Starting phenix.real_space_refine on Sun Sep 29 06:03:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2d_21525/09_2024/6w2d_21525.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2d_21525/09_2024/6w2d_21525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2d_21525/09_2024/6w2d_21525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2d_21525/09_2024/6w2d_21525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2d_21525/09_2024/6w2d_21525.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2d_21525/09_2024/6w2d_21525.cif" } resolution = 4.0 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= 0.005 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 417 5.16 5 C 47220 2.51 5 N 12902 2.21 5 O 13733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 280 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74272 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 10628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 10628 Classifications: {'peptide': 1352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 69, 'TRANS': 1282} Chain breaks: 1 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: 10447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1332, 10447 Classifications: {'peptide': 1332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 69, 'TRANS': 1262} Chain breaks: 1 Chain: "P" Number of atoms: 10113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1283, 10113 Classifications: {'peptide': 1283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1217} Chain breaks: 4 Chain: "v" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2283 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 17, 'TRANS': 274} 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: "u" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 6, 'TRANS': 56} Chain: "f" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2474 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 293} Chain breaks: 3 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: 35.60, per 1000 atoms: 0.48 Number of scatterers: 74272 At special positions: 0 Unit cell: (243.44, 235.28, 228.48, 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 417 16.00 O 13733 8.00 N 12902 7.00 C 47220 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: 16.82 Conformation dependent library (CDL) restraints added in 8.0 seconds 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17828 Finding SS restraints... Secondary structure from input PDB file: 391 helices and 98 sheets defined 44.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.22 Creating SS restraints... Processing helix chain 'J' and resid 24 through 31 Processing helix chain 'J' and resid 41 through 45 removed outlier: 3.537A pdb=" N ASP J 44 " --> pdb=" O VAL J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 removed outlier: 3.805A pdb=" N ALA J 74 " --> pdb=" O THR J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 147 through 187 removed outlier: 3.746A pdb=" N ILE J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 199 removed outlier: 4.301A pdb=" N THR J 196 " --> pdb=" O PHE J 192 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP J 199 " --> pdb=" O GLN J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 206 removed outlier: 3.811A pdb=" N GLU J 204 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG J 205 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY J 206 " --> pdb=" O THR J 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 201 through 206' Processing helix chain 'J' and resid 208 through 226 Processing helix chain 'J' and resid 228 through 236 removed outlier: 3.712A pdb=" N GLU J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN J 235 " --> pdb=" O ASP J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 255 removed outlier: 3.928A pdb=" N VAL J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.834A 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 308 through 323 removed outlier: 5.268A pdb=" N ARG J 314 " --> pdb=" O SER J 310 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 315 " --> pdb=" O PHE J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 337 Processing helix chain 'J' and resid 384 through 390 removed outlier: 3.553A pdb=" N TYR J 388 " --> pdb=" O LEU J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 460 removed outlier: 4.927A pdb=" N LYS J 457 " --> pdb=" O GLN J 453 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL J 458 " --> pdb=" O ASN J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 466 removed outlier: 4.010A pdb=" N HIS J 465 " --> pdb=" O HIS J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 476 Processing helix chain 'J' and resid 498 through 508 removed outlier: 3.653A pdb=" N ILE J 502 " --> pdb=" O ASN J 498 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP J 508 " --> pdb=" O ASP J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 522 Processing helix chain 'J' and resid 525 through 531 removed outlier: 3.581A pdb=" N LEU J 530 " --> pdb=" O THR J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 534 through 539 removed outlier: 4.103A pdb=" N LEU J 538 " --> pdb=" O ASN J 534 " (cutoff:3.500A) Processing helix chain 'J' and resid 554 through 558 Processing helix chain 'J' and resid 577 through 592 Processing helix chain 'J' and resid 599 through 612 removed outlier: 3.808A pdb=" N ILE J 603 " --> pdb=" O ASP J 599 " (cutoff:3.500A) Processing helix chain 'J' and resid 616 through 627 removed outlier: 4.236A 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: 3.855A pdb=" N LEU J 642 " --> pdb=" O PRO J 638 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER J 651 " --> pdb=" O TYR J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 669 removed outlier: 3.550A pdb=" N ILE J 663 " --> pdb=" O SER J 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 676 through 702 removed outlier: 3.764A pdb=" N MET J 682 " --> pdb=" O GLU J 678 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE J 686 " --> pdb=" O MET J 682 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR J 687 " --> pdb=" O TYR J 683 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY J 702 " --> pdb=" O MET J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 716 removed outlier: 3.686A pdb=" N CYS J 716 " --> pdb=" O GLY J 712 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 720 Processing helix chain 'J' and resid 731 through 738 removed outlier: 3.921A 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 775 through 786 Processing helix chain 'J' and resid 806 through 821 removed outlier: 3.835A pdb=" N LYS J 810 " --> pdb=" O ASP J 806 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU J 817 " --> pdb=" O TYR J 813 " (cutoff:3.500A) Proline residue: J 818 - end of helix Processing helix chain 'J' and resid 831 through 841 removed outlier: 3.621A pdb=" N THR J 838 " --> pdb=" O HIS J 834 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU J 839 " --> pdb=" O VAL J 835 " (cutoff:3.500A) Processing helix chain 'J' and resid 856 through 860 removed outlier: 3.725A pdb=" N LEU J 860 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing helix chain 'J' and resid 863 through 872 Processing helix chain 'J' and resid 877 through 886 Processing helix chain 'J' and resid 887 through 890 Processing helix chain 'J' and resid 905 through 909 Processing helix chain 'J' and resid 913 through 917 Processing helix chain 'J' and resid 936 through 942 removed outlier: 4.123A 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: 3.810A pdb=" N GLY J1002 " --> pdb=" O ARG J 998 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU J1007 " --> pdb=" O LYS J1003 " (cutoff:3.500A) Processing helix chain 'J' and resid 1011 through 1021 Processing helix chain 'J' and resid 1026 through 1037 removed outlier: 3.720A pdb=" N LYS J1035 " --> pdb=" O ILE J1031 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1123 through 1128 removed outlier: 3.627A pdb=" N VAL J1127 " --> pdb=" O ASP J1123 " (cutoff:3.500A) Processing helix chain 'J' and resid 1135 through 1146 Processing helix chain 'J' and resid 1193 through 1198 removed outlier: 3.833A pdb=" N LYS J1198 " --> pdb=" O TYR J1195 " (cutoff:3.500A) Processing helix chain 'J' and resid 1217 through 1225 Processing helix chain 'J' and resid 1241 through 1246 removed outlier: 4.257A 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 1270 through 1276 removed outlier: 4.242A pdb=" N PHE J1274 " --> pdb=" O PRO J1270 " (cutoff:3.500A) 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 1296 Processing helix chain 'J' and resid 1324 through 1329 removed outlier: 4.015A pdb=" N LEU J1328 " --> pdb=" O PRO J1324 " (cutoff:3.500A) Processing helix chain 'J' and resid 1339 through 1349 removed outlier: 3.532A pdb=" N ILE J1343 " --> pdb=" O SER J1339 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 67 through 75 removed outlier: 5.842A pdb=" N ALA K 72 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU K 73 " --> pdb=" O GLU K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 88 Processing helix chain 'K' and resid 135 through 143 removed outlier: 3.854A pdb=" N HIS K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 187 removed outlier: 3.577A pdb=" N HIS K 187 " --> pdb=" O VAL K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 199 removed outlier: 4.397A pdb=" N THR K 196 " --> pdb=" O PHE K 192 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 4.234A pdb=" N THR K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 226 Processing helix chain 'K' and resid 228 through 236 removed outlier: 3.524A pdb=" N ASN K 235 " --> pdb=" O ASP K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 255 removed outlier: 3.945A pdb=" N ARG K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL K 255 " --> pdb=" O MET K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 263 removed outlier: 4.493A pdb=" N GLY K 263 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 295 removed outlier: 3.527A pdb=" N GLY K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 324 removed outlier: 3.584A pdb=" N VAL K 319 " --> pdb=" O GLY K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 339 removed outlier: 3.793A pdb=" N ALA K 336 " --> pdb=" O GLU K 332 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG K 337 " --> pdb=" O HIS K 333 " (cutoff:3.500A) removed outlier: 3.991A 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: 3.948A pdb=" N ALA K 356 " --> pdb=" O LEU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 391 removed outlier: 4.072A pdb=" N TYR K 388 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 460 removed outlier: 4.880A pdb=" N LYS K 457 " --> pdb=" O GLN K 453 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL K 458 " --> pdb=" O ASN K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 465 Processing helix chain 'K' and resid 467 through 476 Processing helix chain 'K' and resid 498 through 508 removed outlier: 4.095A pdb=" N ILE K 502 " --> pdb=" O ASN K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 522 Processing helix chain 'K' and resid 525 through 530 Processing helix chain 'K' and resid 537 through 541 Processing helix chain 'K' and resid 572 through 576 Processing helix chain 'K' and resid 577 through 592 Processing helix chain 'K' and resid 599 through 611 removed outlier: 3.528A pdb=" N ILE K 603 " --> pdb=" O ASP K 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 617 through 627 removed outlier: 3.736A pdb=" N VAL K 621 " --> pdb=" O ALA K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 636 Processing helix chain 'K' and resid 636 through 651 Processing helix chain 'K' and resid 659 through 669 Processing helix chain 'K' and resid 676 through 701 removed outlier: 3.523A pdb=" N MET K 682 " --> pdb=" O GLU K 678 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR K 683 " --> pdb=" O ALA K 679 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 701 " --> pdb=" O LEU K 697 " (cutoff:3.500A) Processing helix chain 'K' and resid 710 through 715 Processing helix chain 'K' and resid 731 through 740 removed outlier: 4.053A pdb=" N HIS K 735 " --> pdb=" O ASP K 731 " (cutoff:3.500A) Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 762 Processing helix chain 'K' and resid 775 through 786 removed outlier: 3.921A pdb=" N VAL K 784 " --> pdb=" O TYR K 780 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN K 785 " --> pdb=" O GLY K 781 " (cutoff:3.500A) Processing helix chain 'K' and resid 806 through 815 removed outlier: 3.699A pdb=" N LYS K 810 " --> pdb=" O ASP K 806 " (cutoff:3.500A) Processing helix chain 'K' and resid 815 through 821 Processing helix chain 'K' and resid 831 through 841 Processing helix chain 'K' and resid 842 through 847 removed outlier: 3.664A pdb=" N PHE K 846 " --> pdb=" O ASN K 842 " (cutoff:3.500A) Processing helix chain 'K' and resid 863 through 873 Processing helix chain 'K' and resid 877 through 887 removed outlier: 4.003A pdb=" N ILE K 881 " --> pdb=" O THR K 877 " (cutoff:3.500A) Processing helix chain 'K' and resid 936 through 943 removed outlier: 5.207A pdb=" N THR K 941 " --> pdb=" O ARG K 938 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLN K 942 " --> pdb=" O ALA K 939 " (cutoff:3.500A) Processing helix chain 'K' and resid 957 through 964 Processing helix chain 'K' and resid 964 through 974 Processing helix chain 'K' and resid 975 through 979 removed outlier: 3.560A pdb=" N ALA K 979 " --> pdb=" O GLN K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 998 through 1008 removed outlier: 3.974A 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 1037 removed outlier: 3.583A pdb=" N LEU K1036 " --> pdb=" O ALA K1032 " (cutoff:3.500A) Processing helix chain 'K' and resid 1123 through 1128 Processing helix chain 'K' and resid 1135 through 1147 Processing helix chain 'K' and resid 1192 through 1198 removed outlier: 3.526A pdb=" N PHE K1196 " --> pdb=" O ASP K1192 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS K1198 " --> pdb=" O ALA K1194 " (cutoff:3.500A) Processing helix chain 'K' and resid 1216 through 1226 removed outlier: 3.639A pdb=" N ILE K1224 " --> pdb=" O ALA K1220 " (cutoff:3.500A) Processing helix chain 'K' and resid 1241 through 1246 removed outlier: 3.840A pdb=" N SER K1245 " --> pdb=" O ASN K1241 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN K1246 " --> pdb=" O PRO K1242 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1241 through 1246' Processing helix chain 'K' and resid 1249 through 1256 Processing helix chain 'K' and resid 1271 through 1276 Processing helix chain 'K' and resid 1276 through 1283 removed outlier: 4.461A pdb=" N ASN K1283 " --> pdb=" O GLU K1279 " (cutoff:3.500A) Processing helix chain 'K' and resid 1286 through 1297 Processing helix chain 'K' and resid 1324 through 1329 removed outlier: 3.894A pdb=" N LEU K1328 " --> pdb=" O PRO K1324 " (cutoff:3.500A) Processing helix chain 'K' and resid 1339 through 1349 removed outlier: 3.508A 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 removed outlier: 3.814A pdb=" N ALA N 45 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 75 removed outlier: 5.751A pdb=" N ALA N 72 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU N 73 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 3.751A pdb=" N ARG N 87 " --> pdb=" O ASP N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 141 Processing helix chain 'N' and resid 147 through 187 removed outlier: 3.609A pdb=" N GLY N 168 " --> pdb=" O ALA N 164 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS N 187 " --> pdb=" O VAL N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 199 removed outlier: 4.666A pdb=" N THR N 196 " --> pdb=" O PHE N 192 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 197 " --> pdb=" O ILE N 193 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP N 199 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 226 removed outlier: 3.748A pdb=" N LYS N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA N 217 " --> pdb=" O SER N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 237 removed outlier: 4.875A pdb=" N GLU N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN N 235 " --> pdb=" O ASP N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 255 removed outlier: 3.706A pdb=" N VAL N 255 " --> pdb=" O MET N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 264 removed outlier: 4.594A pdb=" N GLY N 263 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 295 Processing helix chain 'N' and resid 316 through 324 Processing helix chain 'N' and resid 330 through 339 removed outlier: 3.832A 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: 3.558A pdb=" N ALA N 356 " --> pdb=" O LEU N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 391 Processing helix chain 'N' and resid 451 through 460 removed outlier: 4.023A pdb=" N ALA N 455 " --> pdb=" O ASN N 451 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS N 457 " --> pdb=" O GLN N 453 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL N 458 " --> pdb=" O ASN N 454 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU N 459 " --> pdb=" O ALA N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 476 Processing helix chain 'N' and resid 498 through 508 removed outlier: 4.014A pdb=" N ILE N 502 " --> pdb=" O ASN N 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 516 through 522 removed outlier: 3.574A 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 537 through 541 Processing helix chain 'N' and resid 567 through 571 Processing helix chain 'N' and resid 577 through 593 Processing helix chain 'N' and resid 599 through 611 removed outlier: 3.529A pdb=" N ILE N 603 " --> pdb=" O ASP N 599 " (cutoff:3.500A) Processing helix chain 'N' and resid 616 through 627 removed outlier: 3.558A pdb=" N TYR N 620 " --> pdb=" O PRO N 616 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS N 627 " --> pdb=" O GLU N 623 " (cutoff:3.500A) Processing helix chain 'N' and resid 629 through 636 Processing helix chain 'N' and resid 636 through 651 removed outlier: 3.669A 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 677 through 701 removed outlier: 3.582A pdb=" N SER N 681 " --> pdb=" O LYS N 677 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET N 682 " --> pdb=" O GLU N 678 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR N 683 " --> pdb=" O ALA N 679 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU N 694 " --> pdb=" O LEU N 690 " (cutoff:3.500A) Processing helix chain 'N' and resid 711 through 716 removed outlier: 3.775A pdb=" N VAL N 715 " --> pdb=" O VAL N 711 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS N 716 " --> pdb=" O GLY N 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 711 through 716' Processing helix chain 'N' and resid 732 through 740 Processing helix chain 'N' and resid 758 through 762 Processing helix chain 'N' and resid 770 through 774 removed outlier: 4.480A pdb=" N ALA N 774 " --> pdb=" O GLU N 771 " (cutoff:3.500A) Processing helix chain 'N' and resid 775 through 786 removed outlier: 3.556A pdb=" N LEU N 779 " --> pdb=" O GLN N 775 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG N 783 " --> pdb=" O LEU N 779 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL N 784 " --> pdb=" O TYR N 780 " (cutoff:3.500A) Processing helix chain 'N' and resid 806 through 815 Processing helix chain 'N' and resid 815 through 821 Processing helix chain 'N' and resid 831 through 841 removed outlier: 3.584A pdb=" N VAL N 835 " --> pdb=" O ASP N 831 " (cutoff:3.500A) Processing helix chain 'N' and resid 842 through 847 removed outlier: 3.974A pdb=" N PHE N 846 " --> pdb=" O ASN N 842 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER N 847 " --> pdb=" O GLY N 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 842 through 847' Processing helix chain 'N' and resid 855 through 859 Processing helix chain 'N' and resid 863 through 872 removed outlier: 3.518A pdb=" N ASP N 867 " --> pdb=" O GLY N 863 " (cutoff:3.500A) Processing helix chain 'N' and resid 877 through 887 removed outlier: 3.604A pdb=" N ILE N 881 " --> pdb=" O THR N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 888 through 890 No H-bonds generated for 'chain 'N' and resid 888 through 890' Processing helix chain 'N' and resid 913 through 917 removed outlier: 3.692A pdb=" N LYS N 917 " --> pdb=" O ASN N 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 913 through 917' Processing helix chain 'N' and resid 951 through 955 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: 3.670A pdb=" N ALA N 979 " --> pdb=" O GLN N 976 " (cutoff:3.500A) Processing helix chain 'N' and resid 998 through 1007 removed outlier: 3.918A pdb=" N GLY N1002 " --> pdb=" O ARG N 998 " (cutoff:3.500A) Processing helix chain 'N' and resid 1011 through 1021 removed outlier: 3.556A pdb=" N ILE N1015 " --> pdb=" O SER N1011 " (cutoff:3.500A) Processing helix chain 'N' and resid 1026 through 1037 removed outlier: 3.806A pdb=" N ALA N1032 " --> pdb=" O MET N1028 " (cutoff:3.500A) Processing helix chain 'N' and resid 1123 through 1128 Processing helix chain 'N' and resid 1135 through 1147 removed outlier: 3.576A pdb=" N GLY N1147 " --> pdb=" O LYS N1143 " (cutoff:3.500A) Processing helix chain 'N' and resid 1192 through 1198 removed outlier: 3.844A pdb=" N PHE N1196 " --> pdb=" O ASP N1192 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS N1198 " --> pdb=" O ALA N1194 " (cutoff:3.500A) Processing helix chain 'N' and resid 1216 through 1226 removed outlier: 3.788A pdb=" N ALA N1220 " --> pdb=" O ASN N1216 " (cutoff:3.500A) Processing helix chain 'N' and resid 1249 through 1256 Processing helix chain 'N' and resid 1271 through 1276 Processing helix chain 'N' and resid 1276 through 1283 removed outlier: 4.007A pdb=" N ASN N1283 " --> pdb=" O GLU N1279 " (cutoff:3.500A) Processing helix chain 'N' and resid 1286 through 1297 removed outlier: 3.576A pdb=" N SER N1295 " --> pdb=" O VAL N1291 " (cutoff:3.500A) Processing helix chain 'N' and resid 1324 through 1329 removed outlier: 3.813A pdb=" N LEU N1328 " --> pdb=" O PRO N1324 " (cutoff:3.500A) Processing helix chain 'N' and resid 1339 through 1349 removed outlier: 4.153A pdb=" N ILE N1343 " --> pdb=" O SER N1339 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP N1344 " --> pdb=" O ARG N1340 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 75 removed outlier: 3.565A pdb=" N ALA O 74 " --> pdb=" O THR O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 143 removed outlier: 3.746A pdb=" N ILE O 140 " --> pdb=" O LEU O 136 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS O 142 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 187 removed outlier: 3.646A pdb=" N HIS O 187 " --> pdb=" O VAL O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 198 removed outlier: 4.605A pdb=" N THR O 196 " --> pdb=" O PHE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 228 through 233 Processing helix chain 'O' and resid 239 through 255 removed outlier: 3.530A pdb=" N VAL O 255 " --> pdb=" O MET O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 295 removed outlier: 3.571A pdb=" N GLY O 295 " --> pdb=" O LEU O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 314 through 323 removed outlier: 4.101A pdb=" N THR O 320 " --> pdb=" O GLU O 316 " (cutoff:3.500A) Processing helix chain 'O' and resid 330 through 339 removed outlier: 3.812A 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 Processing helix chain 'O' and resid 384 through 391 removed outlier: 3.861A pdb=" N TYR O 388 " --> pdb=" O LEU O 384 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 460 removed outlier: 4.625A pdb=" N LYS O 457 " --> pdb=" O GLN O 453 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL O 458 " --> pdb=" O ASN O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 461 through 466 removed outlier: 4.231A pdb=" N HIS O 465 " --> pdb=" O HIS O 461 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR O 466 " --> pdb=" O PRO O 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 461 through 466' Processing helix chain 'O' and resid 467 through 476 Processing helix chain 'O' and resid 498 through 507 Processing helix chain 'O' and resid 517 through 522 Processing helix chain 'O' and resid 525 through 530 Processing helix chain 'O' and resid 537 through 541 Processing helix chain 'O' and resid 577 through 593 Processing helix chain 'O' and resid 599 through 611 removed outlier: 3.614A pdb=" N ILE O 603 " --> pdb=" O ASP O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 617 through 627 removed outlier: 3.641A pdb=" N VAL O 621 " --> pdb=" O ALA O 617 " (cutoff:3.500A) Processing helix chain 'O' and resid 629 through 636 removed outlier: 3.634A pdb=" N ASN O 636 " --> pdb=" O LYS O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 651 removed outlier: 3.526A pdb=" N ARG O 650 " --> pdb=" O THR O 646 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER O 651 " --> pdb=" O TYR O 647 " (cutoff:3.500A) Processing helix chain 'O' and resid 659 through 670 removed outlier: 3.528A pdb=" N ILE O 663 " --> pdb=" O SER O 659 " (cutoff:3.500A) Processing helix chain 'O' and resid 676 through 702 removed outlier: 3.800A pdb=" N MET O 682 " --> pdb=" O GLU O 678 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR O 683 " --> pdb=" O ALA O 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 removed outlier: 3.785A pdb=" N CYS O 716 " --> pdb=" O GLY O 712 " (cutoff:3.500A) Processing helix chain 'O' and resid 731 through 739 removed outlier: 3.909A pdb=" N HIS O 735 " --> pdb=" O ASP O 731 " (cutoff:3.500A) Processing helix chain 'O' and resid 755 through 757 No H-bonds generated for 'chain 'O' and resid 755 through 757' Processing helix chain 'O' and resid 758 through 762 Processing helix chain 'O' and resid 775 through 786 Processing helix chain 'O' and resid 787 through 791 removed outlier: 3.671A pdb=" N HIS O 790 " --> pdb=" O ASP O 787 " (cutoff:3.500A) Processing helix chain 'O' and resid 807 through 815 Processing helix chain 'O' and resid 815 through 822 removed outlier: 3.666A pdb=" N THR O 819 " --> pdb=" O VAL O 815 " (cutoff:3.500A) Processing helix chain 'O' and resid 831 through 841 removed outlier: 3.789A pdb=" N VAL O 835 " --> pdb=" O ASP O 831 " (cutoff:3.500A) Processing helix chain 'O' and resid 856 through 860 removed outlier: 3.518A pdb=" N LEU O 860 " --> pdb=" O LEU O 857 " (cutoff:3.500A) Processing helix chain 'O' and resid 863 through 873 removed outlier: 3.568A pdb=" N ASP O 867 " --> pdb=" O GLY O 863 " (cutoff:3.500A) removed outlier: 3.830A 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 890 removed outlier: 3.546A pdb=" N THR O 890 " --> pdb=" O SER O 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 887 through 890' Processing helix chain 'O' and resid 905 through 909 Processing helix chain 'O' and resid 934 through 942 Processing helix chain 'O' and resid 956 through 964 removed outlier: 4.169A pdb=" N THR O 962 " --> pdb=" O ARG O 958 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET O 963 " --> pdb=" O VAL O 959 " (cutoff:3.500A) Processing helix chain 'O' and resid 964 through 974 removed outlier: 3.523A pdb=" N ASN O 974 " --> pdb=" O PHE O 970 " (cutoff:3.500A) Processing helix chain 'O' and resid 975 through 979 removed outlier: 4.003A pdb=" N ALA O 979 " --> pdb=" O GLN O 976 " (cutoff:3.500A) Processing helix chain 'O' and resid 998 through 1008 Processing helix chain 'O' and resid 1011 through 1022 removed outlier: 3.566A pdb=" N ILE O1015 " --> pdb=" O SER O1011 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER O1016 " --> pdb=" O LEU O1012 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS O1022 " --> pdb=" O MET O1018 " (cutoff:3.500A) Processing helix chain 'O' and resid 1026 through 1037 Processing helix chain 'O' and resid 1135 through 1146 removed outlier: 3.510A pdb=" N ASN O1139 " --> pdb=" O ASN O1135 " (cutoff:3.500A) Processing helix chain 'O' and resid 1192 through 1198 removed outlier: 3.739A pdb=" N PHE O1196 " --> pdb=" O ASP O1192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS