_start: 0.8562 (mp) cc_final: 0.8272 (mt) REVERT: N 1190 THR cc_start: 0.9131 (p) cc_final: 0.8441 (m) REVERT: O 186 ARG cc_start: 0.7141 (mmm-85) cc_final: 0.6922 (tpp80) REVERT: O 248 LEU cc_start: 0.7959 (mp) cc_final: 0.7359 (mt) REVERT: O 251 MET cc_start: 0.7750 (tpp) cc_final: 0.7203 (tpp) REVERT: O 365 VAL cc_start: 0.6783 (t) cc_final: 0.6491 (t) REVERT: O 553 ASP cc_start: 0.6169 (p0) cc_final: 0.5839 (p0) REVERT: O 739 VAL cc_start: 0.8305 (t) cc_final: 0.8001 (t) REVERT: O 838 THR cc_start: 0.8588 (p) cc_final: 0.8266 (t) REVERT: O 887 SER cc_start: 0.6734 (p) cc_final: 0.6469 (p) REVERT: O 1019 THR cc_start: 0.7466 (p) cc_final: 0.7040 (m) REVERT: O 1028 MET cc_start: 0.7968 (mmm) cc_final: 0.6916 (mmt) REVERT: O 1067 MET cc_start: 0.8652 (tpp) cc_final: 0.8153 (tpt) REVERT: O 1099 LEU cc_start: 0.8653 (mm) cc_final: 0.8294 (mt) REVERT: O 1119 ILE cc_start: 0.6410 (mm) cc_final: 0.5829 (mm) REVERT: O 1290 MET cc_start: 0.7663 (mmt) cc_final: 0.7257 (mmp) REVERT: O 1347 MET cc_start: 0.8767 (mmm) cc_final: 0.8546 (mmm) REVERT: O 1373 LEU cc_start: 0.9033 (mm) cc_final: 0.8653 (mm) REVERT: v 28 MET cc_start: 0.6865 (tpp) cc_final: 0.6422 (tpp) REVERT: v 31 LEU cc_start: 0.6449 (mp) cc_final: 0.6134 (tt) REVERT: v 388 GLU cc_start: 0.6676 (tp30) cc_final: 0.6374 (tp30) REVERT: v 462 CYS cc_start: 0.6940 (m) cc_final: 0.6675 (m) REVERT: v 475 LEU cc_start: 0.9000 (tp) cc_final: 0.8490 (tp) REVERT: v 484 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8132 (mmtt) REVERT: x 62 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7158 (mtpt) REVERT: x 65 LEU cc_start: 0.5920 (mt) cc_final: 0.5691 (mt) REVERT: y 3148 TYR cc_start: 0.5490 (m-80) cc_final: 0.4991 (m-80) REVERT: a 19 PRO cc_start: 0.4013 (Cg_exo) cc_final: 0.3780 (Cg_endo) REVERT: a 41 ARG cc_start: 0.5961 (ttp80) cc_final: 0.5506 (ttp80) REVERT: d 24 LEU cc_start: 0.7988 (mt) cc_final: 0.7699 (mt) REVERT: e 72 ARG cc_start: 0.5687 (mtm180) cc_final: 0.5160 (mtm180) REVERT: f 135 MET cc_start: 0.6226 (mtm) cc_final: 0.5982 (mtp) REVERT: f 183 ASN cc_start: 0.8047 (m110) cc_final: 0.7710 (t0) REVERT: f 192 VAL cc_start: 0.7499 (t) cc_final: 0.7261 (t) REVERT: f 193 GLU cc_start: 0.6032 (pt0) cc_final: 0.5082 (pt0) REVERT: f 261 ASP cc_start: 0.7140 (m-30) cc_final: 0.6894 (m-30) REVERT: h 295 ILE cc_start: 0.8567 (tt) cc_final: 0.8235 (tt) REVERT: k 235 LEU cc_start: 0.5739 (pt) cc_final: 0.5343 (pp) REVERT: k 264 MET cc_start: 0.6540 (ppp) cc_final: 0.5186 (tmm) REVERT: k 283 ARG cc_start: 0.5068 (ppt170) cc_final: 0.4304 (tmm160) REVERT: m 24 ARG cc_start: 0.7194 (tpp-160) cc_final: 0.6772 (tpp-160) REVERT: m 211 ILE cc_start: 0.7744 (mm) cc_final: 0.7537 (mm) REVERT: m 267 MET cc_start: 0.7573 (ttp) cc_final: 0.7370 (ttp) REVERT: m 274 LEU cc_start: 0.8363 (mm) cc_final: 0.8039 (mm) REVERT: p 119 GLU cc_start: 0.7443 (pm20) cc_final: 0.7189 (tp30) REVERT: p 161 MET cc_start: 0.5579 (ptm) cc_final: 0.4867 (ttp) REVERT: p 173 HIS cc_start: 0.6897 (m170) cc_final: 0.6621 (m170) REVERT: p 211 ILE cc_start: 0.8456 (mt) cc_final: 0.8132 (mm) REVERT: r 35 HIS cc_start: 0.6960 (m-70) cc_final: 0.6627 (m170) REVERT: r 138 LEU cc_start: 0.8643 (tp) cc_final: 0.8354 (tp) REVERT: r 140 THR cc_start: 0.8105 (m) cc_final: 0.7771 (m) REVERT: r 221 MET cc_start: 0.7206 (tpp) cc_final: 0.6466 (tpt) REVERT: r 240 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8014 (tm-30) REVERT: r 242 MET cc_start: 0.8089 (mmm) cc_final: 0.7614 (tpp) outliers start: 5 outliers final: 1 residues processed: 1602 average time/residue: 0.5792 time to fit residues: 1591.6660 Evaluate side-chains 1293 residues out of total 6806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1292 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 7.9990 chunk 492 optimal weight: 10.0000 chunk 660 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 572 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 621 optimal weight: 0.4980 chunk 260 optimal weight: 7.9990 chunk 638 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN ** J 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 788 HIS J 921 GLN J1022 HIS ** J1122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 GLN K 722 ASN ** K 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 822 ASN K 833 GLN ** K1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1351 GLN N 222 HIS ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 695 GLN ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 ASN ** N 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 333 HIS ** O 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 695 GLN ** O 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 96 HIS ** x 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 HIS f 208 HIS ** f 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 GLN ** m 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 23 GLN ** r 148 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125118 restraints weight = 165122.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127837 restraints weight = 97535.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129588 restraints weight = 59951.243| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.9894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 63966 Z= 0.236 Angle : 0.728 15.283 86932 Z= 0.368 Chirality : 0.046 0.233 9795 Planarity : 0.006 0.101 11336 Dihedral : 5.256 34.895 8722 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.55 % Rotamer: Outliers : 0.04 % Allowed : 0.47 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 7881 helix: 0.09 (0.09), residues: 2957 sheet: -0.11 (0.15), residues: 1087 loop : -1.49 (0.10), residues: 3837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP v 403 HIS 0.011 0.001 HIS O 104 PHE 0.031 0.002 PHE J1320 TYR 0.031 0.002 TYR O 535 ARG 0.011 0.001 ARG w 85 =============================================================================== Job complete usr+sys time: 22779.06 seconds wall clock time: 393 minutes 56.42 seconds (23636.42 seconds total)