O1198 " --> pdb=" O ALA O1194 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1225 Processing helix chain 'O' and resid 1241 through 1246 removed outlier: 3.552A pdb=" N SER O1245 " --> pdb=" O ASN O1241 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN O1246 " --> pdb=" O PRO O1242 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1241 through 1246' 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 1283 removed outlier: 3.837A pdb=" N ASN O1283 " --> pdb=" O GLU O1279 " (cutoff:3.500A) Processing helix chain 'O' and resid 1286 through 1297 removed outlier: 3.593A pdb=" N SER O1295 " --> pdb=" O VAL O1291 " (cutoff:3.500A) Processing helix chain 'O' and resid 1323 through 1329 removed outlier: 4.493A pdb=" N PHE O1327 " --> pdb=" O GLN O1323 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU O1328 " --> pdb=" O PRO O1324 " (cutoff:3.500A) Processing helix chain 'O' and resid 1339 through 1349 removed outlier: 3.782A pdb=" N ILE O1343 " --> pdb=" O SER O1339 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 42 removed outlier: 3.775A pdb=" N LEU P 40 " --> pdb=" O SER P 36 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY P 42 " --> pdb=" O ASP P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 75 removed outlier: 6.092A pdb=" N ALA P 72 " --> pdb=" O LEU P 69 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU P 73 " --> pdb=" O GLU P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 141 removed outlier: 3.569A pdb=" N LEU P 141 " --> pdb=" O ASP P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 187 removed outlier: 3.523A pdb=" N TYR P 151 " --> pdb=" O THR P 147 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA P 152 " --> pdb=" O PRO P 148 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU P 153 " --> pdb=" O VAL P 149 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS P 187 " --> pdb=" O VAL P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 199 removed outlier: 5.050A pdb=" N THR P 196 " --> pdb=" O PHE P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 203 Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.592A pdb=" N LEU P 215 " --> pdb=" O VAL P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 236 removed outlier: 3.605A pdb=" N ARG P 232 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN P 235 " --> pdb=" O ASP P 231 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 254 Processing helix chain 'P' and resid 283 through 295 removed outlier: 3.870A pdb=" N THR P 292 " --> pdb=" O ARG P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 323 through 337 Processing helix chain 'P' and resid 384 through 390 removed outlier: 3.723A pdb=" N TYR P 388 " --> pdb=" O LEU P 384 " (cutoff:3.500A) Processing helix chain 'P' and resid 452 through 454 No H-bonds generated for 'chain 'P' and resid 452 through 454' Processing helix chain 'P' and resid 455 through 460 Processing helix chain 'P' and resid 467 through 476 Processing helix chain 'P' and resid 498 through 507 removed outlier: 3.929A pdb=" N ILE P 502 " --> pdb=" O ASN P 498 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR P 507 " --> pdb=" O VAL P 503 " (cutoff:3.500A) Processing helix chain 'P' and resid 516 through 524 removed outlier: 3.776A pdb=" N LEU P 524 " --> pdb=" O LEU P 520 " (cutoff:3.500A) Processing helix chain 'P' and resid 525 through 531 Processing helix chain 'P' and resid 534 through 539 Processing helix chain 'P' and resid 567 through 571 Processing helix chain 'P' and resid 572 through 576 Processing helix chain 'P' and resid 577 through 592 Processing helix chain 'P' and resid 599 through 612 removed outlier: 3.621A pdb=" N ILE P 603 " --> pdb=" O ASP P 599 " (cutoff:3.500A) Processing helix chain 'P' and resid 616 through 627 removed outlier: 4.223A pdb=" N TYR P 620 " --> pdb=" O PRO P 616 " (cutoff:3.500A) Processing helix chain 'P' and resid 629 through 636 removed outlier: 3.721A pdb=" N ASN P 636 " --> pdb=" O LYS P 632 " (cutoff:3.500A) Processing helix chain 'P' and resid 636 through 651 removed outlier: 3.779A pdb=" N VAL P 640 " --> pdb=" O ASN P 636 " (cutoff:3.500A) Processing helix chain 'P' and resid 659 through 669 removed outlier: 3.594A pdb=" N ILE P 663 " --> pdb=" O SER P 659 " (cutoff:3.500A) Processing helix chain 'P' and resid 676 through 702 removed outlier: 3.526A pdb=" N MET P 682 " --> pdb=" O GLU P 678 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU P 690 " --> pdb=" O ILE P 686 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE P 691 " --> pdb=" O TYR P 687 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA P 692 " --> pdb=" O GLY P 688 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU P 697 " --> pdb=" O LEU P 693 " (cutoff:3.500A) Processing helix chain 'P' and resid 711 through 716 removed outlier: 4.072A pdb=" N CYS P 716 " --> pdb=" O GLY P 712 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 740 removed outlier: 4.253A pdb=" N HIS P 735 " --> pdb=" O ASP P 731 " (cutoff:3.500A) Processing helix chain 'P' and resid 758 through 762 Processing helix chain 'P' and resid 772 through 781 Processing helix chain 'P' and resid 806 through 821 removed outlier: 4.061A pdb=" N LYS P 810 " --> pdb=" O ASP P 806 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU P 817 " --> pdb=" O TYR P 813 " (cutoff:3.500A) Proline residue: P 818 - end of helix Processing helix chain 'P' and resid 831 through 840 removed outlier: 3.891A pdb=" N VAL P 835 " --> pdb=" O ASP P 831 " (cutoff:3.500A) Processing helix chain 'P' and resid 842 through 847 removed outlier: 4.123A pdb=" N PHE P 846 " --> pdb=" O ASN P 842 " (cutoff:3.500A) Processing helix chain 'P' and resid 863 through 873 Processing helix chain 'P' and resid 877 through 881 Processing helix chain 'P' and resid 884 through 888 removed outlier: 3.568A pdb=" N SER P 887 " --> pdb=" O LEU P 884 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE P 888 " --> pdb=" O SER P 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 884 through 888' Processing helix chain 'P' and resid 905 through 909 removed outlier: 3.573A pdb=" N GLN P 909 " --> pdb=" O VAL P 906 " (cutoff:3.500A) Processing helix chain 'P' and resid 934 through 944 removed outlier: 3.985A pdb=" N CYS P 943 " --> pdb=" O ALA P 939 " (cutoff:3.500A) Processing helix chain 'P' and resid 956 through 964 removed outlier: 3.581A pdb=" N ALA P 960 " --> pdb=" O ASP P 956 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR P 962 " --> pdb=" O ARG P 958 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET P 963 " --> pdb=" O VAL P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 965 through 974 removed outlier: 3.838A pdb=" N THR P 969 " --> pdb=" O GLN P 965 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN P 974 " --> pdb=" O PHE P 970 " (cutoff:3.500A) Processing helix chain 'P' and resid 975 through 978 Processing helix chain 'P' and resid 991 through 995 removed outlier: 3.538A pdb=" N ARG P 994 " --> pdb=" O ALA P 991 " (cutoff:3.500A) Processing helix chain 'P' and resid 998 through 1007 removed outlier: 3.788A pdb=" N GLY P1002 " --> pdb=" O ARG P 998 " (cutoff:3.500A) Processing helix chain 'P' and resid 1011 through 1021 Processing helix chain 'P' and resid 1026 through 1036 removed outlier: 4.023A pdb=" N LYS P1035 " --> pdb=" O ILE P1031 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU P1036 " --> pdb=" O ALA P1032 " (cutoff:3.500A) Processing helix chain 'P' and resid 1123 through 1128 Processing helix chain 'P' and resid 1135 through 1147 Processing helix chain 'P' and resid 1193 through 1198 removed outlier: 3.860A pdb=" N LYS P1198 " --> pdb=" O ALA P1194 " (cutoff:3.500A) Processing helix chain 'P' and resid 1218 through 1226 removed outlier: 4.497A pdb=" N GLY P1222 " --> pdb=" O GLU P1218 " (cutoff:3.500A) Processing helix chain 'P' and resid 1249 through 1256 Processing helix chain 'P' and resid 1271 through 1276 Processing helix chain 'P' and resid 1276 through 1296 Processing helix chain 'P' and resid 1323 through 1329 Processing helix chain 'P' and resid 1341 through 1348 Processing helix chain 'v' and resid 2 through 9 removed outlier: 4.327A pdb=" N VAL v 9 " --> pdb=" O ILE v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 29 Processing helix chain 'v' and resid 332 through 360 removed outlier: 5.565A pdb=" N GLU v 338 " --> pdb=" O ALA v 334 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE v 339 " --> pdb=" O PRO v 335 " (cutoff:3.500A) Processing helix chain 'v' and resid 381 through 396 removed outlier: 4.072A pdb=" N ILE v 386 " --> pdb=" O ASN v 382 " (cutoff:3.500A) Processing helix chain 'v' and resid 401 through 408 removed outlier: 3.711A pdb=" N ILE v 408 " --> pdb=" O VAL v 404 " (cutoff:3.500A) Processing helix chain 'v' and resid 412 through 417 removed outlier: 3.822A pdb=" N ASP v 416 " --> pdb=" O PRO v 412 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA v 417 " --> pdb=" O LYS v 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 412 through 417' Processing helix chain 'v' and resid 427 through 429 No H-bonds generated for 'chain 'v' and resid 427 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: 3.926A pdb=" N ARG w 64 " --> pdb=" O VAL w 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU w 70 " --> pdb=" O LEU w 66 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL w 92 " --> pdb=" O LEU w 88 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA w 93 " --> pdb=" O ASP w 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU w 98 " --> pdb=" O PHE w 94 " (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 97 removed outlier: 4.258A pdb=" N GLU x 40 " --> pdb=" O PRO x 36 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU x 41 " --> pdb=" O GLU x 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 3114 through 3148 removed outlier: 4.406A pdb=" N SER y3120 " --> pdb=" O SER y3116 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG y3121 " --> pdb=" O ARG y3117 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL y3123 " --> pdb=" O LEU y3119 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS y3129 " --> pdb=" O GLN y3125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG y3132 " --> pdb=" O ARG y3128 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER y3133 " --> pdb=" O LYS y3129 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR y3134 " --> pdb=" O LEU y3130 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU y3142 " --> pdb=" O ILE y3138 " (cutoff:3.500A) Processing helix chain 'z' and resid 3114 through 3149 removed outlier: 4.080A pdb=" N SER z3120 " --> pdb=" O SER z3116 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL z3123 " --> pdb=" O LEU z3119 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS z3129 " --> pdb=" O GLN z3125 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG z3132 " --> pdb=" O ARG z3128 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER z3133 " --> pdb=" O LYS z3129 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR z3134 " --> pdb=" O LEU z3130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 18 Processing helix chain 'Z' and resid 23 through 28 Processing helix chain 'Z' and resid 36 through 65 Processing helix chain 'Z' and resid 68 through 76 removed outlier: 3.509A pdb=" N ARG Z 72 " --> pdb=" O PRO Z 68 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA Z 73 " --> pdb=" O ARG Z 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 17 Processing helix chain 'a' and resid 23 through 28 Processing helix chain 'a' and resid 36 through 65 removed outlier: 4.411A pdb=" N PHE a 65 " --> pdb=" O VAL a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 76 Processing helix chain 'd' and resid 13 through 18 Processing helix chain 'd' and resid 22 through 29 removed outlier: 4.315A pdb=" N LYS d 26 " --> pdb=" O PRO d 22 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU d 29 " --> pdb=" O PRO d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 65 removed outlier: 4.104A pdb=" N PHE d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 76 removed outlier: 4.265A pdb=" N ARG d 72 " --> pdb=" O PRO d 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 13 through 18 removed outlier: 3.505A pdb=" N ASP e 17 " --> pdb=" O ARG e 13 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE e 18 " --> pdb=" O LEU e 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 13 through 18' Processing helix chain 'e' and resid 22 through 28 removed outlier: 4.596A pdb=" N LYS e 26 " --> pdb=" O PRO e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 36 through 65 removed outlier: 3.713A pdb=" N GLN e 62 " --> pdb=" O GLU e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 74 removed outlier: 3.773A pdb=" N ARG e 72 " --> pdb=" O PRO e 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 30 removed outlier: 4.079A pdb=" N LEU u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 65 removed outlier: 3.992A pdb=" N ARG u 41 " --> pdb=" O ASN u 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU u 42 " --> pdb=" O ASP u 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 20 removed outlier: 3.910A pdb=" N LEU f 12 " --> pdb=" O ASP f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 50 Processing helix chain 'f' and resid 127 through 136 Processing helix chain 'f' and resid 151 through 159 Processing helix chain 'f' and resid 162 through 169 removed outlier: 3.787A pdb=" N VAL f 169 " --> pdb=" O LEU f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 171 through 176 Processing helix chain 'f' and resid 180 through 185 removed outlier: 3.875A pdb=" N PHE f 184 " --> pdb=" O ARG f 180 " (cutoff:3.500A) Processing helix chain 'f' and resid 285 through 302 removed outlier: 4.256A pdb=" N MET f 290 " --> pdb=" O HIS f 286 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN f 291 " --> pdb=" O CYS f 287 " (cutoff:3.500A) Proline residue: f 299 - end of helix Processing helix chain 'f' and resid 303 through 306 removed outlier: 4.068A pdb=" N ALA f 306 " --> pdb=" O HIS f 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 303 through 306' Processing helix chain 'h' and resid 11 through 20 removed outlier: 3.720A pdb=" N ARG h 15 " --> pdb=" O ARG h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 44 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 161 through 167 removed outlier: 4.031A pdb=" N LEU h 165 " --> pdb=" O SER h 161 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 179 removed outlier: 3.515A pdb=" N ALA h 177 " --> pdb=" O GLY h 173 " (cutoff:3.500A) Processing helix chain 'h' and resid 180 through 184 removed outlier: 3.920A pdb=" N PHE h 184 " --> pdb=" O ARG h 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 180 through 184' Processing helix chain 'h' and resid 232 through 237 removed outlier: 4.127A pdb=" N TRP h 236 " --> pdb=" O ASP h 232 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU h 237 " --> pdb=" O LEU h 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 232 through 237' Processing helix chain 'h' and resid 285 through 305 Proline residue: h 299 - end of helix Processing helix chain 'h' and resid 312 through 316 removed outlier: 3.850A pdb=" N LEU h 316 " --> pdb=" O ILE h 313 " (cutoff:3.500A) Processing helix chain 'k' and resid 17 through 23 Processing helix chain 'k' and resid 56 through 67 Processing helix chain 'k' and resid 117 through 121 removed outlier: 3.610A 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 160 removed outlier: 3.978A pdb=" N ARG k 158 " --> pdb=" O ASN k 154 " (cutoff:3.500A) Processing helix chain 'k' and resid 164 through 174 removed outlier: 3.798A pdb=" N LEU k 170 " --> pdb=" O ASN k 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP k 171 " --> pdb=" O ALA k 167 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL k 172 " --> pdb=" O ASP k 168 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS k 173 " --> pdb=" O MET k 169 " (cutoff:3.500A) Processing helix chain 'k' and resid 198 through 214 removed outlier: 3.979A pdb=" N LEU k 202 " --> pdb=" O GLY k 198 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN k 204 " --> pdb=" O ALA k 200 " (cutoff:3.500A) Processing helix chain 'k' and resid 218 through 231 removed outlier: 3.993A pdb=" N ARG k 229 " --> pdb=" O ARG k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 234 through 238 removed outlier: 3.990A pdb=" N LEU k 238 " --> pdb=" O LEU k 235 " (cutoff:3.500A) Processing helix chain 'k' and resid 244 through 252 removed outlier: 3.972A pdb=" N ALA k 248 " --> pdb=" O PRO k 244 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU k 252 " --> pdb=" O ALA k 248 " (cutoff:3.500A) Processing helix chain 'k' and resid 256 through 272 removed outlier: 3.860A pdb=" N SER k 262 " --> pdb=" O ALA k 258 " (cutoff:3.500A) Processing helix chain 'k' and resid 273 through 280 removed outlier: 4.021A pdb=" N LEU k 277 " --> pdb=" O SER k 273 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU k 280 " --> pdb=" O SER k 276 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 23 Processing helix chain 'm' and resid 56 through 67 removed outlier: 3.815A pdb=" N MET m 60 " --> pdb=" O ASP m 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP m 66 " --> pdb=" O ASN m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 140 through 160 Processing helix chain 'm' and resid 161 through 163 No H-bonds generated for 'chain 'm' and resid 161 through 163' Processing helix chain 'm' and resid 165 through 174 removed outlier: 3.919A pdb=" N MET m 169 " --> pdb=" O GLY m 165 " (cutoff:3.500A) Processing helix chain 'm' and resid 197 through 213 removed outlier: 4.144A pdb=" N ASN m 204 " --> pdb=" O ALA m 200 " (cutoff:3.500A) Processing helix chain 'm' and resid 214 through 216 No H-bonds generated for 'chain 'm' and resid 214 through 216' Processing helix chain 'm' and resid 217 through 231 removed outlier: 4.006A pdb=" N MET m 221 " --> pdb=" O PRO m 217 " (cutoff:3.500A) Processing helix chain 'm' and resid 244 through 251 removed outlier: 3.777A pdb=" N ALA m 248 " --> pdb=" O PRO m 244 " (cutoff:3.500A) Processing helix chain 'm' and resid 256 through 278 removed outlier: 4.024A pdb=" N SER m 273 " --> pdb=" O THR m 269 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER m 276 " --> pdb=" O GLN m 272 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU m 277 " --> pdb=" O SER m 273 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE m 278 " --> pdb=" O LEU m 274 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 24 removed outlier: 4.002A pdb=" N ALA p 19 " --> pdb=" O THR p 15 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS p 20 " --> pdb=" O ASP p 16 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET p 21 " --> pdb=" O GLU p 17 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 43 removed outlier: 3.875A pdb=" N GLY p 42 " --> pdb=" O ASN p 39 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 67 removed outlier: 4.043A pdb=" N MET p 60 " --> pdb=" O ASP p 56 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP p 66 " --> pdb=" O ASN p 62 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 122 Processing helix chain 'p' and resid 140 through 163 Processing helix chain 'p' and resid 168 through 177 Processing helix chain 'p' and resid 201 through 228 removed outlier: 4.681A pdb=" N LEU p 205 " --> pdb=" O LEU p 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE p 209 " --> pdb=" O LEU p 205 " (cutoff:3.500A) Proline residue: p 217 - end of helix removed outlier: 3.586A pdb=" N ILE p 228 " --> pdb=" O VAL p 224 " (cutoff:3.500A) Processing helix chain 'p' and resid 233 through 240 removed outlier: 4.158A pdb=" N ASN p 237 " --> pdb=" O HIS p 233 " (cutoff:3.500A) Processing helix chain 'p' and resid 244 through 249 Processing helix chain 'p' and resid 256 through 279 removed outlier: 4.146A pdb=" N SER p 276 " --> pdb=" O GLN p 272 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU p 277 " --> pdb=" O SER p 273 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE p 278 " --> pdb=" O LEU p 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 24 removed outlier: 3.821A pdb=" N ARG r 24 " --> pdb=" O LYS r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 43 removed outlier: 4.075A pdb=" N GLY r 42 " --> pdb=" O ASN r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 56 through 66 Processing helix chain 'r' and resid 117 through 121 removed outlier: 3.815A pdb=" N ALA r 121 " --> pdb=" O GLY r 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 117 through 121' Processing helix chain 'r' and resid 140 through 163 Processing helix chain 'r' and resid 164 through 167 removed outlier: 3.834A 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 203 through 228 removed outlier: 3.501A pdb=" N LEU r 207 " --> pdb=" O ASP r 203 " (cutoff:3.500A) Proline residue: r 217 - end of helix removed outlier: 3.814A pdb=" N MET r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG r 222 " --> pdb=" O ARG r 218 " (cutoff:3.500A) Processing helix chain 'r' and resid 233 through 240 removed outlier: 4.320A pdb=" N ASN r 237 " --> pdb=" O HIS r 233 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU r 238 " --> pdb=" O ASP r 234 " (cutoff:3.500A) Processing helix chain 'r' and resid 244 through 249 Processing helix chain 'r' and resid 256 through 278 removed outlier: 3.696A pdb=" N ASP r 260 " --> pdb=" O SER r 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 53 through 54 removed outlier: 7.039A pdb=" N GLU J 53 " --> pdb=" O VAL K 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.477A pdb=" N TYR J 59 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER K 98 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 4.172A 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 80 removed outlier: 6.255A pdb=" N VAL J 78 " --> pdb=" O MET J1067 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE J1069 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR J 80 " --> pdb=" O ILE J1069 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 77 through 80 removed outlier: 6.255A pdb=" N VAL J 78 " --> pdb=" O MET J1067 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE J1069 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR J 80 " --> pdb=" O ILE J1069 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA J1083 " --> pdb=" O ALA J1079 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA J1079 " --> pdb=" O ALA J1083 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR J1085 " --> pdb=" O ARG J1077 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 114 through 117 removed outlier: 4.477A pdb=" N ARG J 114 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG J 96 " --> pdb=" O THR O 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 268 through 269 Processing sheet with id=AA7, first strand: chain 'J' and resid 370 through 374 removed outlier: 3.891A pdb=" N ALA J 370 " --> pdb=" O VAL J 381 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY J 278 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU J 382 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE J 280 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 1183 through 1187 removed outlier: 7.674A pdb=" N GLU J1051 " --> pdb=" O ALA J1112 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA J1112 " --> pdb=" O GLU J1051 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU J1053 " --> pdb=" O VAL J1110 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL J1110 " --> pdb=" O LEU J1053 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU J1055 " --> pdb=" O ALA J1108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 1103 through 1112 removed outlier: 6.767A pdb=" N GLU J1055 " --> pdb=" O ALA J1108 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL J1110 " --> pdb=" O LEU J1053 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU J1053 " --> pdb=" O VAL J1110 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA J1112 " --> pdb=" O GLU J1051 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU J1051 " --> pdb=" O ALA J1112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE J1332 " --> pdb=" O SER J 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 1332 through 1333 removed outlier: 3.606A pdb=" N PHE J1332 " --> pdb=" O SER J 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 370 through 374 removed outlier: 3.891A pdb=" N ALA J 370 " --> pdb=" O VAL J 381 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY J 278 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU J 382 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE J 280 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 447 through 450 removed outlier: 3.672A pdb=" N SER J1336 " --> pdb=" O ILE J1363 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 546 through 550 Processing sheet with id=AB5, first strand: chain 'J' and resid 727 through 728 Processing sheet with id=AB6, first strand: chain 'J' and resid 763 through 765 Processing sheet with id=AB7, first strand: chain 'J' and resid 928 through 930 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: 9.452A pdb=" N ALA K 309 " --> pdb=" O CYS K 77 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN K 79 " --> pdb=" O ALA K 309 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE K 311 " --> pdb=" O ASN K 79 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU K 81 " --> pdb=" O PHE K 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 123 through 134 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 370 through 374 removed outlier: 3.886A pdb=" N ALA K 370 " --> pdb=" O VAL K 381 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY K 278 " --> pdb=" O ALA K 380 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU K 382 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE K 280 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 1103 through 1113 removed outlier: 7.363A pdb=" N SER K1103 " --> pdb=" O SER K1061 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER K1061 " --> pdb=" O SER K1103 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET K1105 " --> pdb=" O PHE K1059 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE K1059 " --> pdb=" O MET K1105 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE K1057 " --> pdb=" O PRO K1107 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU K1053 " --> pdb=" O ALA K1111 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE K1113 " --> pdb=" O GLU K1051 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLU K1051 " --> pdb=" O ILE K1113 " (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 549 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: 3.757A 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: 4.317A pdb=" N ARG O 114 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE N 52 " --> pdb=" O THR O 89 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY O 91 " --> pdb=" O PHE N 52 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 54 " --> pdb=" O GLY O 91 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE O 93 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU N 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 10.257A pdb=" N PHE O 95 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL N 58 " --> pdb=" O PHE O 95 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N ILE O 97 " --> pdb=" O VAL N 58 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N THR N 60 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N VAL O 99 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.075A 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: 5.920A pdb=" N VAL N 78 " --> pdb=" O MET N1067 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE N1069 " --> pdb=" O VAL N 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR N 80 " --> pdb=" O ILE N1069 " (cutoff:3.500A) removed outlier: 9.760A pdb=" N ALA N 309 " --> pdb=" O CYS N 77 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN N 79 " --> pdb=" O ALA N 309 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE N 311 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 6.895A 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 93 through 99 removed outlier: 3.919A 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: 4.270A pdb=" N GLY N 278 " --> pdb=" O ALA N 378 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 1103 through 1113 removed outlier: 6.687A pdb=" N GLU N1055 " --> pdb=" O ALA N1108 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL N1110 " --> pdb=" O LEU N1053 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU N1053 " --> pdb=" O VAL N1110 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA N1112 " --> pdb=" O GLU N1051 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLU N1051 " --> pdb=" O ALA N1112 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N PHE N1332 " --> pdb=" O GLN N 402 " (cutoff:3.500A) removed outlier: 6.035A 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: 3.504A 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: 3.897A pdb=" N LEU N 928 " --> pdb=" O LEU N 828 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 1336 through 1337 Processing sheet with id=AE7, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.908A pdb=" N PHE O 37 " --> pdb=" O VAL O 54 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU O 56 " --> pdb=" O HIS O 35 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS O 35 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 123 through 134 removed outlier: 6.149A pdb=" N VAL O 78 " --> pdb=" O MET O1067 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE O1069 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR O 80 " --> pdb=" O ILE O1069 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N ALA O 309 " --> pdb=" O CYS O 77 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN O 79 " --> pdb=" O ALA O 309 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE O 311 " --> pdb=" O ASN O 79 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU O 81 " --> pdb=" O PHE O 311 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 123 through 134 removed outlier: 6.720A pdb=" N ALA O1083 " --> pdb=" O ALA O1079 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA O1079 " --> pdb=" O ALA O1083 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR O1085 " --> pdb=" O ARG O1077 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 268 through 269 Processing sheet with id=AF2, first strand: chain 'O' and resid 370 through 374 removed outlier: 3.787A pdb=" N ALA O 370 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA O 380 " --> pdb=" O GLY O 277 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL O 279 " --> pdb=" O ALA O 380 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU O 382 " --> pdb=" O VAL O 279 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE O 281 " --> pdb=" O GLU O 382 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 1183 through 1187 removed outlier: 6.875A pdb=" N LEU O1053 " --> pdb=" O ALA O1111 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE O1057 " --> pdb=" O PRO O1107 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE O1059 " --> pdb=" O MET O1105 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N MET O1105 " --> pdb=" O PHE O1059 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER O1061 " --> pdb=" O SER O1103 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER O1103 " --> pdb=" O SER O1061 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 1103 through 1112 removed outlier: 7.017A pdb=" N SER O1103 " --> pdb=" O SER O1061 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER O1061 " --> pdb=" O SER O1103 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N MET O1105 " --> pdb=" O PHE O1059 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE O1059 " --> pdb=" O MET O1105 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE O1057 " --> pdb=" O PRO O1107 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU O1053 " --> pdb=" O ALA O1111 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N PHE O1332 " --> pdb=" O GLN O 402 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER O 404 " --> pdb=" O PHE O1332 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 1332 through 1333 removed outlier: 9.361A pdb=" N PHE O1332 " --> pdb=" O GLN O 402 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER O 404 " --> pdb=" O PHE O1332 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG O 400 " --> pdb=" O GLU O1322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'O' and resid 370 through 374 removed outlier: 3.787A pdb=" N ALA O 370 " --> pdb=" O VAL O 381 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA O 380 " --> pdb=" O GLY O 277 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL O 279 " --> pdb=" O ALA O 380 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU O 382 " --> pdb=" O VAL O 279 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE O 281 " --> pdb=" O GLU O 382 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG O 400 " --> pdb=" O GLU O1322 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 438 through 441 Processing sheet with id=AF8, first strand: chain 'O' and resid 546 through 549 Processing sheet with id=AF9, first strand: chain 'O' and resid 727 through 728 Processing sheet with id=AG1, first strand: chain 'O' and resid 763 through 765 Processing sheet with id=AG2, first strand: chain 'O' and resid 928 through 930 Processing sheet with id=AG3, first strand: chain 'O' and resid 1336 through 1337 Processing sheet with id=AG4, first strand: chain 'O' and resid 1373 through 1375 Processing sheet with id=AG5, first strand: chain 'P' and resid 77 through 81 removed outlier: 6.077A pdb=" N VAL P 78 " --> pdb=" O MET P1067 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE P1069 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR P 80 " --> pdb=" O ILE P1069 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 77 through 81 removed outlier: 6.077A pdb=" N VAL P 78 " --> pdb=" O MET P1067 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE P1069 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR P 80 " --> pdb=" O ILE P1069 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG f 25 " --> pdb=" O VAL P1074 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 92 through 99 Processing sheet with id=AG8, first strand: chain 'P' and resid 268 through 269 Processing sheet with id=AG9, first strand: chain 'P' and resid 370 through 374 removed outlier: 3.627A pdb=" N ALA P 370 " --> pdb=" O VAL P 381 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA P 380 " --> pdb=" O GLY P 277 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL P 279 " --> pdb=" O ALA P 380 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU P 382 " --> pdb=" O VAL P 279 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE P 281 " --> pdb=" O GLU P 382 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 1103 through 1113 removed outlier: 4.808A pdb=" N GLU P1055 " --> pdb=" O ALA P1108 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL P1110 " --> pdb=" O LEU P1053 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU P1053 " --> pdb=" O VAL P1110 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA P1112 " --> pdb=" O GLU P1051 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU P1051 " --> pdb=" O ALA P1112 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N PHE P1332 " --> pdb=" O GLN P 402 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER P 404 " --> pdb=" O PHE P1332 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 440 through 441 Processing sheet with id=AH3, first strand: chain 'P' and resid 546 through 549 Processing sheet with id=AH4, first strand: chain 'P' and resid 727 through 728 Processing sheet with id=AH5, first strand: chain 'P' and resid 763 through 765 removed outlier: 4.326A pdb=" N LEU P 796 " --> pdb=" O GLU P 764 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 928 through 930 removed outlier: 3.875A pdb=" N LEU P 928 " --> pdb=" O LEU P 828 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 1336 through 1337 Processing sheet with id=AH8, first strand: chain 'v' and resid 22 through 23 Processing sheet with id=AH9, first strand: chain 'v' and resid 43 through 44 Processing sheet with id=AI1, first strand: chain 'v' and resid 285 through 289 Processing sheet with id=AI2, first strand: chain 'v' and resid 436 through 438 removed outlier: 3.580A pdb=" N LEU v 419 " --> pdb=" O ILE v 438 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 90 through 96 removed outlier: 7.777A pdb=" N LEU f 200 " --> pdb=" O LYS f 196 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS f 196 " --> pdb=" O LEU f 200 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS f 202 " --> pdb=" O ASN f 194 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN f 194 " --> pdb=" O LYS f 202 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR f 204 " --> pdb=" O VAL f 192 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU f 110 " --> pdb=" O VAL f 188 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'f' and resid 208 through 210 removed outlier: 4.372A pdb=" N LEU f 324 " --> pdb=" O ASN f 356 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU f 264 " --> pdb=" O LEU f 324 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR f 326 " --> pdb=" O ALA f 262 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA f 262 " --> pdb=" O THR f 326 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 208 through 210 removed outlier: 4.372A pdb=" N LEU f 324 " --> pdb=" O ASN f 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY f 319 " --> pdb=" O ILE f 363 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'f' and resid 223 through 226 Processing sheet with id=AI7, first strand: chain 'h' and resid 89 through 96 removed outlier: 5.609A pdb=" N VAL h 206 " --> pdb=" O LEU h 191 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU h 191 " --> pdb=" O VAL h 206 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU h 110 " --> pdb=" O VAL h 188 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 209 through 210 removed outlier: 6.420A pdb=" N LEU h 264 " --> pdb=" O LEU h 324 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR h 326 " --> pdb=" O ALA h 262 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA h 262 " --> pdb=" O THR h 326 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 209 through 210 Processing sheet with id=AJ1, first strand: chain 'h' and resid 223 through 226 Processing sheet with id=AJ2, first strand: chain 'k' and resid 28 through 31 removed outlier: 3.679A pdb=" N THR k 68 " --> pdb=" O LEU k 31 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU k 72 " --> pdb=" O THR k 83 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR k 83 " --> pdb=" O LEU k 72 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL k 6 " --> pdb=" O GLN k 38 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'k' and resid 93 through 94 removed outlier: 6.500A pdb=" N THR k 297 " --> pdb=" O ALA k 287 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'k' and resid 122 through 125 Processing sheet with id=AJ5, first strand: chain 'k' and resid 178 through 181 Processing sheet with id=AJ6, first strand: chain 'm' and resid 28 through 31 removed outlier: 6.561A pdb=" N ILE m 81 " --> pdb=" O ASP m 73 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL m 75 " --> pdb=" O SER m 79 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER m 79 " --> pdb=" O VAL m 75 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL m 6 " --> pdb=" O GLN m 38 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'm' and resid 91 through 94 removed outlier: 6.881A pdb=" N THR m 295 " --> pdb=" O TYR m 289 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR m 289 " --> pdb=" O THR m 295 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR m 297 " --> pdb=" O ALA m 287 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA m 285 " --> pdb=" O TRP m 299 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'm' and resid 122 through 125 Processing sheet with id=AJ9, first strand: chain 'm' and resid 178 through 181 Processing sheet with id=AK1, first strand: chain 'p' and resid 4 through 8 removed outlier: 6.699A pdb=" N SER p 79 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL p 75 " --> pdb=" O SER p 79 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE p 81 " --> pdb=" O ASP p 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR p 68 " --> pdb=" O LEU p 31 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'p' and resid 91 through 93 removed outlier: 6.702A pdb=" N THR p 295 " --> pdb=" O TYR p 289 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR p 289 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR p 297 " --> pdb=" O ALA p 287 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'p' and resid 123 through 125 Processing sheet with id=AK4, first strand: chain 'p' and resid 178 through 181 Processing sheet with id=AK5, first strand: chain 'r' and resid 28 through 31 removed outlier: 3.875A pdb=" N THR r 68 " --> pdb=" O LEU r 31 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE r 81 " --> pdb=" O ASP r 73 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL r 75 " --> pdb=" O SER r 79 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER r 79 " --> pdb=" O VAL r 75 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLN r 38 " --> pdb=" O LYS r 4 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL r 6 " --> pdb=" O GLN r 38 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'r' and resid 91 through 94 removed outlier: 6.524A pdb=" N THR r 295 " --> pdb=" O TYR r 289 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR r 289 " --> pdb=" O THR r 295 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR r 297 " --> pdb=" O ALA r 287 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP r 299 " --> pdb=" O ALA r 285 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'r' and resid 122 through 125 Processing sheet with id=AK8, first strand: chain 'r' and resid 178 through 181 3173 hydrogen bonds defined for protein. 8871 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: 42.49 Time building geometry restraints manager: 20.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19805 1.33 - 1.45: 14159 1.45 - 1.57: 41309 1.57 - 1.70: 1 1.70 - 1.82: 709 Bond restraints: 75983 Sorted by residual: bond pdb=" C ALA J 477 " pdb=" N PRO J 478 " ideal model delta sigma weight residual 1.337 1.298 0.039 1.24e-02 6.50e+03 1.01e+01 bond pdb=" CB ASP J 482 " pdb=" CG ASP J 482 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.21e+00 bond pdb=" CB PRO J 480 " pdb=" CG PRO J 480 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.69e+00 bond pdb=" CG1 ILE J 93 " pdb=" CD1 ILE J 93 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.89e+00 bond pdb=" CA ASP J 482 " pdb=" C ASP J 482 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.30e-02 5.92e+03 4.55e+00 ... (remaining 75978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 101527 2.30 - 4.60: 1526 4.60 - 6.90: 166 6.90 - 9.20: 18 9.20 - 11.50: 7 Bond angle restraints: 103244 Sorted by residual: angle pdb=" C GLY J 304 " pdb=" N PRO J 305 " pdb=" CA PRO J 305 " ideal model delta sigma weight residual 119.84 129.40 -9.56 1.25e+00 6.40e-01 5.85e+01 angle pdb=" N VAL P 319 " pdb=" CA VAL P 319 " pdb=" C VAL P 319 " ideal model delta sigma weight residual 113.20 107.60 5.60 9.60e-01 1.09e+00 3.41e+01 angle pdb=" N PRO J 366 " pdb=" CA PRO J 366 " pdb=" C PRO J 366 " ideal model delta sigma weight residual 112.47 100.97 11.50 2.06e+00 2.36e-01 3.11e+01 angle pdb=" N ASP K 299 " pdb=" CA ASP K 299 " pdb=" C ASP K 299 " ideal model delta sigma weight residual 111.28 105.44 5.84 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N VAL K 940 " pdb=" CA VAL K 940 " pdb=" C VAL K 940 " ideal model delta sigma weight residual 111.81 107.54 4.27 8.60e-01 1.35e+00 2.47e+01 ... (remaining 103239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 41644 17.79 - 35.58: 3291 35.58 - 53.37: 618 53.37 - 71.15: 105 71.15 - 88.94: 19 Dihedral angle restraints: 45677 sinusoidal: 18085 harmonic: 27592 Sorted by residual: dihedral pdb=" CA GLN a 32 " pdb=" C GLN a 32 " pdb=" N ASN a 33 " pdb=" CA ASN a 33 " 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 98 " pdb=" C GLN k 98 " pdb=" N PRO k 99 " pdb=" CA PRO k 99 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ALA J 805 " pdb=" C ALA J 805 " pdb=" N ASP J 806 " pdb=" CA ASP J 806 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 45674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 9481 0.057 - 0.114: 1920 0.114 - 0.171: 203 0.171 - 0.228: 7 0.228 - 0.285: 3 Chirality restraints: 11614 Sorted by residual: chirality pdb=" CG LEU J 456 " pdb=" CB LEU J 456 " pdb=" CD1 LEU J 456 " pdb=" CD2 LEU J 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.87 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASP N 873 " pdb=" N ASP N 873 " pdb=" C ASP N 873 " pdb=" CB ASP N 873 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN p 38 " pdb=" N GLN p 38 " pdb=" C GLN p 38 " pdb=" CB GLN p 38 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.63e+00 ... (remaining 11611 not shown) Planarity restraints: 13471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE f 216 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO f 217 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO f 217 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO f 217 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 843 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO J 844 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO J 844 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 844 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 482 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" CG ASP J 482 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP J 482 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 482 " -0.015 2.00e-02 2.50e+03 ... (remaining 13468 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 14 2.07 - 2.78: 17395 2.78 - 3.48: 100914 3.48 - 4.19: 164511 4.19 - 4.90: 288417 Nonbonded interactions: 571251 Sorted by model distance: nonbonded pdb=" OD2 ASP v 25 " pdb=" O ARG v 74 " model vdw 1.362 3.040 nonbonded pdb=" ND2 ASN N 672 " pdb=" O ILE O 871 " model vdw 1.666 3.120 nonbonded pdb=" CD2 LEU N 670 " pdb=" CB ALA N 674 " model vdw 1.678 3.880 nonbonded pdb=" CG GLU O 258 " pdb=" CD LYS O 262 " model vdw 1.745 3.840 nonbonded pdb=" O VAL J 365 " pdb=" O PRO J 366 " model vdw 1.765 3.040 ... (remaining 571246 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 29 through 256 or resid 266 through 1147 or resid 1177 thr \ ough 1299 or resid 1312 through 1381)) selection = (chain 'K' and (resid 29 through 256 or resid 266 through 337 or resid 365 throu \ gh 1147 or resid 1177 through 1299 or resid 1312 through 1381)) selection = (chain 'N' and (resid 29 through 256 or resid 266 through 337 or resid 365 throu \ gh 1147 or resid 1177 through 1299 or resid 1312 through 1381)) selection = (chain 'O' and (resid 29 through 256 or resid 266 through 337 or resid 365 throu \ gh 1147 or resid 1177 through 1299 or resid 1312 through 1381)) selection = (chain 'P' and (resid 29 through 337 or resid 365 through 1381)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'f' and (resid 1 through 238 or resid 255 through 364)) selection = (chain 'h' and (resid 1 through 62 or resid 84 through 149 or resid 151 through \ 364)) } 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: 2.090 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: 0.080 Extract box with map and model: 2.190 Check model and map are aligned: 0.460 Set scattering table: 0.530 Process input model: 157.400 Find NCS groups from input model: 4.620 Set up NCS constraints: 0.570 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: 0.030 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 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 0.139 75983 Z= 0.366 Angle : 0.736 11.497 103244 Z= 0.416 Chirality : 0.045 0.285 11614 Planarity : 0.005 0.074 13471 Dihedral : 13.329 88.943 27849 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.03 % Favored : 94.60 % Rotamer: Outliers : 5.51 % Allowed : 9.58 % Favored : 84.91 % 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: -2.57 (0.08), residues: 9356 helix: -1.39 (0.08), residues: 3379 sheet: -0.79 (0.14), residues: 1247 loop : -2.20 (0.08), residues: 4730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP x 54 HIS 0.009 0.001 HIS J 35 PHE 0.026 0.002 PHE P 990 TYR 0.029 0.002 TYR P 780 ARG 0.007 0.001 ARG k 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3406 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 445 poor density : 2961 time to evaluate : 6.317 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: J 5 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5564 (mp0) REVERT: J 544 PRO cc_start: 0.7970 (Cg_exo) cc_final: 0.7758 (Cg_endo) REVERT: J 838 THR cc_start: 0.5552 (p) cc_final: 0.5069 (p) REVERT: J 871 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6765 (tp) REVERT: J 1209 VAL cc_start: 0.6671 (OUTLIER) cc_final: 0.6393 (t) REVERT: J 1332 PHE cc_start: 0.7334 (m-80) cc_final: 0.7024 (m-80) REVERT: K 1 MET cc_start: 0.0527 (mtt) cc_final: -0.0117 (mtm) REVERT: K 96 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.5056 (mtm-85) REVERT: K 314 ARG cc_start: 0.7298 (ptm-80) cc_final: 0.6921 (mmt180) REVERT: K 448 LEU cc_start: 0.5421 (mt) cc_final: 0.4482 (mt) REVERT: K 464 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5704 (mm) REVERT: K 662 MET cc_start: 0.5447 (mmm) cc_final: 0.5183 (mmt) REVERT: K 815 VAL cc_start: 0.5338 (t) cc_final: 0.4734 (t) REVERT: K 883 ASP cc_start: 0.5758 (m-30) cc_final: 0.5393 (m-30) REVERT: K 1161 TYR cc_start: 0.5358 (p90) cc_final: 0.4909 (t80) REVERT: K 1215 TYR cc_start: 0.5415 (m-80) cc_final: 0.5181 (m-10) REVERT: K 1254 MET cc_start: 0.7012 (mtm) cc_final: 0.6689 (ttm) REVERT: K 1288 TYR cc_start: 0.6343 (m-80) cc_final: 0.5267 (p90) REVERT: N 1 MET cc_start: 0.5606 (mmm) cc_final: 0.5155 (ptm) REVERT: N 33 LEU cc_start: 0.6622 (tp) cc_final: 0.6403 (mt) REVERT: N 328 MET cc_start: 0.4436 (tpt) cc_final: 0.4079 (mtp) REVERT: N 501 VAL cc_start: 0.6011 (OUTLIER) cc_final: 0.5612 (p) REVERT: N 567 MET cc_start: 0.4750 (ptp) cc_final: 0.4205 (ptp) REVERT: N 654 LEU cc_start: 0.7088 (pp) cc_final: 0.6470 (pp) REVERT: N 762 PHE cc_start: 0.3982 (m-80) cc_final: 0.3675 (m-80) REVERT: N 846 PHE cc_start: 0.3632 (m-80) cc_final: 0.3403 (m-80) REVERT: N 1067 MET cc_start: 0.6744 (mmm) cc_final: 0.5937 (mmm) REVERT: N 1081 VAL cc_start: 0.4281 (OUTLIER) cc_final: 0.4016 (m) REVERT: N 1210 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6889 (t) REVERT: N 1249 SER cc_start: 0.4494 (p) cc_final: 0.3757 (m) REVERT: N 1294 TYR cc_start: 0.6127 (t80) cc_final: 0.5813 (t80) REVERT: N 1304 THR cc_start: 0.7092 (p) cc_final: 0.6769 (t) REVERT: O 47 GLU cc_start: 0.2839 (OUTLIER) cc_final: -0.0008 (tt0) REVERT: O 121 ASN cc_start: 0.4657 (OUTLIER) cc_final: 0.4228 (p0) REVERT: O 426 MET cc_start: 0.6451 (ttm) cc_final: 0.6193 (mtm) REVERT: O 598 VAL cc_start: 0.6491 (OUTLIER) cc_final: 0.6197 (p) REVERT: O 801 ASP cc_start: 0.7292 (p0) cc_final: 0.6751 (p0) REVERT: O 914 PRO cc_start: 0.6502 (Cg_endo) cc_final: 0.6221 (Cg_exo) REVERT: O 1347 MET cc_start: 0.5710 (mmp) cc_final: 0.5323 (mmt) REVERT: P 149 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7432 (t) REVERT: P 167 PHE cc_start: 0.7172 (m-80) cc_final: 0.6926 (m-10) REVERT: P 174 ARG cc_start: 0.6691 (mmt90) cc_final: 0.4570 (tmt170) REVERT: P 251 MET cc_start: 0.5919 (ttm) cc_final: 0.5591 (ttm) REVERT: P 293 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: P 414 PRO cc_start: 0.5708 (Cg_exo) cc_final: 0.4591 (Cg_endo) REVERT: P 861 GLU cc_start: 0.4266 (pm20) cc_final: 0.3308 (pm20) REVERT: P 906 VAL cc_start: 0.6549 (t) cc_final: 0.6251 (m) REVERT: P 1178 GLN cc_start: 0.5448 (tm-30) cc_final: 0.4807 (mp10) REVERT: P 1268 TYR cc_start: 0.6821 (t80) cc_final: 0.6520 (t80) REVERT: P 1335 LEU cc_start: 0.8423 (tt) cc_final: 0.8140 (tt) REVERT: v 9 VAL cc_start: 0.3298 (OUTLIER) cc_final: 0.2806 (m) REVERT: v 13 LEU cc_start: 0.3936 (tt) cc_final: 0.3428 (tt) REVERT: v 57 VAL cc_start: 0.4447 (OUTLIER) cc_final: 0.4159 (m) REVERT: a 56 CYS cc_start: 0.6000 (m) cc_final: 0.5630 (m) REVERT: d 75 ASP cc_start: 0.6375 (p0) cc_final: 0.5238 (m-30) REVERT: u 24 LEU cc_start: 0.6054 (tp) cc_final: 0.5828 (tt) REVERT: f 164 THR cc_start: 0.5755 (OUTLIER) cc_final: 0.5417 (m) REVERT: f 214 LYS cc_start: 0.3944 (OUTLIER) cc_final: 0.3089 (tptt) REVERT: f 290 MET cc_start: 0.6105 (mmm) cc_final: 0.5852 (mmt) REVERT: k 271 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.3968 (mt) REVERT: m 252 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4143 (pp) REVERT: p 60 MET cc_start: 0.3060 (mtm) cc_final: 0.2799 (mtm) REVERT: p 62 ASN cc_start: 0.4887 (m-40) cc_final: 0.4685 (m110) REVERT: p 89 GLN cc_start: 0.5243 (mp-120) cc_final: 0.5028 (tp-100) REVERT: r 125 LEU cc_start: 0.5655 (mt) cc_final: 0.5216 (mt) REVERT: r 239 PHE cc_start: 0.7077 (m-10) cc_final: 0.6837 (m-80) outliers start: 445 outliers final: 113 residues processed: 3253 average time/residue: 0.7111 time to fit residues: 3914.0119 Evaluate side-chains 1910 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1778 time to evaluate : 6.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 5 GLU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 308 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain J residue 847 SER Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 871 ILE Chi-restraints excluded: chain J residue 1065 THR Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1161 TYR Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1187 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 752 VAL Chi-restraints excluded: chain K residue 919 THR Chi-restraints excluded: chain K residue 1013 VAL Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1155 LEU Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1187 THR Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1305 SER Chi-restraints excluded: chain K residue 1352 THR Chi-restraints excluded: chain K residue 1369 VAL Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 371 VAL Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 501 VAL Chi-restraints excluded: chain N residue 550 ILE Chi-restraints excluded: chain N residue 571 LEU Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 670 LEU Chi-restraints excluded: chain N residue 675 ILE Chi-restraints excluded: chain N residue 769 MET Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 1048 ARG Chi-restraints excluded: chain N residue 1081 VAL Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1210 VAL Chi-restraints excluded: chain N residue 1256 ASN Chi-restraints excluded: chain N residue 1313 VAL Chi-restraints excluded: chain N residue 1336 SER Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 121 ASN Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 313 VAL Chi-restraints excluded: chain O residue 592 THR Chi-restraints excluded: chain O residue 598 VAL Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 681 SER Chi-restraints excluded: chain O residue 856 ILE Chi-restraints excluded: chain O residue 885 SER Chi-restraints excluded: chain O residue 902 VAL Chi-restraints excluded: chain O residue 940 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1309 VAL Chi-restraints excluded: chain O residue 1319 VAL Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 901 SER Chi-restraints excluded: chain P residue 929 VAL Chi-restraints excluded: chain P residue 1106 THR Chi-restraints excluded: chain P residue 1110 VAL Chi-restraints excluded: chain P residue 1119 ILE Chi-restraints excluded: chain P residue 1187 THR Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain v residue 57 VAL Chi-restraints excluded: chain v residue 100 LEU Chi-restraints excluded: chain v residue 284 LEU Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 371 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 409 SER Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain f residue 164 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 214 LYS Chi-restraints excluded: chain f residue 313 ILE Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 197 SER Chi-restraints excluded: chain h residue 224 THR Chi-restraints excluded: chain h residue 300 SER Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 331 ASP Chi-restraints excluded: chain k residue 69 LEU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 271 LEU Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 247 ILE Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain r residue 255 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 786 optimal weight: 3.9990 chunk 705 optimal weight: 6.9990 chunk 391 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 475 optimal weight: 0.8980 chunk 376 optimal weight: 10.0000 chunk 729 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 443 optimal weight: 8.9990 chunk 543 optimal weight: 20.0000 chunk 845 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 104 HIS J 126 HIS J 195 GLN J 444 ASN J 445 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 HIS J 531 HIS J 560 HIS ** J 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 ASN J 669 HIS J 695 GLN J 722 ASN J 790 HIS ** J 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 848 HIS J 862 ASN ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 997 HIS J1022 HIS ** J1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1090 HIS J1120 HIS J1176 HIS J1292 ASN K 94 GLN K 104 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN K 385 GLN K 415 ASN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 HIS K 531 HIS ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 570 ASN K 627 HIS K 788 HIS K 824 HIS ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 HIS K 977 GLN K 984 ASN K1137 GLN ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1178 GLN K1256 ASN K1353 HIS N 104 HIS N 123 HIS N 300 ASN N 333 HIS N 385 GLN ** N 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN N 465 HIS N 469 HIS N 491 HIS N 534 ASN ** N 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 645 ASN N 669 HIS N 761 GLN N 804 HIS N 824 HIS ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1073 ASN N1089 HIS ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1256 ASN N1301 HIS N1306 ASN ** N1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 289 GLN O 333 HIS O 377 HIS O 432 GLN O 445 ASN O 465 HIS O 469 HIS ** O 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 581 GLN O 636 ASN O 824 HIS O 909 GLN O 965 GLN ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS O1135 ASN O1227 HIS O1283 ASN O1301 HIS ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1357 HIS P 226 HIS P 402 GLN P 415 ASN P 509 ASN P 586 GLN P 596 HIS P 735 HIS P 750 ASN P 837 GLN P1120 HIS P1178 GLN ** P1357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 7 ASN v 45 GLN ** v 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 295 HIS v 360 GLN v 461 HIS ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Z 28 GLN Z 54 GLN Z 71 GLN ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 GLN e 31 ASN e 32 GLN u 44 GLN f 102 ASN f 208 HIS f 303 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 288 GLN h 291 ASN ** k 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 41 GLN k 62 ASN k 184 HIS k 233 HIS ** m 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 148 GLN m 185 HIS m 230 HIS m 233 HIS ** m 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 GLN p 89 GLN p 95 ASN p 128 ASN p 185 HIS p 204 ASN ** p 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 41 GLN r 47 GLN ** r 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 128 ASN ** r 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 GLN Total number of N/Q/H flips: 125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 75983 Z= 0.273 Angle : 0.754 12.918 103244 Z= 0.389 Chirality : 0.047 0.241 11614 Planarity : 0.006 0.084 13471 Dihedral : 6.624 83.243 10554 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 5.43 % Allowed : 18.81 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.08), residues: 9356 helix: -0.39 (0.08), residues: 3419 sheet: -0.45 (0.14), residues: 1254 loop : -1.87 (0.08), residues: 4683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP m 103 HIS 0.015 0.002 HIS N1301 PHE 0.052 0.002 PHE u 50 TYR 0.047 0.002 TYR P 780 ARG 0.021 0.001 ARG P 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2446 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 438 poor density : 2008 time to evaluate : 6.486 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: J 40 LEU cc_start: 0.7008 (mt) cc_final: 0.6729 (mt) REVERT: J 871 ILE cc_start: 0.7334 (tp) cc_final: 0.6898 (tp) REVERT: J 896 ARG cc_start: 0.6470 (mtt90) cc_final: 0.4776 (ttt180) REVERT: K 39 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.5949 (pp) REVERT: K 178 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8306 (t0) REVERT: K 697 LEU cc_start: 0.6614 (tt) cc_final: 0.6231 (tt) REVERT: K 772 MET cc_start: 0.6605 (mmm) cc_final: 0.6148 (mmt) REVERT: K 792 PHE cc_start: 0.6984 (m-10) cc_final: 0.6545 (m-10) REVERT: K 880 MET cc_start: 0.5630 (mpp) cc_final: 0.5022 (mtm) REVERT: K 883 ASP cc_start: 0.5433 (m-30) cc_final: 0.5177 (m-30) REVERT: K 952 MET cc_start: 0.7162 (tpt) cc_final: 0.6763 (tpt) REVERT: K 953 PHE cc_start: 0.5775 (m-10) cc_final: 0.5551 (m-10) REVERT: K 1068 PHE cc_start: 0.6678 (m-80) cc_final: 0.6469 (m-80) REVERT: K 1161 TYR cc_start: 0.5701 (p90) cc_final: 0.4908 (t80) REVERT: K 1185 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7683 (mm) REVERT: K 1199 SER cc_start: 0.6556 (OUTLIER) cc_final: 0.6294 (p) REVERT: K 1215 TYR cc_start: 0.6148 (m-80) cc_final: 0.5859 (m-10) REVERT: K 1288 TYR cc_start: 0.6858 (m-80) cc_final: 0.5607 (p90) REVERT: K 1358 TYR cc_start: 0.6737 (m-10) cc_final: 0.6247 (m-10) REVERT: N 1 MET cc_start: 0.6140 (mmm) cc_final: 0.5929 (ptm) REVERT: N 550 ILE cc_start: 0.3612 (OUTLIER) cc_final: 0.3308 (mp) REVERT: N 587 GLN cc_start: 0.7706 (pt0) cc_final: 0.7471 (pt0) REVERT: N 635 MET cc_start: 0.6068 (tpt) cc_final: 0.5844 (tpt) REVERT: N 762 PHE cc_start: 0.3770 (m-80) cc_final: 0.3477 (m-80) REVERT: N 928 LEU cc_start: 0.5830 (pt) cc_final: 0.5101 (pp) REVERT: N 1001 MET cc_start: 0.6853 (mtp) cc_final: 0.6183 (mtp) REVERT: N 1067 MET cc_start: 0.7100 (mmm) cc_final: 0.6535 (mmt) REVERT: N 1086 PHE cc_start: 0.6948 (m-10) cc_final: 0.6724 (m-80) REVERT: O 47 GLU cc_start: 0.2881 (OUTLIER) cc_final: 0.1145 (tt0) REVERT: O 225 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: O 426 MET cc_start: 0.6852 (ttm) cc_final: 0.6496 (mtm) REVERT: O 556 GLU cc_start: 0.5328 (pm20) cc_final: 0.4946 (pp20) REVERT: O 573 THR cc_start: 0.7921 (p) cc_final: 0.7382 (m) REVERT: O 594 LEU cc_start: 0.7601 (tp) cc_final: 0.7102 (tp) REVERT: O 598 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7265 (p) REVERT: O 811 ILE cc_start: 0.7211 (pt) cc_final: 0.6993 (pt) REVERT: O 1254 MET cc_start: 0.5276 (mtt) cc_final: 0.4954 (mtt) REVERT: O 1344 ASP cc_start: 0.5765 (m-30) cc_final: 0.5473 (m-30) REVERT: P 174 ARG cc_start: 0.7174 (mmt90) cc_final: 0.4767 (tmt170) REVERT: P 293 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6121 (m-10) REVERT: P 401 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5356 (mtm) REVERT: P 698 MET cc_start: 0.6176 (mmp) cc_final: 0.5916 (mmm) REVERT: P 1178 GLN cc_start: 0.5840 (OUTLIER) cc_final: 0.5009 (mp10) REVERT: v 396 ARG cc_start: 0.5815 (mmt90) cc_final: 0.5302 (mmt90) REVERT: v 427 TYR cc_start: 0.5868 (m-80) cc_final: 0.5449 (m-80) REVERT: x 54 TRP cc_start: 0.5593 (m100) cc_final: 0.5379 (m100) REVERT: x 101 MET cc_start: 0.3899 (mtt) cc_final: 0.3471 (mtt) REVERT: Z 1 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.4866 (mmt) REVERT: Z 38 ASP cc_start: 0.5544 (p0) cc_final: 0.4822 (p0) REVERT: Z 76 LYS cc_start: 0.6922 (tptt) cc_final: 0.6224 (mttm) REVERT: a 1 MET cc_start: 0.3215 (OUTLIER) cc_final: 0.2870 (ptm) REVERT: d 56 CYS cc_start: 0.6923 (m) cc_final: 0.6677 (m) REVERT: d 75 ASP cc_start: 0.5532 (p0) cc_final: 0.4889 (m-30) REVERT: h 154 MET cc_start: 0.4549 (tpp) cc_final: 0.4281 (tpp) REVERT: h 237 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6018 (tm) REVERT: k 21 MET cc_start: 0.6119 (mmm) cc_final: 0.5500 (mmt) REVERT: k 60 MET cc_start: 0.6931 (mpp) cc_final: 0.6674 (mtm) REVERT: m 18 ILE cc_start: 0.6625 (tp) cc_final: 0.6310 (tp) REVERT: m 252 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4628 (pp) REVERT: p 20 LYS cc_start: 0.4032 (mtmm) cc_final: 0.3792 (mtmt) REVERT: p 49 TYR cc_start: 0.6274 (t80) cc_final: 0.6031 (t80) REVERT: p 62 ASN cc_start: 0.4943 (m-40) cc_final: 0.4415 (m-40) REVERT: p 150 ILE cc_start: 0.8115 (tt) cc_final: 0.7597 (tp) REVERT: p 267 MET cc_start: 0.5594 (ptm) cc_final: 0.5185 (tmm) REVERT: p 291 GLN cc_start: 0.4706 (pm20) cc_final: 0.4088 (tt0) REVERT: p 293 THR cc_start: 0.5542 (m) cc_final: 0.5207 (m) REVERT: r 169 MET cc_start: 0.4857 (mmp) cc_final: 0.4435 (mmm) outliers start: 438 outliers final: 229 residues processed: 2291 average time/residue: 0.6873 time to fit residues: 2738.2490 Evaluate side-chains 1869 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1625 time to evaluate : 6.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 CYS Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain J residue 401 MET Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 516 THR Chi-restraints excluded: chain J residue 571 LEU Chi-restraints excluded: chain J residue 596 HIS Chi-restraints excluded: chain J residue 613 THR Chi-restraints excluded: chain J residue 641 SER Chi-restraints excluded: chain J residue 669 HIS Chi-restraints excluded: chain J residue 710 SER Chi-restraints excluded: chain J residue 716 CYS Chi-restraints excluded: chain J residue 849 HIS Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 895 THR Chi-restraints excluded: chain J residue 925 VAL Chi-restraints excluded: chain J residue 999 SER Chi-restraints excluded: chain J residue 1011 SER Chi-restraints excluded: chain J residue 1042 VAL Chi-restraints excluded: chain J residue 1065 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1161 TYR Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1218 GLU Chi-restraints excluded: chain J residue 1365 GLU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 ASN Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 319 VAL Chi-restraints excluded: chain K residue 415 ASN Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain K residue 469 HIS Chi-restraints excluded: chain K residue 613 THR Chi-restraints excluded: chain K residue 621 VAL Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 790 HIS Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 868 LEU Chi-restraints excluded: chain K residue 891 CYS Chi-restraints excluded: chain K residue 956 ASP Chi-restraints excluded: chain K residue 964 HIS Chi-restraints excluded: chain K residue 1013 VAL Chi-restraints excluded: chain K residue 1014 SER Chi-restraints excluded: chain K residue 1045 THR Chi-restraints excluded: chain K residue 1047 VAL Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1088 VAL Chi-restraints excluded: chain K residue 1105 MET Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1185 ILE Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1349 VAL Chi-restraints excluded: chain K residue 1350 LYS Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 218 MET Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 437 GLU Chi-restraints excluded: chain N residue 452 LEU Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 489 LEU Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 550 ILE Chi-restraints excluded: chain N residue 609 THR Chi-restraints excluded: chain N residue 634 VAL Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 732 ILE Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 757 LEU Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1181 THR Chi-restraints excluded: chain N residue 1182 CYS Chi-restraints excluded: chain N residue 1193 VAL Chi-restraints excluded: chain N residue 1313 VAL Chi-restraints excluded: chain N residue 1356 ILE Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 177 ILE Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 225 GLU Chi-restraints excluded: chain O residue 256 SER Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 302 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 340 ASP Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 590 THR Chi-restraints excluded: chain O residue 598 VAL Chi-restraints excluded: chain O residue 613 THR Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 839 LEU Chi-restraints excluded: chain O residue 971 VAL Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1044 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1090 HIS Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1183 GLU Chi-restraints excluded: chain O residue 1293 GLU Chi-restraints excluded: chain O residue 1325 CYS Chi-restraints excluded: chain O residue 1373 LEU Chi-restraints excluded: chain O residue 1379 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 242 GLN Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 400 ARG Chi-restraints excluded: chain P residue 401 MET Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 642 LEU Chi-restraints excluded: chain P residue 808 LEU Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 1055 GLU Chi-restraints excluded: chain P residue 1073 ASN Chi-restraints excluded: chain P residue 1178 GLN Chi-restraints excluded: chain P residue 1181 THR Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1211 SER Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1328 LEU Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 100 LEU Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3126 LEU Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 40 PHE Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 32 GLN Chi-restraints excluded: chain e residue 40 PHE Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 152 THR Chi-restraints excluded: chain f residue 191 LEU Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 326 THR Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain h residue 46 HIS Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain h residue 165 LEU Chi-restraints excluded: chain h residue 237 LEU Chi-restraints excluded: chain h residue 295 ILE Chi-restraints excluded: chain h residue 300 SER Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 331 ASP Chi-restraints excluded: chain k residue 41 GLN Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 138 LEU Chi-restraints excluded: chain k residue 170 LEU Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 245 ASP Chi-restraints excluded: chain k residue 298 CYS Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 210 CYS Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain m residue 297 THR Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 95 ASN Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 179 VAL Chi-restraints excluded: chain p residue 249 ARG Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 469 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 703 optimal weight: 30.0000 chunk 575 optimal weight: 0.2980 chunk 233 optimal weight: 20.0000 chunk 846 optimal weight: 3.9990 chunk 914 optimal weight: 8.9990 chunk 754 optimal weight: 9.9990 chunk 839 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 679 optimal weight: 5.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 389 ASN J 415 ASN J 445 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 669 HIS J 833 GLN ** J 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 842 ASN J 848 HIS J 859 ASN ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1353 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 377 HIS ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 570 ASN K 587 GLN K 636 ASN K 788 HIS K 834 HIS ** K 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 HIS K1167 ASN K1176 HIS K1353 HIS N 79 ASN N 104 HIS N 178 ASN ** N 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 444 ASN N 472 ASN N 600 GLN ** N 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 669 HIS N 673 ASN N 761 GLN N 795 HIS ** N 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 909 GLN N 974 ASN ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 HIS O 377 HIS O 398 ASN O 496 HIS ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 837 GLN ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1090 HIS O1284 ASN O1296 GLN ** O1329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN P 289 GLN P 402 GLN P 433 GLN P 442 ASN P 534 ASN ** P 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 837 GLN P 951 HIS P1178 GLN P1241 ASN v 34 ASN ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 295 HIS v 424 HIS v 461 HIS w 59 GLN x 59 GLN x 77 HIS ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 32 GLN u 31 ASN u 62 GLN f 28 ASN f 46 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 GLN k 41 GLN k 102 GLN k 148 GLN ** k 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 GLN ** m 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 185 HIS ** m 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 GLN ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 95 ASN r 102 GLN ** r 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 173 HIS Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 75983 Z= 0.289 Angle : 0.743 13.702 103244 Z= 0.383 Chirality : 0.047 0.261 11614 Planarity : 0.006 0.094 13471 Dihedral : 6.017 76.677 10437 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 6.20 % Allowed : 20.43 % Favored : 73.37 % 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: -1.38 (0.08), residues: 9356 helix: -0.09 (0.09), residues: 3444 sheet: -0.39 (0.14), residues: 1236 loop : -1.70 (0.09), residues: 4676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP v 362 HIS 0.052 0.002 HIS J 669 PHE 0.050 0.002 PHE u 50 TYR 0.035 0.002 TYR J 395 ARG 0.012 0.001 ARG u 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2376 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 500 poor density : 1876 time to evaluate : 6.571 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: J 115 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6880 (p) REVERT: J 567 MET cc_start: 0.6129 (mmt) cc_final: 0.5545 (mmt) REVERT: J 666 ILE cc_start: 0.6493 (mm) cc_final: 0.6205 (mm) REVERT: J 856 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6233 (tp) REVERT: J 871 ILE cc_start: 0.7491 (tp) cc_final: 0.7186 (tp) REVERT: J 928 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5522 (pp) REVERT: J 952 MET cc_start: 0.6501 (tpt) cc_final: 0.6165 (tpp) REVERT: J 1156 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4044 (tmt170) REVERT: J 1257 SER cc_start: 0.7511 (m) cc_final: 0.6901 (m) REVERT: J 1276 ASN cc_start: 0.6004 (t0) cc_final: 0.5461 (t0) REVERT: J 1358 TYR cc_start: 0.6181 (m-10) cc_final: 0.5914 (m-80) REVERT: K 1 MET cc_start: 0.1362 (mtt) cc_final: 0.0367 (mtm) REVERT: K 163 SER cc_start: 0.8129 (p) cc_final: 0.7275 (t) REVERT: K 178 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8627 (t0) REVERT: K 266 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7499 (t) REVERT: K 384 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8306 (pp) REVERT: K 801 ASP cc_start: 0.3949 (p0) cc_final: 0.3643 (p0) REVERT: K 880 MET cc_start: 0.5874 (mpp) cc_final: 0.5335 (mtm) REVERT: K 995 GLU cc_start: 0.5572 (tp30) cc_final: 0.5189 (tp30) REVERT: K 1033 GLN cc_start: 0.7667 (mt0) cc_final: 0.6980 (mt0) REVERT: K 1067 MET cc_start: 0.8554 (mmt) cc_final: 0.8234 (mmm) REVERT: K 1080 ARG cc_start: 0.6922 (mtm-85) cc_final: 0.6624 (tpt170) REVERT: K 1136 GLN cc_start: 0.5087 (OUTLIER) cc_final: 0.4611 (tm-30) REVERT: K 1161 TYR cc_start: 0.6681 (p90) cc_final: 0.5273 (t80) REVERT: K 1199 SER cc_start: 0.6808 (OUTLIER) cc_final: 0.6503 (p) REVERT: K 1215 TYR cc_start: 0.6737 (m-80) cc_final: 0.6281 (m-10) REVERT: K 1275 PHE cc_start: 0.7005 (m-10) cc_final: 0.6714 (m-10) REVERT: K 1369 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7204 (p) REVERT: N 1 MET cc_start: 0.6502 (mmm) cc_final: 0.5898 (ptm) REVERT: N 22 LEU cc_start: 0.7526 (mp) cc_final: 0.7198 (tp) REVERT: N 138 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7047 (mt) REVERT: N 178 ASN cc_start: 0.7027 (t0) cc_final: 0.6548 (t0) REVERT: N 290 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8403 (mt) REVERT: N 405 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6606 (t80) REVERT: N 466 THR cc_start: 0.7047 (p) cc_final: 0.6783 (m) REVERT: N 546 TYR cc_start: 0.6141 (m-80) cc_final: 0.5843 (m-10) REVERT: N 813 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5161 (m-80) REVERT: N 867 ASP cc_start: 0.5779 (OUTLIER) cc_final: 0.4942 (m-30) REVERT: N 928 LEU cc_start: 0.5837 (pt) cc_final: 0.5025 (pp) REVERT: N 1044 MET cc_start: 0.7915 (mpp) cc_final: 0.7642 (mtm) REVERT: N 1077 ARG cc_start: 0.3468 (OUTLIER) cc_final: 0.3247 (ptt180) REVERT: N 1329 GLN cc_start: 0.6410 (tm-30) cc_final: 0.6074 (tm-30) REVERT: N 1345 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5533 (mt-10) REVERT: O 47 GLU cc_start: 0.2905 (OUTLIER) cc_final: 0.0639 (tt0) REVERT: O 101 THR cc_start: 0.8019 (t) cc_final: 0.7725 (t) REVERT: O 158 VAL cc_start: 0.8016 (m) cc_final: 0.7795 (p) REVERT: O 197 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7773 (mm) REVERT: O 267 TYR cc_start: 0.5559 (m-80) cc_final: 0.5272 (m-80) REVERT: O 352 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8144 (tt) REVERT: O 426 MET cc_start: 0.7493 (ttm) cc_final: 0.7035 (mtm) REVERT: O 452 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7140 (tt) REVERT: O 546 TYR cc_start: 0.7013 (m-80) cc_final: 0.6414 (m-80) REVERT: O 570 ASN cc_start: 0.6667 (m-40) cc_final: 0.6412 (m-40) REVERT: O 573 THR cc_start: 0.8330 (p) cc_final: 0.7766 (m) REVERT: O 1174 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6442 (pp) REVERT: O 1288 TYR cc_start: 0.6774 (m-80) cc_final: 0.5162 (p90) REVERT: P 37 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6650 (t80) REVERT: P 95 PHE cc_start: 0.4413 (OUTLIER) cc_final: 0.3036 (m-80) REVERT: P 281 ILE cc_start: 0.8894 (pt) cc_final: 0.8618 (mt) REVERT: P 401 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6229 (mtm) REVERT: P 594 LEU cc_start: 0.5072 (tt) cc_final: 0.4548 (tp) REVERT: P 952 MET cc_start: 0.6752 (tpp) cc_final: 0.5881 (tpp) REVERT: P 1025 MET cc_start: 0.5860 (mpp) cc_final: 0.4875 (mpp) REVERT: P 1026 SER cc_start: 0.5873 (m) cc_final: 0.5336 (p) REVERT: P 1178 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: P 1268 TYR cc_start: 0.7345 (t80) cc_final: 0.7095 (t80) REVERT: P 1294 TYR cc_start: 0.7818 (t80) cc_final: 0.7465 (t80) REVERT: x 41 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6977 (tt) REVERT: x 101 MET cc_start: 0.4447 (mtt) cc_final: 0.4112 (mtt) REVERT: Z 60 TYR cc_start: 0.6264 (t80) cc_final: 0.5607 (t80) REVERT: Z 76 LYS cc_start: 0.6880 (tptt) cc_final: 0.6012 (mmtt) REVERT: a 1 MET cc_start: 0.3316 (OUTLIER) cc_final: 0.2787 (ptm) REVERT: a 59 GLU cc_start: 0.4485 (tt0) cc_final: 0.4255 (tt0) REVERT: d 40 PHE cc_start: 0.2394 (OUTLIER) cc_final: 0.2126 (t80) REVERT: d 48 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7354 (mt) REVERT: d 75 ASP cc_start: 0.5901 (p0) cc_final: 0.4960 (m-30) REVERT: e 40 PHE cc_start: 0.5537 (OUTLIER) cc_final: 0.5244 (t80) REVERT: f 335 ARG cc_start: 0.4181 (OUTLIER) cc_final: 0.3955 (ptp-170) REVERT: h 134 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7696 (tp) REVERT: h 154 MET cc_start: 0.5786 (tpp) cc_final: 0.5437 (tpp) REVERT: h 237 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6271 (tm) REVERT: k 75 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.6728 (p) REVERT: k 212 MET cc_start: 0.3307 (mmt) cc_final: 0.2865 (mmt) REVERT: k 245 ASP cc_start: 0.4912 (OUTLIER) cc_final: 0.4413 (t70) REVERT: m 145 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6642 (tt0) REVERT: m 252 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4803 (pp) REVERT: m 267 MET cc_start: 0.7961 (mmm) cc_final: 0.6728 (ttm) REVERT: p 150 ILE cc_start: 0.8322 (tt) cc_final: 0.8083 (tp) REVERT: p 174 MET cc_start: 0.5695 (ppp) cc_final: 0.5455 (ptp) REVERT: p 201 LEU cc_start: 0.4640 (tt) cc_final: 0.4345 (tt) REVERT: r 161 MET cc_start: 0.6103 (mtt) cc_final: 0.5649 (mtm) REVERT: r 169 MET cc_start: 0.5035 (mmp) cc_final: 0.4697 (mmm) outliers start: 500 outliers final: 275 residues processed: 2179 average time/residue: 0.6794 time to fit residues: 2579.8222 Evaluate side-chains 1911 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1600 time to evaluate : 6.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain J residue 401 MET Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 516 THR Chi-restraints excluded: chain J residue 596 HIS Chi-restraints excluded: chain J residue 641 SER Chi-restraints excluded: chain J residue 710 SER Chi-restraints excluded: chain J residue 716 CYS Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 919 THR Chi-restraints excluded: chain J residue 925 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 1011 SER Chi-restraints excluded: chain J residue 1088 VAL Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1115 THR Chi-restraints excluded: chain J residue 1156 ARG Chi-restraints excluded: chain J residue 1161 TYR Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1287 LEU Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain J residue 1369 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 ASN Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 266 THR Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 580 PHE Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 757 LEU Chi-restraints excluded: chain K residue 763 ILE Chi-restraints excluded: chain K residue 788 HIS Chi-restraints excluded: chain K residue 790 HIS Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 828 LEU Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 868 LEU Chi-restraints excluded: chain K residue 910 LEU Chi-restraints excluded: chain K residue 1014 SER Chi-restraints excluded: chain K residue 1022 HIS Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1088 VAL Chi-restraints excluded: chain K residue 1095 ILE Chi-restraints excluded: chain K residue 1136 GLN Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1187 THR Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1349 VAL Chi-restraints excluded: chain K residue 1350 LYS Chi-restraints excluded: chain K residue 1353 HIS Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1369 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 218 MET Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 313 VAL Chi-restraints excluded: chain N residue 319 VAL Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 420 THR Chi-restraints excluded: chain N residue 421 SER Chi-restraints excluded: chain N residue 452 LEU Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 495 ASN Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 548 ILE Chi-restraints excluded: chain N residue 609 THR Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 675 ILE Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 802 GLU Chi-restraints excluded: chain N residue 813 TYR Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 919 THR Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 1045 THR Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1077 ARG Chi-restraints excluded: chain N residue 1099 LEU Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1181 THR Chi-restraints excluded: chain N residue 1182 CYS Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1274 PHE Chi-restraints excluded: chain N residue 1313 VAL Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain N residue 1343 ILE Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 236 MET Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 302 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 398 ASN Chi-restraints excluded: chain O residue 443 LYS Chi-restraints excluded: chain O residue 452 LEU Chi-restraints excluded: chain O residue 497 MET Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 516 THR Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 598 VAL Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 971 VAL Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1095 ILE Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1236 TYR Chi-restraints excluded: chain O residue 1239 THR Chi-restraints excluded: chain O residue 1325 CYS Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain O residue 1374 LYS Chi-restraints excluded: chain O residue 1379 VAL Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 143 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 401 MET Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 486 THR Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 660 PHE Chi-restraints excluded: chain P residue 718 LEU Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 835 VAL Chi-restraints excluded: chain P residue 838 THR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 929 VAL Chi-restraints excluded: chain P residue 1088 VAL Chi-restraints excluded: chain P residue 1178 GLN Chi-restraints excluded: chain P residue 1187 THR Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 78 THR Chi-restraints excluded: chain v residue 100 LEU Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 284 LEU Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 41 LEU Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain d residue 40 PHE Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 PHE Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 225 VAL Chi-restraints excluded: chain f residue 265 TYR Chi-restraints excluded: chain f residue 279 PHE Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 326 THR Chi-restraints excluded: chain f residue 335 ARG Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain h residue 46 HIS Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain h residue 134 LEU Chi-restraints excluded: chain h residue 151 LEU Chi-restraints excluded: chain h residue 165 LEU Chi-restraints excluded: chain h residue 223 VAL Chi-restraints excluded: chain h residue 224 THR Chi-restraints excluded: chain h residue 237 LEU Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 331 ASP Chi-restraints excluded: chain h residue 363 ILE Chi-restraints excluded: chain k residue 14 TYR Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 138 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 170 LEU Chi-restraints excluded: chain k residue 245 ASP Chi-restraints excluded: chain k residue 257 VAL Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 54 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 147 LEU Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 210 CYS Chi-restraints excluded: chain m residue 221 MET Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 179 VAL Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 238 LEU Chi-restraints excluded: chain p residue 249 ARG Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 284 LEU Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain r residue 81 ILE Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 273 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 836 optimal weight: 9.9990 chunk 636 optimal weight: 4.9990 chunk 439 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 404 optimal weight: 10.0000 chunk 568 optimal weight: 20.0000 chunk 850 optimal weight: 9.9990 chunk 899 optimal weight: 5.9990 chunk 444 optimal weight: 8.9990 chunk 805 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 285 ASN J 445 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 HIS J 596 HIS ** J 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 862 ASN ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1122 GLN J1292 ASN K 94 GLN K 126 HIS K 392 GLN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 570 ASN K 600 GLN K 788 HIS K 951 HIS ** K1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1151 ASN K1169 ASN N 385 GLN N 402 GLN N 496 HIS N 587 GLN ** N 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 669 HIS N 761 GLN N 834 HIS N 974 ASN N1090 HIS N1178 GLN ** N1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN O 123 HIS O 125 HIS O 377 HIS O 398 ASN ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 695 GLN O 837 GLN O 859 ASN ** O 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1283 ASN O1289 ASN O1296 GLN ** P 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 926 ASN P 942 GLN P 964 HIS P1217 GLN ** P1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1353 HIS ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 461 HIS ** v 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 208 HIS k 62 ASN ** k 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 38 GLN m 185 HIS p 23 GLN p 173 HIS r 23 GLN r 104 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.7919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 75983 Z= 0.365 Angle : 0.810 15.859 103244 Z= 0.419 Chirality : 0.049 0.339 11614 Planarity : 0.006 0.107 13471 Dihedral : 6.174 64.869 10423 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 7.63 % Allowed : 21.79 % Favored : 70.57 % Cbeta Deviations : 0.01 % 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: -1.53 (0.08), residues: 9356 helix: -0.21 (0.08), residues: 3476 sheet: -0.51 (0.14), residues: 1301 loop : -1.81 (0.09), residues: 4579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP v 362 HIS 0.064 0.002 HIS K1353 PHE 0.044 0.002 PHE N 506 TYR 0.032 0.002 TYR v 427 ARG 0.012 0.001 ARG Z 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2424 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 616 poor density : 1808 time to evaluate : 6.556 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: J 38 ASP cc_start: 0.7339 (t0) cc_final: 0.7006 (t0) REVERT: J 393 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.7186 (m) REVERT: J 497 MET cc_start: 0.6878 (tmm) cc_final: 0.6505 (tpp) REVERT: J 567 MET cc_start: 0.6213 (mmt) cc_final: 0.5951 (mmt) REVERT: J 629 PHE cc_start: 0.7308 (t80) cc_final: 0.7087 (t80) REVERT: J 641 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7695 (m) REVERT: J 825 MET cc_start: 0.6335 (mmt) cc_final: 0.6090 (mmt) REVERT: J 874 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8164 (mp) REVERT: J 1021 MET cc_start: 0.8133 (mtt) cc_final: 0.7924 (mtt) REVERT: J 1059 PHE cc_start: 0.8968 (t80) cc_final: 0.8576 (t80) REVERT: J 1257 SER cc_start: 0.8560 (m) cc_final: 0.8333 (m) REVERT: J 1271 CYS cc_start: 0.7318 (m) cc_final: 0.6680 (m) REVERT: K 1 MET cc_start: 0.1877 (mtt) cc_final: 0.0831 (mtm) REVERT: K 90 ASP cc_start: 0.7280 (m-30) cc_final: 0.7005 (m-30) REVERT: K 104 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6340 (p90) REVERT: K 163 SER cc_start: 0.7834 (p) cc_final: 0.7133 (t) REVERT: K 384 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8479 (pp) REVERT: K 429 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7678 (t0) REVERT: K 611 TYR cc_start: 0.7863 (m-10) cc_final: 0.7568 (m-10) REVERT: K 790 HIS cc_start: 0.6737 (t-90) cc_final: 0.6474 (t-90) REVERT: K 801 ASP cc_start: 0.4712 (p0) cc_final: 0.4379 (p0) REVERT: K 825 MET cc_start: 0.7380 (mtm) cc_final: 0.7063 (mtm) REVERT: K 839 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7263 (mp) REVERT: K 864 THR cc_start: 0.7718 (p) cc_final: 0.7441 (p) REVERT: K 880 MET cc_start: 0.5914 (mpp) cc_final: 0.5698 (mtt) REVERT: K 1199 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7063 (p) REVERT: K 1231 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7789 (p0) REVERT: N 28 SER cc_start: 0.8465 (m) cc_final: 0.7989 (t) REVERT: N 50 ILE cc_start: 0.8851 (tp) cc_final: 0.8528 (pt) REVERT: N 134 SER cc_start: 0.7306 (t) cc_final: 0.6955 (m) REVERT: N 224 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8349 (tt) REVERT: N 290 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8872 (mp) REVERT: N 405 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6891 (t80) REVERT: N 507 TYR cc_start: 0.7999 (m-80) cc_final: 0.7577 (m-80) REVERT: N 747 ILE cc_start: 0.7446 (mp) cc_final: 0.6887 (mp) REVERT: N 769 MET cc_start: 0.4689 (ttt) cc_final: 0.4233 (ttt) REVERT: N 867 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5006 (m-30) REVERT: N 889 MET cc_start: 0.7057 (mmm) cc_final: 0.6212 (mtp) REVERT: N 910 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8192 (mt) REVERT: N 928 LEU cc_start: 0.6738 (pt) cc_final: 0.6405 (pp) REVERT: N 1021 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6373 (ttt) REVERT: N 1124 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7347 (t80) REVERT: O 47 GLU cc_start: 0.2849 (OUTLIER) cc_final: 0.0179 (tt0) REVERT: O 185 LEU cc_start: 0.8380 (tp) cc_final: 0.8123 (tp) REVERT: O 223 LEU cc_start: 0.8292 (tt) cc_final: 0.7999 (tp) REVERT: O 334 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: O 426 MET cc_start: 0.7783 (ttm) cc_final: 0.7457 (mtm) REVERT: O 443 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8404 (tttp) REVERT: O 546 TYR cc_start: 0.7416 (m-80) cc_final: 0.7137 (m-80) REVERT: O 573 THR cc_start: 0.8674 (p) cc_final: 0.8006 (m) REVERT: O 592 THR cc_start: 0.8330 (t) cc_final: 0.8101 (t) REVERT: O 859 ASN cc_start: 0.7270 (m-40) cc_final: 0.6901 (m-40) REVERT: O 972 MET cc_start: 0.6253 (tmm) cc_final: 0.5999 (tmm) REVERT: O 1174 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7411 (pp) REVERT: O 1239 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8360 (m) REVERT: O 1269 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8287 (p) REVERT: O 1375 PHE cc_start: 0.7066 (t80) cc_final: 0.6834 (t80) REVERT: P 37 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6703 (t80) REVERT: P 95 PHE cc_start: 0.4718 (OUTLIER) cc_final: 0.2784 (m-80) REVERT: P 112 LYS cc_start: 0.3253 (OUTLIER) cc_final: 0.2352 (tppt) REVERT: P 698 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5992 (mmm) REVERT: P 951 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.6137 (t-90) REVERT: P 1358 TYR cc_start: 0.6152 (t80) cc_final: 0.5814 (t80) REVERT: v 365 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7426 (mm-40) REVERT: w 74 MET cc_start: 0.5349 (tmm) cc_final: 0.4693 (tmm) REVERT: x 101 MET cc_start: 0.4497 (mtt) cc_final: 0.4137 (mtt) REVERT: Z 60 TYR cc_start: 0.6518 (t80) cc_final: 0.6311 (t80) REVERT: Z 76 LYS cc_start: 0.6808 (tptt) cc_final: 0.5795 (mmtt) REVERT: d 14 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6944 (tp) REVERT: d 40 PHE cc_start: 0.2767 (OUTLIER) cc_final: 0.2121 (t80) REVERT: d 75 ASP cc_start: 0.6060 (p0) cc_final: 0.4930 (m-30) REVERT: e 24 LEU cc_start: 0.6356 (tt) cc_final: 0.6154 (tt) REVERT: e 40 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.5522 (t80) REVERT: u 9 THR cc_start: 0.6085 (m) cc_final: 0.5741 (p) REVERT: f 1 MET cc_start: 0.4632 (ttm) cc_final: 0.4270 (ttm) REVERT: f 201 ASN cc_start: 0.3041 (m110) cc_final: 0.2583 (m-40) REVERT: h 151 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7849 (tt) REVERT: h 302 MET cc_start: 0.8270 (tpp) cc_final: 0.7224 (mtt) REVERT: h 311 LEU cc_start: 0.3620 (OUTLIER) cc_final: 0.3315 (pp) REVERT: k 245 ASP cc_start: 0.5449 (OUTLIER) cc_final: 0.5086 (t70) REVERT: m 145 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6892 (tt0) REVERT: m 149 LYS cc_start: 0.8244 (mmmt) cc_final: 0.8007 (mmmt) REVERT: m 182 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3956 (pp) REVERT: m 267 MET cc_start: 0.8158 (mmm) cc_final: 0.7709 (tpp) REVERT: p 150 ILE cc_start: 0.8244 (tt) cc_final: 0.8016 (tp) REVERT: p 169 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6541 (mmm) REVERT: p 229 ARG cc_start: 0.6050 (ttp-170) cc_final: 0.5815 (ttp-170) REVERT: r 60 MET cc_start: 0.7463 (mtp) cc_final: 0.7261 (mtp) REVERT: r 68 THR cc_start: 0.8217 (p) cc_final: 0.7997 (p) REVERT: r 161 MET cc_start: 0.5963 (mtt) cc_final: 0.5649 (mtm) REVERT: r 169 MET cc_start: 0.5602 (mmp) cc_final: 0.5182 (mmm) REVERT: r 208 TYR cc_start: 0.7946 (m-10) cc_final: 0.7709 (m-10) REVERT: r 211 ILE cc_start: 0.7976 (mm) cc_final: 0.7622 (mt) REVERT: r 239 PHE cc_start: 0.7421 (m-80) cc_final: 0.7210 (m-80) outliers start: 616 outliers final: 359 residues processed: 2208 average time/residue: 0.6861 time to fit residues: 2638.1950 Evaluate side-chains 1920 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 1525 time to evaluate : 6.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 CYS Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain J residue 401 MET Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 516 THR Chi-restraints excluded: chain J residue 613 THR Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 641 SER Chi-restraints excluded: chain J residue 710 SER Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 919 THR Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1011 SER Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1047 VAL Chi-restraints excluded: chain J residue 1065 THR Chi-restraints excluded: chain J residue 1075 SER Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1115 THR Chi-restraints excluded: chain J residue 1143 LYS Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1210 VAL Chi-restraints excluded: chain J residue 1287 LEU Chi-restraints excluded: chain J residue 1304 THR Chi-restraints excluded: chain J residue 1308 GLU Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 429 ASN Chi-restraints excluded: chain K residue 491 HIS Chi-restraints excluded: chain K residue 580 PHE Chi-restraints excluded: chain K residue 598 VAL Chi-restraints excluded: chain K residue 621 VAL Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 693 LEU Chi-restraints excluded: chain K residue 709 GLU Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 747 ILE Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 828 LEU Chi-restraints excluded: chain K residue 835 VAL Chi-restraints excluded: chain K residue 838 THR Chi-restraints excluded: chain K residue 839 LEU Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 910 LEU Chi-restraints excluded: chain K residue 1014 SER Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1084 VAL Chi-restraints excluded: chain K residue 1088 VAL Chi-restraints excluded: chain K residue 1095 ILE Chi-restraints excluded: chain K residue 1106 THR Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1121 THR Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1186 VAL Chi-restraints excluded: chain K residue 1187 THR Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1210 VAL Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1231 ASP Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1342 LEU Chi-restraints excluded: chain K residue 1349 VAL Chi-restraints excluded: chain K residue 1350 LYS Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 135 MET Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 218 MET Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 319 VAL Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 355 VAL Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 460 CYS Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 495 ASN Chi-restraints excluded: chain N residue 515 VAL Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 548 ILE Chi-restraints excluded: chain N residue 568 VAL Chi-restraints excluded: chain N residue 609 THR Chi-restraints excluded: chain N residue 621 VAL Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 732 ILE Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 757 LEU Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 893 THR Chi-restraints excluded: chain N residue 910 LEU Chi-restraints excluded: chain N residue 919 THR Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 1021 MET Chi-restraints excluded: chain N residue 1045 THR Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1124 PHE Chi-restraints excluded: chain N residue 1175 CYS Chi-restraints excluded: chain N residue 1181 THR Chi-restraints excluded: chain N residue 1182 CYS Chi-restraints excluded: chain N residue 1210 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1295 SER Chi-restraints excluded: chain N residue 1319 VAL Chi-restraints excluded: chain N residue 1320 PHE Chi-restraints excluded: chain N residue 1321 LEU Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 52 PHE Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 292 THR Chi-restraints excluded: chain O residue 302 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 334 PHE Chi-restraints excluded: chain O residue 340 ASP Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 424 ILE Chi-restraints excluded: chain O residue 443 LYS Chi-restraints excluded: chain O residue 497 MET Chi-restraints excluded: chain O residue 501 VAL Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 665 PHE Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 794 LEU Chi-restraints excluded: chain O residue 807 VAL Chi-restraints excluded: chain O residue 856 ILE Chi-restraints excluded: chain O residue 864 THR Chi-restraints excluded: chain O residue 898 VAL Chi-restraints excluded: chain O residue 906 VAL Chi-restraints excluded: chain O residue 928 LEU Chi-restraints excluded: chain O residue 938 ARG Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1044 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1181 THR Chi-restraints excluded: chain O residue 1224 ILE Chi-restraints excluded: chain O residue 1239 THR Chi-restraints excluded: chain O residue 1247 LEU Chi-restraints excluded: chain O residue 1253 ILE Chi-restraints excluded: chain O residue 1269 SER Chi-restraints excluded: chain O residue 1293 GLU Chi-restraints excluded: chain O residue 1321 LEU Chi-restraints excluded: chain O residue 1325 CYS Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain O residue 1345 GLU Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 143 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 436 VAL Chi-restraints excluded: chain P residue 447 LEU Chi-restraints excluded: chain P residue 486 THR Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 605 THR Chi-restraints excluded: chain P residue 621 VAL Chi-restraints excluded: chain P residue 698 MET Chi-restraints excluded: chain P residue 700 LEU Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 735 HIS Chi-restraints excluded: chain P residue 741 ASP Chi-restraints excluded: chain P residue 756 THR Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 832 PHE Chi-restraints excluded: chain P residue 835 VAL Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 900 VAL Chi-restraints excluded: chain P residue 951 HIS Chi-restraints excluded: chain P residue 1019 THR Chi-restraints excluded: chain P residue 1028 MET Chi-restraints excluded: chain P residue 1088 VAL Chi-restraints excluded: chain P residue 1106 THR Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1192 ASP Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1291 VAL Chi-restraints excluded: chain P residue 1319 VAL Chi-restraints excluded: chain P residue 1328 LEU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 78 THR Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 284 LEU Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 365 GLN Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 456 LEU Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 41 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 57 CYS Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3126 LEU Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain d residue 40 PHE Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 PHE Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 165 LEU Chi-restraints excluded: chain f residue 205 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 265 TYR Chi-restraints excluded: chain f residue 279 PHE Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 326 THR Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain h residue 38 ASP Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain h residue 125 VAL Chi-restraints excluded: chain h residue 151 LEU Chi-restraints excluded: chain h residue 165 LEU Chi-restraints excluded: chain h residue 223 VAL Chi-restraints excluded: chain h residue 224 THR Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 352 SER Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 138 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 169 MET Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 215 LEU Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain k residue 245 ASP Chi-restraints excluded: chain k residue 257 VAL Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 210 CYS Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 221 MET Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain m residue 286 THR Chi-restraints excluded: chain m residue 298 CYS Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 169 MET Chi-restraints excluded: chain p residue 202 LEU Chi-restraints excluded: chain p residue 238 LEU Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 260 ASP Chi-restraints excluded: chain p residue 284 LEU Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 76 SER Chi-restraints excluded: chain r residue 81 ILE Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 224 VAL Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 255 LEU Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 273 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 749 optimal weight: 5.9990 chunk 510 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 670 optimal weight: 0.9990 chunk 371 optimal weight: 2.9990 chunk 767 optimal weight: 6.9990 chunk 622 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 459 optimal weight: 0.8980 chunk 807 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 187 HIS J 445 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 795 HIS ** J 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 964 HIS J1360 HIS K 35 HIS K 222 HIS ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 735 HIS K 788 HIS K1122 GLN K1137 GLN ** K1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 HIS N 402 GLN ** N 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 495 ASN ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1149 GLN N1217 GLN ** N1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1276 ASN N1306 ASN O 301 GLN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 398 ASN O 454 ASN ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 695 GLN O 837 GLN O 964 HIS ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1139 ASN ** O1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1283 ASN O1284 ASN O1296 GLN ** P 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 289 GLN P 402 GLN ** P 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 788 HIS P 942 GLN P1122 GLN ** P1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1360 HIS ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 461 HIS ** v 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS y3135 HIS ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 GLN h 201 ASN k 102 GLN k 175 HIS k 233 HIS ** m 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 185 HIS p 23 GLN r 47 GLN r 154 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.8408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 75983 Z= 0.204 Angle : 0.700 14.348 103244 Z= 0.349 Chirality : 0.045 0.234 11614 Planarity : 0.005 0.085 13471 Dihedral : 5.657 59.799 10413 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 4.73 % Allowed : 25.81 % Favored : 69.46 % 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: -1.21 (0.08), residues: 9356 helix: 0.12 (0.09), residues: 3510 sheet: -0.48 (0.14), residues: 1328 loop : -1.65 (0.09), residues: 4518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP v 362 HIS 0.013 0.001 HIS O 377 PHE 0.037 0.002 PHE u 50 TYR 0.029 0.002 TYR P1255 ARG 0.013 0.001 ARG p 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2079 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1697 time to evaluate : 6.485 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: J 38 ASP cc_start: 0.7365 (t0) cc_final: 0.7009 (t0) REVERT: J 193 ILE cc_start: 0.8800 (mm) cc_final: 0.8479 (mt) REVERT: J 497 MET cc_start: 0.6760 (tmm) cc_final: 0.6293 (tpp) REVERT: J 620 TYR cc_start: 0.7561 (m-80) cc_final: 0.7277 (m-80) REVERT: J 825 MET cc_start: 0.6319 (mmt) cc_final: 0.5733 (mmm) REVERT: J 928 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6000 (pp) REVERT: J 1021 MET cc_start: 0.8235 (mtt) cc_final: 0.7901 (mtt) REVERT: J 1049 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8817 (p) REVERT: J 1235 GLU cc_start: 0.6301 (tt0) cc_final: 0.6096 (tt0) REVERT: J 1241 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7418 (t0) REVERT: J 1271 CYS cc_start: 0.7591 (m) cc_final: 0.7217 (m) REVERT: K 1 MET cc_start: 0.1618 (mtt) cc_final: 0.0684 (mtm) REVERT: K 163 SER cc_start: 0.7823 (p) cc_final: 0.7182 (t) REVERT: K 343 GLU cc_start: 0.6659 (pm20) cc_final: 0.6159 (pm20) REVERT: K 384 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8148 (pp) REVERT: K 473 SER cc_start: 0.7778 (p) cc_final: 0.7569 (m) REVERT: K 796 LEU cc_start: 0.7464 (mp) cc_final: 0.7207 (mp) REVERT: K 913 ASN cc_start: 0.8432 (t0) cc_final: 0.7888 (t0) REVERT: K 942 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6561 (pp30) REVERT: K 1084 VAL cc_start: 0.8761 (t) cc_final: 0.8461 (m) REVERT: K 1347 MET cc_start: 0.8013 (mtm) cc_final: 0.7304 (mtm) REVERT: K 1348 SER cc_start: 0.8440 (p) cc_final: 0.8154 (m) REVERT: N 28 SER cc_start: 0.8450 (m) cc_final: 0.7729 (t) REVERT: N 84 ASP cc_start: 0.7465 (p0) cc_final: 0.7080 (p0) REVERT: N 134 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6533 (m) REVERT: N 135 MET cc_start: 0.8181 (mpp) cc_final: 0.7980 (pmm) REVERT: N 224 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8219 (tt) REVERT: N 236 MET cc_start: 0.6084 (mmm) cc_final: 0.5260 (tmm) REVERT: N 290 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8798 (mp) REVERT: N 405 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6827 (t80) REVERT: N 485 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: N 532 PRO cc_start: 0.8834 (Cg_exo) cc_final: 0.8583 (Cg_endo) REVERT: N 547 ASP cc_start: 0.7260 (t0) cc_final: 0.7050 (t0) REVERT: N 747 ILE cc_start: 0.7379 (mp) cc_final: 0.6335 (mp) REVERT: N 769 MET cc_start: 0.4431 (ttt) cc_final: 0.3962 (ttt) REVERT: N 867 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5065 (m-30) REVERT: N 893 THR cc_start: 0.7917 (p) cc_final: 0.7686 (p) REVERT: N 910 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8361 (mt) REVERT: N 928 LEU cc_start: 0.6870 (pt) cc_final: 0.6482 (pp) REVERT: O 47 GLU cc_start: 0.2497 (OUTLIER) cc_final: -0.0150 (tt0) REVERT: O 387 MET cc_start: 0.7626 (ppp) cc_final: 0.7174 (ppp) REVERT: O 401 MET cc_start: 0.7408 (tpp) cc_final: 0.7171 (tpt) REVERT: O 413 MET cc_start: 0.7521 (mmm) cc_final: 0.7225 (mmt) REVERT: O 420 THR cc_start: 0.7562 (p) cc_final: 0.7294 (p) REVERT: O 426 MET cc_start: 0.7580 (ttm) cc_final: 0.7378 (mtm) REVERT: O 443 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8389 (tttp) REVERT: O 546 TYR cc_start: 0.7429 (m-80) cc_final: 0.7017 (m-80) REVERT: O 573 THR cc_start: 0.8640 (p) cc_final: 0.7926 (m) REVERT: O 594 LEU cc_start: 0.7604 (tt) cc_final: 0.7044 (tp) REVERT: O 698 MET cc_start: 0.5477 (ptt) cc_final: 0.5255 (ptt) REVERT: O 956 ASP cc_start: 0.6213 (t0) cc_final: 0.5548 (t0) REVERT: O 981 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: O 1174 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7181 (pp) REVERT: O 1253 ILE cc_start: 0.8598 (tt) cc_final: 0.8306 (tt) REVERT: O 1375 PHE cc_start: 0.6929 (t80) cc_final: 0.6523 (t80) REVERT: P 37 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6784 (t80) REVERT: P 95 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.2683 (m-80) REVERT: P 112 LYS cc_start: 0.3042 (OUTLIER) cc_final: 0.1694 (mttp) REVERT: P 958 ARG cc_start: 0.6278 (mtm-85) cc_final: 0.6073 (mpt90) REVERT: P 1044 MET cc_start: 0.7335 (mtm) cc_final: 0.7095 (mtm) REVERT: P 1105 MET cc_start: 0.7654 (mtp) cc_final: 0.7447 (mtp) REVERT: P 1347 MET cc_start: 0.6929 (mmm) cc_final: 0.6402 (mtp) REVERT: v 103 TYR cc_start: 0.3149 (OUTLIER) cc_final: 0.2509 (p90) REVERT: v 468 THR cc_start: 0.6089 (t) cc_final: 0.5790 (t) REVERT: w 74 MET cc_start: 0.5415 (tmm) cc_final: 0.4789 (tmm) REVERT: x 101 MET cc_start: 0.4388 (mtt) cc_final: 0.4001 (mtt) REVERT: Z 76 LYS cc_start: 0.6639 (tptt) cc_final: 0.5870 (mmtt) REVERT: d 75 ASP cc_start: 0.5370 (p0) cc_final: 0.4828 (m-30) REVERT: u 9 THR cc_start: 0.6264 (m) cc_final: 0.5812 (p) REVERT: f 201 ASN cc_start: 0.2731 (m110) cc_final: 0.2513 (m-40) REVERT: f 277 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.5222 (p90) REVERT: h 302 MET cc_start: 0.8246 (tpp) cc_final: 0.7508 (mtt) REVERT: h 311 LEU cc_start: 0.3466 (OUTLIER) cc_final: 0.3210 (pp) REVERT: m 96 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7371 (tptp) REVERT: m 159 VAL cc_start: 0.7936 (t) cc_final: 0.7683 (p) REVERT: m 182 LEU cc_start: 0.4193 (OUTLIER) cc_final: 0.3901 (pp) REVERT: m 252 LEU cc_start: 0.4750 (OUTLIER) cc_final: 0.4073 (pp) REVERT: m 267 MET cc_start: 0.8019 (mmm) cc_final: 0.7372 (tpp) REVERT: p 38 GLN cc_start: 0.4704 (mm110) cc_final: 0.4296 (pt0) REVERT: p 242 MET cc_start: 0.5304 (ttp) cc_final: 0.5094 (ttp) REVERT: p 291 GLN cc_start: 0.5782 (pm20) cc_final: 0.4863 (tt0) REVERT: r 60 MET cc_start: 0.7384 (mtp) cc_final: 0.7140 (mtp) REVERT: r 169 MET cc_start: 0.5403 (mmp) cc_final: 0.5154 (mmm) REVERT: r 208 TYR cc_start: 0.7847 (m-10) cc_final: 0.7530 (m-10) outliers start: 382 outliers final: 239 residues processed: 1947 average time/residue: 0.6626 time to fit residues: 2261.0378 Evaluate side-chains 1780 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1516 time to evaluate : 6.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1011 SER Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1049 THR Chi-restraints excluded: chain J residue 1058 LEU Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1115 THR Chi-restraints excluded: chain J residue 1143 LYS Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1241 ASN Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 491 HIS Chi-restraints excluded: chain K residue 580 PHE Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 706 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 763 ILE Chi-restraints excluded: chain K residue 789 ASP Chi-restraints excluded: chain K residue 828 LEU Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 868 LEU Chi-restraints excluded: chain K residue 910 LEU Chi-restraints excluded: chain K residue 942 GLN Chi-restraints excluded: chain K residue 1014 SER Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1092 MET Chi-restraints excluded: chain K residue 1095 ILE Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1121 THR Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1219 VAL Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 65 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 495 ASN Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 609 THR Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 654 LEU Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 757 LEU Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 910 LEU Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 1045 THR Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1210 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1320 PHE Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 284 ASP Chi-restraints excluded: chain O residue 302 ILE Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 443 LYS Chi-restraints excluded: chain O residue 497 MET Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 568 VAL Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 898 VAL Chi-restraints excluded: chain O residue 981 GLU Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1044 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1183 GLU Chi-restraints excluded: chain O residue 1247 LEU Chi-restraints excluded: chain O residue 1283 ASN Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 502 ILE Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 944 LEU Chi-restraints excluded: chain P residue 1019 THR Chi-restraints excluded: chain P residue 1033 GLN Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1192 ASP Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1296 GLN Chi-restraints excluded: chain P residue 1328 LEU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 35 ARG Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 284 LEU Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 57 CYS Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3126 LEU Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 PHE Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 265 TYR Chi-restraints excluded: chain f residue 277 PHE Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 313 ILE Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 GLN Chi-restraints excluded: chain h residue 125 VAL Chi-restraints excluded: chain h residue 165 LEU Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 295 ILE Chi-restraints excluded: chain h residue 298 SER Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 138 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 175 HIS Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 96 LYS Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 245 ASP Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 175 HIS Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 245 ASP Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 64 LEU Chi-restraints excluded: chain r residue 81 ILE Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 238 LEU Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 293 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 302 optimal weight: 20.0000 chunk 810 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 528 optimal weight: 10.0000 chunk 222 optimal weight: 40.0000 chunk 900 optimal weight: 7.9990 chunk 747 optimal weight: 30.0000 chunk 417 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 472 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 445 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 862 ASN ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 735 HIS ** K 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 ASN N 385 GLN ** N 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 GLN ** N 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 HIS ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 587 GLN O 750 ASN O 837 GLN ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 997 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1284 ASN ** P 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 946 HIS P1178 GLN ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1296 GLN ** P1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 8 GLN v 45 GLN ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 382 ASN v 461 HIS x 77 HIS y3135 HIS ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 GLN m 185 HIS p 95 ASN ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 47 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.9517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 75983 Z= 0.358 Angle : 0.784 15.713 103244 Z= 0.399 Chirality : 0.048 0.407 11614 Planarity : 0.006 0.089 13471 Dihedral : 5.931 59.890 10409 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.88 % Favored : 93.05 % Rotamer: Outliers : 6.63 % Allowed : 24.85 % Favored : 68.52 % 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: -1.38 (0.08), residues: 9356 helix: -0.00 (0.09), residues: 3520 sheet: -0.56 (0.14), residues: 1303 loop : -1.77 (0.09), residues: 4533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP J 996 HIS 0.065 0.002 HIS k 175 PHE 0.035 0.003 PHE J1059 TYR 0.040 0.003 TYR v 427 ARG 0.017 0.001 ARG J 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2176 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 535 poor density : 1641 time to evaluate : 6.549 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: J 43 LYS cc_start: 0.7880 (pttt) cc_final: 0.7317 (tptp) REVERT: J 193 ILE cc_start: 0.8880 (mm) cc_final: 0.8557 (mt) REVERT: J 271 LYS cc_start: 0.2696 (OUTLIER) cc_final: 0.1126 (mtmm) REVERT: J 497 MET cc_start: 0.6860 (tmm) cc_final: 0.6293 (tpp) REVERT: J 567 MET cc_start: 0.6583 (mmt) cc_final: 0.6341 (mmt) REVERT: J 637 VAL cc_start: 0.8127 (p) cc_final: 0.7740 (t) REVERT: J 697 LEU cc_start: 0.8536 (mm) cc_final: 0.8298 (mm) REVERT: J 825 MET cc_start: 0.6757 (mmt) cc_final: 0.6249 (mmm) REVERT: J 928 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6347 (pp) REVERT: J 976 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: J 1021 MET cc_start: 0.8296 (mtt) cc_final: 0.8048 (mtt) REVERT: J 1183 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: J 1235 GLU cc_start: 0.6576 (tt0) cc_final: 0.6281 (tt0) REVERT: K 1 MET cc_start: 0.1918 (mtt) cc_final: 0.1001 (mtm) REVERT: K 53 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5540 (mm-30) REVERT: K 104 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.6726 (p90) REVERT: K 163 SER cc_start: 0.8003 (p) cc_final: 0.7361 (t) REVERT: K 194 LEU cc_start: 0.8475 (tt) cc_final: 0.8133 (tp) REVERT: K 287 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (tp) REVERT: K 384 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8471 (pp) REVERT: K 473 SER cc_start: 0.8186 (p) cc_final: 0.7847 (m) REVERT: K 741 ASP cc_start: 0.6986 (m-30) cc_final: 0.6756 (m-30) REVERT: K 770 ASP cc_start: 0.6279 (t70) cc_final: 0.6076 (t70) REVERT: K 913 ASN cc_start: 0.8461 (t0) cc_final: 0.8063 (t0) REVERT: K 942 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7043 (pp30) REVERT: K 1117 MET cc_start: 0.8243 (mpp) cc_final: 0.7666 (mtp) REVERT: K 1154 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8261 (pp) REVERT: K 1199 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7460 (p) REVERT: K 1231 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7809 (p0) REVERT: K 1348 SER cc_start: 0.8423 (p) cc_final: 0.8145 (m) REVERT: N 16 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7759 (p) REVERT: N 28 SER cc_start: 0.8213 (m) cc_final: 0.7623 (t) REVERT: N 84 ASP cc_start: 0.7606 (p0) cc_final: 0.7186 (p0) REVERT: N 134 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.6548 (m) REVERT: N 224 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8550 (tt) REVERT: N 236 MET cc_start: 0.6415 (mmm) cc_final: 0.5626 (tmm) REVERT: N 299 ASP cc_start: 0.4926 (t70) cc_final: 0.4659 (t0) REVERT: N 405 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6949 (t80) REVERT: N 547 ASP cc_start: 0.7654 (t0) cc_final: 0.7376 (t0) REVERT: N 736 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8188 (tt) REVERT: N 747 ILE cc_start: 0.7849 (mp) cc_final: 0.7334 (mp) REVERT: N 867 ASP cc_start: 0.5608 (OUTLIER) cc_final: 0.4631 (m-30) REVERT: N 889 MET cc_start: 0.6790 (mmm) cc_final: 0.6080 (mmm) REVERT: N 910 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8470 (mt) REVERT: N 1074 VAL cc_start: 0.8474 (t) cc_final: 0.8270 (p) REVERT: N 1353 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7402 (t-90) REVERT: O 47 GLU cc_start: 0.2767 (OUTLIER) cc_final: 0.0021 (tt0) REVERT: O 187 HIS cc_start: 0.7056 (m-70) cc_final: 0.6822 (m-70) REVERT: O 251 MET cc_start: 0.7408 (mmm) cc_final: 0.6970 (mtt) REVERT: O 335 MET cc_start: 0.6984 (mmm) cc_final: 0.6774 (tpt) REVERT: O 546 TYR cc_start: 0.7759 (m-80) cc_final: 0.7175 (m-80) REVERT: O 594 LEU cc_start: 0.7714 (tt) cc_final: 0.7091 (tp) REVERT: O 698 MET cc_start: 0.6138 (ptt) cc_final: 0.5357 (ptt) REVERT: O 793 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7383 (mtp180) REVERT: O 956 ASP cc_start: 0.6953 (t0) cc_final: 0.6433 (t0) REVERT: O 1174 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7610 (pp) REVERT: O 1239 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8346 (m) REVERT: O 1327 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6838 (t80) REVERT: O 1361 TYR cc_start: 0.8823 (p90) cc_final: 0.8402 (p90) REVERT: P 37 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6796 (t80) REVERT: P 92 LYS cc_start: 0.7800 (mmmt) cc_final: 0.6746 (mttt) REVERT: P 95 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.2705 (m-80) REVERT: P 112 LYS cc_start: 0.3091 (OUTLIER) cc_final: 0.1682 (mttm) REVERT: P 185 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9116 (tp) REVERT: P 223 LEU cc_start: 0.8758 (tt) cc_final: 0.8506 (tt) REVERT: P 250 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7465 (mm-30) REVERT: P 723 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6048 (mm) REVERT: P 1019 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7857 (t) REVERT: P 1123 ASP cc_start: 0.7431 (t0) cc_final: 0.7210 (t0) REVERT: P 1178 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.5468 (tt0) REVERT: P 1292 ASN cc_start: 0.7554 (m-40) cc_final: 0.7346 (t0) REVERT: v 103 TYR cc_start: 0.3230 (OUTLIER) cc_final: 0.2622 (p90) REVERT: v 302 TYR cc_start: 0.5103 (t80) cc_final: 0.4684 (t80) REVERT: v 365 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7341 (mm-40) REVERT: w 74 MET cc_start: 0.5366 (tmm) cc_final: 0.4772 (tmm) REVERT: x 101 MET cc_start: 0.4391 (mtt) cc_final: 0.4112 (mtt) REVERT: Z 76 LYS cc_start: 0.6999 (tptt) cc_final: 0.6134 (mmtt) REVERT: a 3 ARG cc_start: 0.6562 (mtt180) cc_final: 0.6361 (mtt180) REVERT: d 53 SER cc_start: 0.6616 (p) cc_final: 0.6000 (p) REVERT: d 75 ASP cc_start: 0.5573 (p0) cc_final: 0.4656 (m-30) REVERT: e 1 MET cc_start: 0.4988 (tmm) cc_final: 0.4787 (tmm) REVERT: f 201 ASN cc_start: 0.2353 (m110) cc_final: 0.2139 (m-40) REVERT: h 27 LEU cc_start: 0.7382 (tt) cc_final: 0.7025 (tp) REVERT: h 115 GLN cc_start: 0.7966 (mm110) cc_final: 0.7532 (mm110) REVERT: h 212 VAL cc_start: 0.8608 (t) cc_final: 0.8383 (m) REVERT: h 302 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7549 (mtt) REVERT: k 13 LEU cc_start: 0.6749 (tt) cc_final: 0.6473 (tp) REVERT: k 161 MET cc_start: 0.4745 (tmm) cc_final: 0.4196 (tmm) REVERT: k 206 SER cc_start: 0.6501 (p) cc_final: 0.6276 (t) REVERT: k 269 THR cc_start: 0.7315 (p) cc_final: 0.6882 (m) REVERT: m 25 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7258 (mm) REVERT: m 39 ASN cc_start: 0.8724 (t0) cc_final: 0.8273 (t0) REVERT: m 96 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7015 (tptp) REVERT: m 159 VAL cc_start: 0.8453 (t) cc_final: 0.8176 (p) REVERT: m 173 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6365 (t70) REVERT: m 252 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4115 (pp) REVERT: m 255 LEU cc_start: 0.7913 (mm) cc_final: 0.7637 (mm) REVERT: m 267 MET cc_start: 0.7915 (mmm) cc_final: 0.7216 (ttm) REVERT: m 274 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6158 (tt) outliers start: 535 outliers final: 351 residues processed: 1988 average time/residue: 0.7163 time to fit residues: 2505.3734 Evaluate side-chains 1867 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1477 time to evaluate : 6.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 266 THR Chi-restraints excluded: chain J residue 271 LYS Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 VAL Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 598 VAL Chi-restraints excluded: chain J residue 613 THR Chi-restraints excluded: chain J residue 737 LEU Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 940 VAL Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 976 GLN Chi-restraints excluded: chain J residue 1011 SER Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1049 THR Chi-restraints excluded: chain J residue 1058 LEU Chi-restraints excluded: chain J residue 1075 SER Chi-restraints excluded: chain J residue 1088 VAL Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1115 THR Chi-restraints excluded: chain J residue 1143 LYS Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1183 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 167 PHE Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 404 SER Chi-restraints excluded: chain K residue 491 HIS Chi-restraints excluded: chain K residue 580 PHE Chi-restraints excluded: chain K residue 598 VAL Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 747 ILE Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 794 LEU Chi-restraints excluded: chain K residue 828 LEU Chi-restraints excluded: chain K residue 835 VAL Chi-restraints excluded: chain K residue 838 THR Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 881 ILE Chi-restraints excluded: chain K residue 922 THR Chi-restraints excluded: chain K residue 942 GLN Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1092 MET Chi-restraints excluded: chain K residue 1102 SER Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1154 LEU Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1210 VAL Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1219 VAL Chi-restraints excluded: chain K residue 1231 ASP Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1342 LEU Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 34 PHE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 65 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 319 VAL Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 355 VAL Chi-restraints excluded: chain N residue 387 MET Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 494 PRO Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 590 THR Chi-restraints excluded: chain N residue 609 THR Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 732 ILE Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 802 GLU Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 910 LEU Chi-restraints excluded: chain N residue 919 THR Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 999 SER Chi-restraints excluded: chain N residue 1031 ILE Chi-restraints excluded: chain N residue 1045 THR Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1053 LEU Chi-restraints excluded: chain N residue 1113 ILE Chi-restraints excluded: chain N residue 1114 THR Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1122 GLN Chi-restraints excluded: chain N residue 1189 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1295 SER Chi-restraints excluded: chain N residue 1320 PHE Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain N residue 1353 HIS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 180 VAL Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 284 ASP Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 362 GLN Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 424 ILE Chi-restraints excluded: chain O residue 502 ILE Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 568 VAL Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 661 SER Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 795 HIS Chi-restraints excluded: chain O residue 864 THR Chi-restraints excluded: chain O residue 898 VAL Chi-restraints excluded: chain O residue 902 VAL Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1021 MET Chi-restraints excluded: chain O residue 1044 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1074 VAL Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1224 ILE Chi-restraints excluded: chain O residue 1239 THR Chi-restraints excluded: chain O residue 1247 LEU Chi-restraints excluded: chain O residue 1325 CYS Chi-restraints excluded: chain O residue 1327 PHE Chi-restraints excluded: chain O residue 1336 SER Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain O residue 1379 VAL Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 143 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 377 HIS Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 436 VAL Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 605 THR Chi-restraints excluded: chain P residue 621 VAL Chi-restraints excluded: chain P residue 723 LEU Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 741 ASP Chi-restraints excluded: chain P residue 756 THR Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 1019 THR Chi-restraints excluded: chain P residue 1033 GLN Chi-restraints excluded: chain P residue 1088 VAL Chi-restraints excluded: chain P residue 1097 THR Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1178 GLN Chi-restraints excluded: chain P residue 1192 ASP Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1296 GLN Chi-restraints excluded: chain P residue 1319 VAL Chi-restraints excluded: chain P residue 1328 LEU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 35 ARG Chi-restraints excluded: chain v residue 78 THR Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 284 LEU Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 365 GLN Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 41 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 57 CYS Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain y residue 3119 LEU Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3126 LEU Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 31 ASN Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain d residue 74 ILE Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 17 ASP Chi-restraints excluded: chain e residue 40 PHE Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 205 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 225 VAL Chi-restraints excluded: chain f residue 230 PHE Chi-restraints excluded: chain f residue 278 THR Chi-restraints excluded: chain f residue 297 TYR Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 313 ILE Chi-restraints excluded: chain f residue 333 TRP Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain f residue 358 SER Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain h residue 125 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 197 SER Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 223 VAL Chi-restraints excluded: chain h residue 224 THR Chi-restraints excluded: chain h residue 298 SER Chi-restraints excluded: chain h residue 302 MET Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 142 ILE Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 169 MET Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 96 LYS Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain m residue 155 VAL Chi-restraints excluded: chain m residue 173 HIS Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 210 CYS Chi-restraints excluded: chain m residue 211 ILE Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 239 PHE Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 245 ASP Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain m residue 274 LEU Chi-restraints excluded: chain m residue 286 THR Chi-restraints excluded: chain m residue 298 CYS Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 122 THR Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 238 LEU Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 64 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 85 ILE Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 152 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 223 LEU Chi-restraints excluded: chain r residue 227 LEU Chi-restraints excluded: chain r residue 228 ILE Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 252 LEU Chi-restraints excluded: chain r residue 255 LEU Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 273 SER Chi-restraints excluded: chain r residue 293 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 868 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 513 optimal weight: 6.9990 chunk 657 optimal weight: 7.9990 chunk 509 optimal weight: 8.9990 chunk 758 optimal weight: 30.0000 chunk 503 optimal weight: 8.9990 chunk 897 optimal weight: 6.9990 chunk 561 optimal weight: 9.9990 chunk 547 optimal weight: 9.9990 chunk 414 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 445 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 600 GLN K 735 HIS ** K 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN ** N 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 997 HIS O1289 ASN ** P 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 402 GLN P 432 GLN ** P 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1178 GLN ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1296 GLN ** P1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS x 102 GLN ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 44 GLN h 112 GLN h 201 ASN ** k 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 185 HIS r 47 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 1.0171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 75983 Z= 0.303 Angle : 0.759 15.532 103244 Z= 0.381 Chirality : 0.047 0.222 11614 Planarity : 0.006 0.085 13471 Dihedral : 5.831 58.767 10408 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 5.90 % Allowed : 26.33 % Favored : 67.77 % 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: -1.33 (0.08), residues: 9356 helix: 0.08 (0.09), residues: 3534 sheet: -0.60 (0.14), residues: 1305 loop : -1.77 (0.09), residues: 4517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 996 HIS 0.051 0.001 HIS O 377 PHE 0.036 0.002 PHE u 50 TYR 0.036 0.002 TYR K1255 ARG 0.016 0.001 ARG p 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2093 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 1617 time to evaluate : 6.575 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: J 43 LYS cc_start: 0.8058 (pttt) cc_final: 0.7509 (tptp) REVERT: J 193 ILE cc_start: 0.8931 (mm) cc_final: 0.8575 (mt) REVERT: J 497 MET cc_start: 0.6844 (tmm) cc_final: 0.6597 (tpp) REVERT: J 637 VAL cc_start: 0.8244 (p) cc_final: 0.7860 (t) REVERT: J 825 MET cc_start: 0.6903 (mmt) cc_final: 0.6487 (mmm) REVERT: J 928 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6341 (pp) REVERT: J 976 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: J 1021 MET cc_start: 0.8386 (mtt) cc_final: 0.8157 (mtt) REVERT: J 1199 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8825 (p) REVERT: J 1235 GLU cc_start: 0.6643 (tt0) cc_final: 0.6429 (tt0) REVERT: J 1297 ARG cc_start: 0.7577 (tmm-80) cc_final: 0.7363 (ttt90) REVERT: K 1 MET cc_start: 0.2070 (mtt) cc_final: 0.1119 (mtm) REVERT: K 75 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8556 (m) REVERT: K 104 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.6834 (p90) REVERT: K 115 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.7921 (p) REVERT: K 163 SER cc_start: 0.8164 (p) cc_final: 0.7299 (t) REVERT: K 183 VAL cc_start: 0.8458 (t) cc_final: 0.8203 (p) REVERT: K 384 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8351 (pp) REVERT: K 385 GLN cc_start: 0.7999 (tp40) cc_final: 0.7720 (tp-100) REVERT: K 473 SER cc_start: 0.8217 (p) cc_final: 0.7885 (m) REVERT: K 808 LEU cc_start: 0.7166 (mp) cc_final: 0.6922 (mt) REVERT: K 913 ASN cc_start: 0.8506 (t0) cc_final: 0.8175 (t0) REVERT: K 942 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: K 966 ASP cc_start: 0.4662 (m-30) cc_final: 0.4459 (m-30) REVERT: K 1025 MET cc_start: 0.7061 (mtm) cc_final: 0.6753 (mtt) REVERT: K 1199 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7621 (p) REVERT: K 1322 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: K 1347 MET cc_start: 0.8464 (mtm) cc_final: 0.8207 (mtm) REVERT: N 16 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7947 (p) REVERT: N 28 SER cc_start: 0.8392 (m) cc_final: 0.7760 (t) REVERT: N 84 ASP cc_start: 0.7642 (p0) cc_final: 0.7227 (p0) REVERT: N 134 SER cc_start: 0.6749 (OUTLIER) cc_final: 0.6474 (m) REVERT: N 223 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8968 (tp) REVERT: N 236 MET cc_start: 0.6320 (mmm) cc_final: 0.5281 (tmm) REVERT: N 334 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6838 (t80) REVERT: N 403 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: N 405 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7211 (t80) REVERT: N 532 PRO cc_start: 0.8825 (Cg_exo) cc_final: 0.8578 (Cg_endo) REVERT: N 736 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8183 (tt) REVERT: N 860 LEU cc_start: 0.7043 (mt) cc_final: 0.6821 (mt) REVERT: N 867 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5020 (m-30) REVERT: N 889 MET cc_start: 0.6901 (mmm) cc_final: 0.6493 (mmm) REVERT: N 1117 MET cc_start: 0.7628 (tpt) cc_final: 0.7321 (tpt) REVERT: N 1124 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7699 (t80) REVERT: N 1223 LEU cc_start: 0.7875 (mm) cc_final: 0.7620 (tt) REVERT: N 1290 MET cc_start: 0.6816 (mmt) cc_final: 0.6302 (mmt) REVERT: O 47 GLU cc_start: 0.2740 (OUTLIER) cc_final: -0.0225 (tt0) REVERT: O 88 MET cc_start: 0.8400 (tmm) cc_final: 0.7769 (ttt) REVERT: O 194 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8375 (tp) REVERT: O 303 MET cc_start: 0.5713 (mmp) cc_final: 0.5156 (tpp) REVERT: O 387 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6607 (ptt) REVERT: O 413 MET cc_start: 0.8227 (mmm) cc_final: 0.7815 (mmt) REVERT: O 504 ASP cc_start: 0.5618 (m-30) cc_final: 0.5324 (m-30) REVERT: O 546 TYR cc_start: 0.7756 (m-80) cc_final: 0.7098 (m-80) REVERT: O 594 LEU cc_start: 0.7684 (tt) cc_final: 0.7421 (tp) REVERT: O 793 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7537 (mtp180) REVERT: O 956 ASP cc_start: 0.7036 (t0) cc_final: 0.6462 (t0) REVERT: O 1174 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7664 (pp) REVERT: O 1183 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8338 (tp30) REVERT: O 1239 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8336 (m) REVERT: O 1327 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6837 (t80) REVERT: O 1361 TYR cc_start: 0.9048 (p90) cc_final: 0.8610 (p90) REVERT: P 37 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6925 (t80) REVERT: P 92 LYS cc_start: 0.7595 (mmmt) cc_final: 0.7274 (mttt) REVERT: P 95 PHE cc_start: 0.4341 (OUTLIER) cc_final: 0.1872 (m-80) REVERT: P 112 LYS cc_start: 0.3164 (OUTLIER) cc_final: 0.1743 (mttp) REVERT: P 185 LEU cc_start: 0.9346 (mt) cc_final: 0.9059 (tp) REVERT: P 250 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7526 (mm-30) REVERT: P 573 THR cc_start: 0.6471 (p) cc_final: 0.6189 (t) REVERT: P 723 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.5864 (mm) REVERT: P 916 ASP cc_start: 0.6141 (p0) cc_final: 0.5865 (p0) REVERT: P 1019 THR cc_start: 0.8327 (p) cc_final: 0.8056 (t) REVERT: P 1139 ASN cc_start: 0.8366 (m-40) cc_final: 0.7630 (t0) REVERT: P 1178 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6283 (tt0) REVERT: P 1253 ILE cc_start: 0.8397 (mm) cc_final: 0.8140 (mt) REVERT: P 1292 ASN cc_start: 0.7236 (m-40) cc_final: 0.6923 (t0) REVERT: P 1347 MET cc_start: 0.7090 (mmm) cc_final: 0.6780 (mtp) REVERT: v 103 TYR cc_start: 0.3137 (OUTLIER) cc_final: 0.2178 (p90) REVERT: v 302 TYR cc_start: 0.4762 (t80) cc_final: 0.4297 (t80) REVERT: w 74 MET cc_start: 0.5184 (tmm) cc_final: 0.4697 (tmm) REVERT: x 56 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6871 (mtt180) REVERT: x 101 MET cc_start: 0.4270 (mtt) cc_final: 0.3957 (mtt) REVERT: x 102 GLN cc_start: 0.3468 (OUTLIER) cc_final: 0.3102 (mt0) REVERT: Z 76 LYS cc_start: 0.6947 (tptt) cc_final: 0.5988 (mmtt) REVERT: d 53 SER cc_start: 0.6585 (p) cc_final: 0.6113 (p) REVERT: d 75 ASP cc_start: 0.5332 (p0) cc_final: 0.4786 (m-30) REVERT: e 1 MET cc_start: 0.5492 (tmm) cc_final: 0.5170 (tmm) REVERT: u 44 GLN cc_start: 0.3613 (OUTLIER) cc_final: 0.3035 (mt0) REVERT: u 45 ARG cc_start: 0.4727 (OUTLIER) cc_final: 0.3612 (mpt180) REVERT: h 27 LEU cc_start: 0.7450 (tt) cc_final: 0.7215 (tp) REVERT: h 46 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6389 (m170) REVERT: h 212 VAL cc_start: 0.8588 (t) cc_final: 0.8365 (m) REVERT: h 289 ILE cc_start: 0.7869 (mm) cc_final: 0.7655 (mm) REVERT: h 302 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7741 (mtt) REVERT: h 326 THR cc_start: 0.8739 (m) cc_final: 0.8344 (p) REVERT: k 161 MET cc_start: 0.4486 (tmm) cc_final: 0.3969 (tmm) REVERT: k 206 SER cc_start: 0.6435 (p) cc_final: 0.6225 (t) REVERT: m 39 ASN cc_start: 0.8478 (t0) cc_final: 0.7115 (t0) REVERT: m 96 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7529 (tptm) REVERT: m 159 VAL cc_start: 0.8535 (t) cc_final: 0.8315 (p) REVERT: m 173 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6425 (t70) REVERT: m 185 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.6042 (m90) REVERT: m 238 LEU cc_start: 0.7917 (tt) cc_final: 0.7694 (mp) REVERT: m 252 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4575 (pp) REVERT: m 267 MET cc_start: 0.8082 (mmm) cc_final: 0.7649 (ttm) REVERT: m 274 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6285 (tt) REVERT: m 276 SER cc_start: 0.8137 (p) cc_final: 0.7745 (p) REVERT: p 151 LEU cc_start: 0.5643 (tp) cc_final: 0.4536 (tt) REVERT: p 175 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5584 (t-90) REVERT: r 80 LEU cc_start: 0.7867 (pt) cc_final: 0.7628 (pt) REVERT: r 123 VAL cc_start: 0.8040 (t) cc_final: 0.7834 (t) REVERT: r 145 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7321 (mt-10) REVERT: r 255 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6012 (pt) outliers start: 476 outliers final: 321 residues processed: 1930 average time/residue: 0.6741 time to fit residues: 2282.2581 Evaluate side-chains 1841 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1476 time to evaluate : 6.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 448 LEU Chi-restraints excluded: chain J residue 458 VAL Chi-restraints excluded: chain J residue 568 VAL Chi-restraints excluded: chain J residue 592 THR Chi-restraints excluded: chain J residue 727 VAL Chi-restraints excluded: chain J residue 737 LEU Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 976 GLN Chi-restraints excluded: chain J residue 1011 SER Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1049 THR Chi-restraints excluded: chain J residue 1058 LEU Chi-restraints excluded: chain J residue 1065 THR Chi-restraints excluded: chain J residue 1075 SER Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1115 THR Chi-restraints excluded: chain J residue 1143 LYS Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1199 SER Chi-restraints excluded: chain J residue 1210 VAL Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain J residue 1369 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 404 SER Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain K residue 458 VAL Chi-restraints excluded: chain K residue 491 HIS Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 598 VAL Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 709 GLU Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 769 MET Chi-restraints excluded: chain K residue 828 LEU Chi-restraints excluded: chain K residue 835 VAL Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 881 ILE Chi-restraints excluded: chain K residue 922 THR Chi-restraints excluded: chain K residue 942 GLN Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1092 MET Chi-restraints excluded: chain K residue 1099 LEU Chi-restraints excluded: chain K residue 1102 SER Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1219 VAL Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1322 GLU Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1342 LEU Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 65 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 334 PHE Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 403 TYR Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 621 VAL Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 667 CYS Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 757 LEU Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 907 THR Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 928 LEU Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 971 VAL Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1053 LEU Chi-restraints excluded: chain N residue 1105 MET Chi-restraints excluded: chain N residue 1114 THR Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1122 GLN Chi-restraints excluded: chain N residue 1124 PHE Chi-restraints excluded: chain N residue 1181 THR Chi-restraints excluded: chain N residue 1182 CYS Chi-restraints excluded: chain N residue 1189 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1295 SER Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 284 ASP Chi-restraints excluded: chain O residue 292 THR Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 387 MET Chi-restraints excluded: chain O residue 497 MET Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 568 VAL Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 700 LEU Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 830 VAL Chi-restraints excluded: chain O residue 864 THR Chi-restraints excluded: chain O residue 898 VAL Chi-restraints excluded: chain O residue 902 VAL Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1021 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1074 VAL Chi-restraints excluded: chain O residue 1082 ASP Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1124 PHE Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1183 GLU Chi-restraints excluded: chain O residue 1224 ILE Chi-restraints excluded: chain O residue 1239 THR Chi-restraints excluded: chain O residue 1321 LEU Chi-restraints excluded: chain O residue 1327 PHE Chi-restraints excluded: chain O residue 1336 SER Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain O residue 1379 VAL Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 143 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 244 VAL Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 377 HIS Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 436 VAL Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 526 THR Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 602 VAL Chi-restraints excluded: chain P residue 706 VAL Chi-restraints excluded: chain P residue 723 LEU Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 735 HIS Chi-restraints excluded: chain P residue 741 ASP Chi-restraints excluded: chain P residue 756 THR Chi-restraints excluded: chain P residue 808 LEU Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 1033 GLN Chi-restraints excluded: chain P residue 1097 THR Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1178 GLN Chi-restraints excluded: chain P residue 1192 ASP Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1296 GLN Chi-restraints excluded: chain P residue 1319 VAL Chi-restraints excluded: chain P residue 1328 LEU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 115 TYR Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 57 CYS Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 94 PHE Chi-restraints excluded: chain x residue 102 GLN Chi-restraints excluded: chain y residue 3119 LEU Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3126 LEU Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain z residue 3144 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 PHE Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain u residue 44 GLN Chi-restraints excluded: chain u residue 45 ARG Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 205 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 225 VAL Chi-restraints excluded: chain f residue 279 PHE Chi-restraints excluded: chain f residue 297 TYR Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain f residue 358 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 46 HIS Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 112 GLN Chi-restraints excluded: chain h residue 125 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 197 SER Chi-restraints excluded: chain h residue 203 ILE Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 223 VAL Chi-restraints excluded: chain h residue 224 THR Chi-restraints excluded: chain h residue 302 MET Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 169 MET Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 232 HIS Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 96 LYS Chi-restraints excluded: chain m residue 127 SER Chi-restraints excluded: chain m residue 155 VAL Chi-restraints excluded: chain m residue 173 HIS Chi-restraints excluded: chain m residue 185 HIS Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 210 CYS Chi-restraints excluded: chain m residue 211 ILE Chi-restraints excluded: chain m residue 214 THR Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 243 VAL Chi-restraints excluded: chain m residue 245 ASP Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain m residue 274 LEU Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 175 HIS Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 234 ASP Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 64 LEU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 85 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 152 LEU Chi-restraints excluded: chain r residue 170 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 252 LEU Chi-restraints excluded: chain r residue 255 LEU Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 273 SER Chi-restraints excluded: chain r residue 293 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 555 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 535 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 176 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 570 optimal weight: 7.9990 chunk 611 optimal weight: 0.8980 chunk 443 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 705 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 909 GLN ** J 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS K 415 ASN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 564 HIS K 735 HIS K 795 HIS ** K 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 HIS N 402 GLN N 472 ASN N 564 HIS ** N 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1169 ASN ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 301 GLN O 377 HIS ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 636 ASN O 775 GLN O 964 HIS ** O 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 HIS ** P 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 GLN Z 62 GLN ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 201 ASN h 46 HIS h 201 ASN ** k 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 185 HIS r 47 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 1.0394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 75983 Z= 0.219 Angle : 0.730 18.214 103244 Z= 0.362 Chirality : 0.045 0.341 11614 Planarity : 0.005 0.089 13471 Dihedral : 5.593 57.796 10406 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.00 % Favored : 93.95 % Rotamer: Outliers : 4.57 % Allowed : 28.01 % Favored : 67.41 % 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: -1.14 (0.09), residues: 9356 helix: 0.27 (0.09), residues: 3502 sheet: -0.45 (0.14), residues: 1297 loop : -1.69 (0.09), residues: 4557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP x 54 HIS 0.013 0.001 HIS m 185 PHE 0.052 0.002 PHE Z 50 TYR 0.033 0.002 TYR d 60 ARG 0.013 0.001 ARG N 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1942 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1573 time to evaluate : 6.758 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: J 193 ILE cc_start: 0.8893 (mm) cc_final: 0.8509 (mt) REVERT: J 417 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7975 (mttm) REVERT: J 497 MET cc_start: 0.6792 (tmm) cc_final: 0.6552 (tpp) REVERT: J 637 VAL cc_start: 0.8533 (p) cc_final: 0.8036 (t) REVERT: J 928 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6171 (pp) REVERT: J 1023 ILE cc_start: 0.8157 (mm) cc_final: 0.7797 (mm) REVERT: J 1049 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8895 (p) REVERT: J 1297 ARG cc_start: 0.7551 (tmm-80) cc_final: 0.7310 (ttt90) REVERT: K 1 MET cc_start: 0.1866 (mtt) cc_final: 0.0994 (mtm) REVERT: K 75 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8447 (m) REVERT: K 104 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6831 (p90) REVERT: K 163 SER cc_start: 0.7888 (p) cc_final: 0.7011 (t) REVERT: K 183 VAL cc_start: 0.8418 (t) cc_final: 0.8146 (p) REVERT: K 218 MET cc_start: 0.8403 (mmm) cc_final: 0.7921 (mmp) REVERT: K 382 GLU cc_start: 0.7899 (tp30) cc_final: 0.7579 (tp30) REVERT: K 384 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8173 (pp) REVERT: K 385 GLN cc_start: 0.8000 (tp40) cc_final: 0.7735 (tp-100) REVERT: K 473 SER cc_start: 0.8182 (p) cc_final: 0.7836 (m) REVERT: K 808 LEU cc_start: 0.7238 (mp) cc_final: 0.7028 (mt) REVERT: K 913 ASN cc_start: 0.8494 (t0) cc_final: 0.8155 (t0) REVERT: K 942 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7171 (pp30) REVERT: K 1025 MET cc_start: 0.6911 (mtm) cc_final: 0.6588 (mtt) REVERT: N 16 THR cc_start: 0.8188 (m) cc_final: 0.7915 (p) REVERT: N 28 SER cc_start: 0.8343 (m) cc_final: 0.7737 (t) REVERT: N 84 ASP cc_start: 0.7686 (p0) cc_final: 0.7249 (p0) REVERT: N 134 SER cc_start: 0.6777 (t) cc_final: 0.6564 (m) REVERT: N 223 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8920 (tp) REVERT: N 236 MET cc_start: 0.6184 (mmm) cc_final: 0.5237 (tmm) REVERT: N 334 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.6950 (t80) REVERT: N 401 MET cc_start: 0.8356 (tmm) cc_final: 0.8044 (tmm) REVERT: N 405 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7240 (t80) REVERT: N 532 PRO cc_start: 0.8796 (Cg_exo) cc_final: 0.8524 (Cg_endo) REVERT: N 736 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8094 (tt) REVERT: N 813 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: N 889 MET cc_start: 0.6623 (mmm) cc_final: 0.5982 (mmm) REVERT: N 1117 MET cc_start: 0.7529 (tpt) cc_final: 0.7134 (tpt) REVERT: N 1223 LEU cc_start: 0.7699 (mm) cc_final: 0.7483 (tt) REVERT: N 1290 MET cc_start: 0.6820 (mmt) cc_final: 0.6342 (mmt) REVERT: O 47 GLU cc_start: 0.2632 (OUTLIER) cc_final: -0.0406 (tt0) REVERT: O 88 MET cc_start: 0.8317 (tmm) cc_final: 0.7647 (ttt) REVERT: O 194 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (tp) REVERT: O 334 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: O 387 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6590 (ptt) REVERT: O 413 MET cc_start: 0.8194 (mmm) cc_final: 0.7764 (mmt) REVERT: O 546 TYR cc_start: 0.7677 (m-80) cc_final: 0.6986 (m-80) REVERT: O 594 LEU cc_start: 0.7678 (tt) cc_final: 0.7446 (tp) REVERT: O 793 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7379 (mtp180) REVERT: O 956 ASP cc_start: 0.6793 (t0) cc_final: 0.6127 (t0) REVERT: O 1174 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7597 (pp) REVERT: O 1183 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8669 (mm-30) REVERT: O 1327 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6670 (t80) REVERT: O 1361 TYR cc_start: 0.9034 (p90) cc_final: 0.8586 (p90) REVERT: P 37 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6793 (t80) REVERT: P 95 PHE cc_start: 0.4483 (OUTLIER) cc_final: 0.1942 (m-80) REVERT: P 112 LYS cc_start: 0.3143 (OUTLIER) cc_final: 0.1717 (mttp) REVERT: P 185 LEU cc_start: 0.9296 (mt) cc_final: 0.9011 (tp) REVERT: P 191 MET cc_start: 0.8574 (tpp) cc_final: 0.7837 (tpp) REVERT: P 250 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7465 (mm-30) REVERT: P 573 THR cc_start: 0.6401 (p) cc_final: 0.6193 (t) REVERT: P 723 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5807 (mm) REVERT: P 1019 THR cc_start: 0.8382 (p) cc_final: 0.8037 (t) REVERT: P 1139 ASN cc_start: 0.8358 (m-40) cc_final: 0.7739 (t0) REVERT: P 1198 LYS cc_start: 0.8408 (pttt) cc_final: 0.8008 (pptt) REVERT: P 1253 ILE cc_start: 0.8382 (mm) cc_final: 0.8176 (mt) REVERT: P 1292 ASN cc_start: 0.6850 (m-40) cc_final: 0.6600 (t0) REVERT: v 103 TYR cc_start: 0.3232 (OUTLIER) cc_final: 0.2332 (p90) REVERT: v 302 TYR cc_start: 0.4655 (t80) cc_final: 0.4221 (t80) REVERT: w 74 MET cc_start: 0.5212 (tmm) cc_final: 0.4711 (tmm) REVERT: x 56 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6653 (mtt180) REVERT: x 94 PHE cc_start: 0.1232 (OUTLIER) cc_final: -0.2554 (m-80) REVERT: x 101 MET cc_start: 0.3726 (mtt) cc_final: 0.2985 (mtm) REVERT: Z 76 LYS cc_start: 0.6862 (tptt) cc_final: 0.5904 (mmtt) REVERT: a 15 GLU cc_start: 0.6470 (mp0) cc_final: 0.6211 (mp0) REVERT: d 7 LYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4017 (tptt) REVERT: d 18 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: d 53 SER cc_start: 0.6426 (p) cc_final: 0.6086 (p) REVERT: d 75 ASP cc_start: 0.5121 (p0) cc_final: 0.4718 (m-30) REVERT: e 1 MET cc_start: 0.5398 (tmm) cc_final: 0.5146 (tmm) REVERT: f 174 ARG cc_start: 0.6752 (tpt90) cc_final: 0.6443 (tpt170) REVERT: h 46 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6025 (m-70) REVERT: h 289 ILE cc_start: 0.7840 (mm) cc_final: 0.7568 (mm) REVERT: h 302 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7711 (mtt) REVERT: h 326 THR cc_start: 0.8704 (m) cc_final: 0.8361 (p) REVERT: k 149 LYS cc_start: 0.8579 (tppp) cc_final: 0.8229 (tppp) REVERT: k 161 MET cc_start: 0.4331 (tmm) cc_final: 0.3813 (tmm) REVERT: m 35 HIS cc_start: 0.6771 (m90) cc_final: 0.6463 (m-70) REVERT: m 96 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7277 (tptm) REVERT: m 159 VAL cc_start: 0.8463 (t) cc_final: 0.8238 (p) REVERT: m 238 LEU cc_start: 0.7940 (tt) cc_final: 0.7641 (mp) REVERT: m 252 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4729 (pp) REVERT: m 267 MET cc_start: 0.8238 (mmm) cc_final: 0.7692 (ttm) REVERT: m 274 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6478 (tt) REVERT: m 276 SER cc_start: 0.7963 (p) cc_final: 0.7634 (p) REVERT: p 175 HIS cc_start: 0.5770 (OUTLIER) cc_final: 0.5556 (t-90) REVERT: r 145 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7311 (mt-10) outliers start: 369 outliers final: 275 residues processed: 1811 average time/residue: 0.6815 time to fit residues: 2158.4358 Evaluate side-chains 1773 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1465 time to evaluate : 6.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 216 ILE Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 458 VAL Chi-restraints excluded: chain J residue 568 VAL Chi-restraints excluded: chain J residue 653 ARG Chi-restraints excluded: chain J residue 737 LEU Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1049 THR Chi-restraints excluded: chain J residue 1058 LEU Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1143 LYS Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain J residue 1369 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 167 PHE Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 404 SER Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain K residue 458 VAL Chi-restraints excluded: chain K residue 491 HIS Chi-restraints excluded: chain K residue 598 VAL Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 649 GLU Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 709 GLU Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 769 MET Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 838 THR Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 942 GLN Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1092 MET Chi-restraints excluded: chain K residue 1099 LEU Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1155 LEU Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1219 VAL Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1342 LEU Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 65 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 334 PHE Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 654 LEU Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 687 TYR Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 757 LEU Chi-restraints excluded: chain N residue 813 TYR Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 907 THR Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 928 LEU Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 950 PHE Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1053 LEU Chi-restraints excluded: chain N residue 1114 THR Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1189 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1295 SER Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 284 ASP Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 334 PHE Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 387 MET Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 568 VAL Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 898 VAL Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1021 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1074 VAL Chi-restraints excluded: chain O residue 1082 ASP Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1183 GLU Chi-restraints excluded: chain O residue 1293 GLU Chi-restraints excluded: chain O residue 1321 LEU Chi-restraints excluded: chain O residue 1327 PHE Chi-restraints excluded: chain O residue 1336 SER Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 236 MET Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 377 HIS Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 526 THR Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 602 VAL Chi-restraints excluded: chain P residue 706 VAL Chi-restraints excluded: chain P residue 723 LEU Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 741 ASP Chi-restraints excluded: chain P residue 756 THR Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 1033 GLN Chi-restraints excluded: chain P residue 1097 THR Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1192 ASP Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1295 SER Chi-restraints excluded: chain P residue 1319 VAL Chi-restraints excluded: chain P residue 1328 LEU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 115 TYR Chi-restraints excluded: chain v residue 299 VAL Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 94 PHE Chi-restraints excluded: chain y residue 3116 SER Chi-restraints excluded: chain y residue 3119 LEU Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain y residue 3144 LEU Chi-restraints excluded: chain y residue 3149 LEU Chi-restraints excluded: chain z residue 3144 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 31 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 205 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 225 VAL Chi-restraints excluded: chain f residue 265 TYR Chi-restraints excluded: chain f residue 280 PHE Chi-restraints excluded: chain f residue 297 TYR Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 333 TRP Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain f residue 358 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 46 HIS Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 125 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 203 ILE Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 223 VAL Chi-restraints excluded: chain h residue 298 SER Chi-restraints excluded: chain h residue 302 MET Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 169 MET Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 232 HIS Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 28 ILE Chi-restraints excluded: chain m residue 96 LYS Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 210 CYS Chi-restraints excluded: chain m residue 211 ILE Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 245 ASP Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain m residue 274 LEU Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain p residue 54 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 147 LEU Chi-restraints excluded: chain p residue 175 HIS Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 264 MET Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 85 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 152 LEU Chi-restraints excluded: chain r residue 170 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 293 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 816 optimal weight: 1.9990 chunk 859 optimal weight: 6.9990 chunk 784 optimal weight: 1.9990 chunk 836 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 364 optimal weight: 0.8980 chunk 656 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 755 optimal weight: 20.0000 chunk 790 optimal weight: 0.4980 chunk 833 optimal weight: 30.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 842 ASN ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 862 ASN ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 964 HIS ** J 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 415 ASN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 735 HIS ** K 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1149 GLN ** N 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1178 GLN ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 HIS ** O 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 984 ASN ** O1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1296 GLN P1178 GLN ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS x 102 GLN ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 62 GLN h 201 ASN ** k 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 185 HIS ** p 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 1.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 75983 Z= 0.207 Angle : 0.732 16.671 103244 Z= 0.362 Chirality : 0.045 0.383 11614 Planarity : 0.005 0.089 13471 Dihedral : 5.423 57.184 10404 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 4.24 % Allowed : 28.58 % Favored : 67.18 % 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: -1.06 (0.09), residues: 9356 helix: 0.33 (0.09), residues: 3504 sheet: -0.39 (0.14), residues: 1277 loop : -1.64 (0.09), residues: 4575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP x 54 HIS 0.027 0.001 HIS h 46 PHE 0.049 0.002 PHE Z 50 TYR 0.032 0.002 TYR d 60 ARG 0.013 0.001 ARG N 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1933 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1591 time to evaluate : 6.888 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: J 193 ILE cc_start: 0.8795 (mm) cc_final: 0.8545 (mt) REVERT: J 417 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7950 (mttm) REVERT: J 497 MET cc_start: 0.6855 (tmm) cc_final: 0.6489 (tpp) REVERT: J 637 VAL cc_start: 0.8451 (p) cc_final: 0.7961 (t) REVERT: J 825 MET cc_start: 0.7183 (mmt) cc_final: 0.6292 (mmm) REVERT: J 841 TYR cc_start: 0.7971 (t80) cc_final: 0.7531 (t80) REVERT: J 928 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6070 (pp) REVERT: J 1009 LEU cc_start: 0.8302 (tp) cc_final: 0.7905 (mt) REVERT: J 1021 MET cc_start: 0.8346 (mtt) cc_final: 0.8082 (mtt) REVERT: J 1023 ILE cc_start: 0.8424 (mm) cc_final: 0.8079 (mm) REVERT: J 1049 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8830 (p) REVERT: J 1363 ILE cc_start: 0.9424 (mp) cc_final: 0.9124 (mt) REVERT: K 75 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8345 (m) REVERT: K 104 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.6879 (p90) REVERT: K 163 SER cc_start: 0.7975 (p) cc_final: 0.7117 (t) REVERT: K 218 MET cc_start: 0.8350 (mmm) cc_final: 0.8089 (mmp) REVERT: K 382 GLU cc_start: 0.7802 (tp30) cc_final: 0.7585 (tp30) REVERT: K 384 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8077 (pp) REVERT: K 385 GLN cc_start: 0.7942 (tp40) cc_final: 0.7671 (tp-100) REVERT: K 473 SER cc_start: 0.8237 (p) cc_final: 0.7845 (m) REVERT: K 769 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6088 (tpp) REVERT: K 880 MET cc_start: 0.6130 (mtm) cc_final: 0.5880 (mtt) REVERT: K 913 ASN cc_start: 0.8505 (t0) cc_final: 0.8163 (t0) REVERT: K 942 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7104 (pp30) REVERT: K 1025 MET cc_start: 0.6902 (mtm) cc_final: 0.6575 (mtt) REVERT: K 1199 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7571 (p) REVERT: N 16 THR cc_start: 0.8191 (m) cc_final: 0.7937 (p) REVERT: N 28 SER cc_start: 0.8359 (m) cc_final: 0.7740 (t) REVERT: N 84 ASP cc_start: 0.7628 (p0) cc_final: 0.7129 (p0) REVERT: N 236 MET cc_start: 0.6089 (mmm) cc_final: 0.5211 (tmm) REVERT: N 334 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7000 (t80) REVERT: N 405 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7267 (t80) REVERT: N 532 PRO cc_start: 0.8691 (Cg_exo) cc_final: 0.8456 (Cg_endo) REVERT: N 736 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8045 (tt) REVERT: N 747 ILE cc_start: 0.8341 (mm) cc_final: 0.8137 (mm) REVERT: N 813 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: N 867 ASP cc_start: 0.5777 (OUTLIER) cc_final: 0.4840 (m-30) REVERT: N 889 MET cc_start: 0.6715 (mmm) cc_final: 0.6052 (mmm) REVERT: N 1223 LEU cc_start: 0.7693 (mm) cc_final: 0.7452 (tt) REVERT: N 1290 MET cc_start: 0.6862 (mmt) cc_final: 0.6350 (mmt) REVERT: O 47 GLU cc_start: 0.2543 (OUTLIER) cc_final: -0.0490 (tt0) REVERT: O 88 MET cc_start: 0.8371 (tmm) cc_final: 0.7730 (ttt) REVERT: O 194 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8299 (tp) REVERT: O 334 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: O 413 MET cc_start: 0.8226 (mmm) cc_final: 0.7806 (mmt) REVERT: O 546 TYR cc_start: 0.7630 (m-80) cc_final: 0.7015 (m-80) REVERT: O 793 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7400 (mtp180) REVERT: O 956 ASP cc_start: 0.6539 (t0) cc_final: 0.5985 (t0) REVERT: O 1174 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7576 (pp) REVERT: O 1361 TYR cc_start: 0.9021 (p90) cc_final: 0.8604 (p90) REVERT: P 37 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6883 (t80) REVERT: P 95 PHE cc_start: 0.4651 (OUTLIER) cc_final: 0.1517 (m-80) REVERT: P 112 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.1754 (mttp) REVERT: P 165 LEU cc_start: 0.8812 (mm) cc_final: 0.8393 (mt) REVERT: P 185 LEU cc_start: 0.9283 (mt) cc_final: 0.9014 (tp) REVERT: P 191 MET cc_start: 0.8563 (tpp) cc_final: 0.7806 (tpp) REVERT: P 223 LEU cc_start: 0.8797 (tp) cc_final: 0.8348 (tp) REVERT: P 250 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7461 (mm-30) REVERT: P 497 MET cc_start: 0.6487 (mmm) cc_final: 0.6020 (mmp) REVERT: P 582 GLU cc_start: 0.4594 (mt-10) cc_final: 0.4246 (mt-10) REVERT: P 723 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6290 (mm) REVERT: P 1019 THR cc_start: 0.8415 (p) cc_final: 0.8113 (t) REVERT: P 1117 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7005 (mtp) REVERT: P 1139 ASN cc_start: 0.8310 (m-40) cc_final: 0.7692 (t0) REVERT: P 1178 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.5931 (tt0) REVERT: P 1297 ARG cc_start: 0.6431 (tpm170) cc_final: 0.6012 (tpm170) REVERT: v 66 MET cc_start: 0.5526 (mmm) cc_final: 0.5282 (tpp) REVERT: v 302 TYR cc_start: 0.4680 (t80) cc_final: 0.4366 (t80) REVERT: w 74 MET cc_start: 0.5028 (tmm) cc_final: 0.4576 (tmm) REVERT: x 94 PHE cc_start: 0.1169 (OUTLIER) cc_final: -0.2574 (m-80) REVERT: x 101 MET cc_start: 0.4693 (mtt) cc_final: 0.4436 (mtt) REVERT: Z 76 LYS cc_start: 0.6964 (tptt) cc_final: 0.5932 (mmtt) REVERT: a 15 GLU cc_start: 0.6532 (mp0) cc_final: 0.6303 (mp0) REVERT: d 7 LYS cc_start: 0.5621 (OUTLIER) cc_final: 0.4693 (tptt) REVERT: d 53 SER cc_start: 0.6650 (p) cc_final: 0.6234 (p) REVERT: d 75 ASP cc_start: 0.4901 (p0) cc_final: 0.4444 (m-30) REVERT: e 1 MET cc_start: 0.5357 (tmm) cc_final: 0.5103 (tmm) REVERT: u 15 GLU cc_start: 0.4934 (pm20) cc_final: 0.4697 (pm20) REVERT: u 45 ARG cc_start: 0.4556 (OUTLIER) cc_final: 0.3066 (mpt180) REVERT: u 48 LEU cc_start: 0.6046 (mt) cc_final: 0.5327 (tp) REVERT: f 294 ARG cc_start: 0.7280 (ttp80) cc_final: 0.6959 (ttp80) REVERT: h 46 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.6134 (m170) REVERT: h 289 ILE cc_start: 0.7806 (mm) cc_final: 0.7558 (mm) REVERT: h 302 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: h 326 THR cc_start: 0.8711 (m) cc_final: 0.8361 (p) REVERT: k 112 MET cc_start: 0.7269 (ptt) cc_final: 0.6919 (ptt) REVERT: k 149 LYS cc_start: 0.8505 (tppp) cc_final: 0.8188 (tppp) REVERT: m 96 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7088 (tptm) REVERT: m 159 VAL cc_start: 0.8354 (t) cc_final: 0.8152 (p) REVERT: m 238 LEU cc_start: 0.7927 (tt) cc_final: 0.7682 (mp) REVERT: m 252 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4638 (pp) REVERT: m 267 MET cc_start: 0.8208 (mmm) cc_final: 0.7728 (ttm) REVERT: m 276 SER cc_start: 0.8030 (p) cc_final: 0.7667 (p) REVERT: p 175 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.4952 (t-90) REVERT: r 212 MET cc_start: 0.8436 (tpp) cc_final: 0.8184 (ttm) outliers start: 342 outliers final: 256 residues processed: 1809 average time/residue: 0.6994 time to fit residues: 2217.4190 Evaluate side-chains 1789 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1501 time to evaluate : 9.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 458 VAL Chi-restraints excluded: chain J residue 568 VAL Chi-restraints excluded: chain J residue 613 THR Chi-restraints excluded: chain J residue 737 LEU Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1049 THR Chi-restraints excluded: chain J residue 1075 SER Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1322 GLU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain J residue 1369 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 167 PHE Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 404 SER Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain K residue 458 VAL Chi-restraints excluded: chain K residue 598 VAL Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 649 GLU Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 769 MET Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 922 THR Chi-restraints excluded: chain K residue 942 GLN Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1099 LEU Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1155 LEU Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1219 VAL Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1327 PHE Chi-restraints excluded: chain K residue 1342 LEU Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 65 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 323 SER Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 328 MET Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 334 PHE Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 464 LEU Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 654 LEU Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 757 LEU Chi-restraints excluded: chain N residue 813 TYR Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 919 THR Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 928 LEU Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 971 VAL Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1113 ILE Chi-restraints excluded: chain N residue 1114 THR Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1122 GLN Chi-restraints excluded: chain N residue 1189 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1213 GLU Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1295 SER Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 284 ASP Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 334 PHE Chi-restraints excluded: chain O residue 340 ASP Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 568 VAL Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1001 MET Chi-restraints excluded: chain O residue 1021 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1074 VAL Chi-restraints excluded: chain O residue 1082 ASP Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1110 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1328 LEU Chi-restraints excluded: chain O residue 1336 SER Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 236 MET Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 377 HIS Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 436 VAL Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 526 THR Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 566 LEU Chi-restraints excluded: chain P residue 602 VAL Chi-restraints excluded: chain P residue 706 VAL Chi-restraints excluded: chain P residue 723 LEU Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 756 THR Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 1033 GLN Chi-restraints excluded: chain P residue 1117 MET Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1178 GLN Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1319 VAL Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 115 TYR Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 94 PHE Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain z residue 3144 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 31 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain u residue 45 ARG Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 205 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 216 ILE Chi-restraints excluded: chain f residue 225 VAL Chi-restraints excluded: chain f residue 265 TYR Chi-restraints excluded: chain f residue 280 PHE Chi-restraints excluded: chain f residue 297 TYR Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 333 TRP Chi-restraints excluded: chain f residue 338 PHE Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain f residue 358 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 46 HIS Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 125 VAL Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 302 MET Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 232 HIS Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 28 ILE Chi-restraints excluded: chain m residue 96 LYS Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 211 ILE Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 245 ASP Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 175 HIS Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 264 MET Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 85 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 111 VAL Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 152 LEU Chi-restraints excluded: chain r residue 170 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 273 SER Chi-restraints excluded: chain r residue 293 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 549 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 539 optimal weight: 0.2980 chunk 419 optimal weight: 8.9990 chunk 614 optimal weight: 8.9990 chunk 927 optimal weight: 20.0000 chunk 853 optimal weight: 6.9990 chunk 738 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 570 optimal weight: 9.9990 chunk 452 optimal weight: 20.0000 overall best weight: 7.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 195 GLN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 964 HIS K 35 HIS K 166 GLN K 415 ASN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 735 HIS ** K 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 645 ASN ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 804 HIS ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 HIS ** O 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 570 ASN ** O1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1178 GLN ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 394 GLN x 77 HIS ** z3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 62 GLN h 46 HIS ** k 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 185 HIS p 23 GLN ** p 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 175 HIS ** p 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 1.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 75983 Z= 0.312 Angle : 0.786 16.365 103244 Z= 0.394 Chirality : 0.047 0.332 11614 Planarity : 0.006 0.090 13471 Dihedral : 5.665 59.832 10402 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 4.27 % Allowed : 28.91 % Favored : 66.82 % 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: -1.20 (0.09), residues: 9356 helix: 0.23 (0.09), residues: 3520 sheet: -0.49 (0.14), residues: 1282 loop : -1.74 (0.09), residues: 4554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP x 54 HIS 0.017 0.001 HIS O 377 PHE 0.047 0.002 PHE Z 50 TYR 0.035 0.002 TYR d 60 ARG 0.010 0.001 ARG J 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18712 Ramachandran restraints generated. 9356 Oldfield, 0 Emsley, 9356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1844 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1499 time to evaluate : 6.775 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: J 43 LYS cc_start: 0.8537 (pttt) cc_final: 0.7955 (tptp) REVERT: J 94 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7416 (mm110) REVERT: J 193 ILE cc_start: 0.8834 (mm) cc_final: 0.8550 (mt) REVERT: J 417 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8113 (mttm) REVERT: J 497 MET cc_start: 0.7081 (tmm) cc_final: 0.6698 (tpp) REVERT: J 637 VAL cc_start: 0.8463 (p) cc_final: 0.8017 (t) REVERT: J 825 MET cc_start: 0.7036 (mmt) cc_final: 0.6233 (mmm) REVERT: J 841 TYR cc_start: 0.8095 (t80) cc_final: 0.7809 (t80) REVERT: J 928 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6463 (pp) REVERT: J 1009 LEU cc_start: 0.8288 (tp) cc_final: 0.7943 (mt) REVERT: J 1018 MET cc_start: 0.8950 (tpp) cc_final: 0.8649 (tpt) REVERT: J 1021 MET cc_start: 0.8507 (mtt) cc_final: 0.8284 (mtt) REVERT: J 1023 ILE cc_start: 0.8560 (mm) cc_final: 0.8144 (mm) REVERT: J 1049 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9031 (p) REVERT: J 1363 ILE cc_start: 0.9529 (mp) cc_final: 0.9322 (mt) REVERT: K 1 MET cc_start: 0.0922 (mtt) cc_final: 0.0159 (mtm) REVERT: K 75 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8681 (m) REVERT: K 104 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7127 (p90) REVERT: K 163 SER cc_start: 0.8139 (p) cc_final: 0.7328 (t) REVERT: K 218 MET cc_start: 0.8274 (mmm) cc_final: 0.8028 (mmp) REVERT: K 337 ARG cc_start: 0.5632 (ptt180) cc_final: 0.5359 (ptt90) REVERT: K 384 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8096 (pp) REVERT: K 473 SER cc_start: 0.8323 (p) cc_final: 0.7977 (m) REVERT: K 880 MET cc_start: 0.6442 (mtm) cc_final: 0.6160 (mtt) REVERT: K 913 ASN cc_start: 0.8593 (t0) cc_final: 0.8275 (t0) REVERT: K 942 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7234 (pp30) REVERT: K 1116 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7886 (t70) REVERT: K 1199 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7647 (p) REVERT: N 16 THR cc_start: 0.8365 (m) cc_final: 0.8099 (p) REVERT: N 28 SER cc_start: 0.8484 (m) cc_final: 0.7848 (t) REVERT: N 84 ASP cc_start: 0.7726 (p0) cc_final: 0.7242 (p0) REVERT: N 401 MET cc_start: 0.8342 (tmm) cc_final: 0.8054 (tmm) REVERT: N 405 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7446 (t80) REVERT: N 532 PRO cc_start: 0.8895 (Cg_exo) cc_final: 0.8643 (Cg_endo) REVERT: N 736 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8316 (tt) REVERT: N 867 ASP cc_start: 0.5996 (OUTLIER) cc_final: 0.4970 (m-30) REVERT: N 884 LEU cc_start: 0.8360 (mt) cc_final: 0.7959 (mt) REVERT: N 889 MET cc_start: 0.6624 (mmm) cc_final: 0.6113 (mmm) REVERT: N 1223 LEU cc_start: 0.7816 (mm) cc_final: 0.7506 (tt) REVERT: N 1290 MET cc_start: 0.7021 (mmt) cc_final: 0.6523 (mmt) REVERT: N 1340 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7997 (ttm170) REVERT: N 1346 PHE cc_start: 0.8357 (t80) cc_final: 0.8123 (t80) REVERT: O 47 GLU cc_start: 0.2921 (OUTLIER) cc_final: 0.0264 (tt0) REVERT: O 88 MET cc_start: 0.8530 (tmm) cc_final: 0.7883 (ttt) REVERT: O 194 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8485 (tp) REVERT: O 334 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: O 413 MET cc_start: 0.8249 (mmm) cc_final: 0.7800 (mmt) REVERT: O 546 TYR cc_start: 0.7777 (m-80) cc_final: 0.7041 (m-80) REVERT: O 570 ASN cc_start: 0.6862 (m-40) cc_final: 0.6626 (m110) REVERT: O 793 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7442 (mtp180) REVERT: O 880 MET cc_start: 0.5811 (mtp) cc_final: 0.5482 (mtp) REVERT: O 956 ASP cc_start: 0.6900 (t0) cc_final: 0.6385 (t0) REVERT: O 984 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.6029 (p0) REVERT: O 1025 MET cc_start: 0.7570 (mmm) cc_final: 0.6262 (mtt) REVERT: O 1174 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7733 (pp) REVERT: P 37 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6846 (t80) REVERT: P 112 LYS cc_start: 0.3242 (OUTLIER) cc_final: 0.1882 (mttp) REVERT: P 185 LEU cc_start: 0.9350 (mt) cc_final: 0.9041 (tp) REVERT: P 191 MET cc_start: 0.8646 (tpp) cc_final: 0.7790 (tpp) REVERT: P 250 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7538 (mm-30) REVERT: P 723 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6231 (mm) REVERT: P 1019 THR cc_start: 0.8537 (p) cc_final: 0.8128 (t) REVERT: P 1139 ASN cc_start: 0.8129 (m-40) cc_final: 0.7637 (t0) REVERT: P 1178 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: P 1198 LYS cc_start: 0.8327 (pttt) cc_final: 0.7909 (pptt) REVERT: P 1297 ARG cc_start: 0.6441 (tpm170) cc_final: 0.6074 (tpm170) REVERT: v 286 ARG cc_start: 0.6295 (tpt-90) cc_final: 0.5878 (mmt180) REVERT: v 302 TYR cc_start: 0.4641 (t80) cc_final: 0.4302 (t80) REVERT: w 74 MET cc_start: 0.5222 (tmm) cc_final: 0.4856 (tmm) REVERT: x 94 PHE cc_start: 0.1577 (OUTLIER) cc_final: -0.2364 (m-80) REVERT: x 101 MET cc_start: 0.4885 (mtt) cc_final: 0.4493 (mtt) REVERT: Z 76 LYS cc_start: 0.7318 (tptt) cc_final: 0.6306 (mmtt) REVERT: d 7 LYS cc_start: 0.5509 (OUTLIER) cc_final: 0.4442 (tptt) REVERT: d 75 ASP cc_start: 0.5024 (p0) cc_final: 0.4546 (m-30) REVERT: e 1 MET cc_start: 0.5692 (tmm) cc_final: 0.5226 (tmm) REVERT: f 265 TYR cc_start: 0.4376 (OUTLIER) cc_final: 0.4150 (m-80) REVERT: f 272 GLU cc_start: 0.7320 (mp0) cc_final: 0.6993 (tm-30) REVERT: f 294 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7074 (ttp80) REVERT: h 46 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6017 (m-70) REVERT: h 48 GLN cc_start: 0.6922 (pp30) cc_final: 0.6569 (pp30) REVERT: h 302 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: h 326 THR cc_start: 0.8780 (m) cc_final: 0.8440 (p) REVERT: h 340 TYR cc_start: 0.6803 (t80) cc_final: 0.4209 (t80) REVERT: k 112 MET cc_start: 0.7332 (ptt) cc_final: 0.7041 (ptt) REVERT: k 155 VAL cc_start: 0.7023 (t) cc_final: 0.6611 (t) REVERT: m 96 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7278 (tptm) REVERT: m 238 LEU cc_start: 0.8236 (tt) cc_final: 0.8035 (tt) REVERT: m 252 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.4867 (pp) REVERT: m 267 MET cc_start: 0.8293 (mmm) cc_final: 0.7622 (tpp) REVERT: m 276 SER cc_start: 0.8285 (p) cc_final: 0.7992 (p) REVERT: p 60 MET cc_start: 0.4396 (OUTLIER) cc_final: 0.3989 (mtm) REVERT: p 169 MET cc_start: 0.6985 (mmm) cc_final: 0.6702 (mmp) outliers start: 345 outliers final: 278 residues processed: 1727 average time/residue: 0.7355 time to fit residues: 2233.7232 Evaluate side-chains 1729 residues out of total 8071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1422 time to evaluate : 7.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain J residue 458 VAL Chi-restraints excluded: chain J residue 613 THR Chi-restraints excluded: chain J residue 737 LEU Chi-restraints excluded: chain J residue 851 THR Chi-restraints excluded: chain J residue 878 VAL Chi-restraints excluded: chain J residue 928 LEU Chi-restraints excluded: chain J residue 972 MET Chi-restraints excluded: chain J residue 1016 SER Chi-restraints excluded: chain J residue 1049 THR Chi-restraints excluded: chain J residue 1075 SER Chi-restraints excluded: chain J residue 1095 ILE Chi-restraints excluded: chain J residue 1105 MET Chi-restraints excluded: chain J residue 1106 THR Chi-restraints excluded: chain J residue 1110 VAL Chi-restraints excluded: chain J residue 1174 LEU Chi-restraints excluded: chain J residue 1210 VAL Chi-restraints excluded: chain J residue 1321 LEU Chi-restraints excluded: chain J residue 1336 SER Chi-restraints excluded: chain J residue 1369 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 167 PHE Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 207 PHE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 404 SER Chi-restraints excluded: chain K residue 440 ILE Chi-restraints excluded: chain K residue 458 VAL Chi-restraints excluded: chain K residue 598 VAL Chi-restraints excluded: chain K residue 637 VAL Chi-restraints excluded: chain K residue 649 GLU Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 677 LYS Chi-restraints excluded: chain K residue 711 VAL Chi-restraints excluded: chain K residue 736 LEU Chi-restraints excluded: chain K residue 748 ILE Chi-restraints excluded: chain K residue 769 MET Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 848 HIS Chi-restraints excluded: chain K residue 851 THR Chi-restraints excluded: chain K residue 905 ASP Chi-restraints excluded: chain K residue 922 THR Chi-restraints excluded: chain K residue 942 GLN Chi-restraints excluded: chain K residue 1026 SER Chi-restraints excluded: chain K residue 1049 THR Chi-restraints excluded: chain K residue 1099 LEU Chi-restraints excluded: chain K residue 1116 ASP Chi-restraints excluded: chain K residue 1168 VAL Chi-restraints excluded: chain K residue 1199 SER Chi-restraints excluded: chain K residue 1210 VAL Chi-restraints excluded: chain K residue 1213 GLU Chi-restraints excluded: chain K residue 1219 VAL Chi-restraints excluded: chain K residue 1241 ASN Chi-restraints excluded: chain K residue 1253 ILE Chi-restraints excluded: chain K residue 1325 CYS Chi-restraints excluded: chain K residue 1327 PHE Chi-restraints excluded: chain K residue 1342 LEU Chi-restraints excluded: chain K residue 1366 VAL Chi-restraints excluded: chain K residue 1372 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 61 ASN Chi-restraints excluded: chain N residue 65 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 328 MET Chi-restraints excluded: chain N residue 334 PHE Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 405 TYR Chi-restraints excluded: chain N residue 464 LEU Chi-restraints excluded: chain N residue 470 THR Chi-restraints excluded: chain N residue 518 ILE Chi-restraints excluded: chain N residue 637 VAL Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 667 CYS Chi-restraints excluded: chain N residue 687 TYR Chi-restraints excluded: chain N residue 732 ILE Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 756 THR Chi-restraints excluded: chain N residue 826 CYS Chi-restraints excluded: chain N residue 848 HIS Chi-restraints excluded: chain N residue 865 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 919 THR Chi-restraints excluded: chain N residue 925 VAL Chi-restraints excluded: chain N residue 928 LEU Chi-restraints excluded: chain N residue 933 PHE Chi-restraints excluded: chain N residue 950 PHE Chi-restraints excluded: chain N residue 971 VAL Chi-restraints excluded: chain N residue 1018 MET Chi-restraints excluded: chain N residue 1051 GLU Chi-restraints excluded: chain N residue 1113 ILE Chi-restraints excluded: chain N residue 1114 THR Chi-restraints excluded: chain N residue 1116 ASP Chi-restraints excluded: chain N residue 1189 VAL Chi-restraints excluded: chain N residue 1211 SER Chi-restraints excluded: chain N residue 1213 GLU Chi-restraints excluded: chain N residue 1264 VAL Chi-restraints excluded: chain N residue 1295 SER Chi-restraints excluded: chain N residue 1325 CYS Chi-restraints excluded: chain N residue 1352 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 104 HIS Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 LYS Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 279 VAL Chi-restraints excluded: chain O residue 284 ASP Chi-restraints excluded: chain O residue 292 THR Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 334 PHE Chi-restraints excluded: chain O residue 340 ASP Chi-restraints excluded: chain O residue 377 HIS Chi-restraints excluded: chain O residue 515 VAL Chi-restraints excluded: chain O residue 522 CYS Chi-restraints excluded: chain O residue 568 VAL Chi-restraints excluded: chain O residue 588 PHE Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain O residue 661 SER Chi-restraints excluded: chain O residue 748 ILE Chi-restraints excluded: chain O residue 757 LEU Chi-restraints excluded: chain O residue 984 ASN Chi-restraints excluded: chain O residue 1021 MET Chi-restraints excluded: chain O residue 1046 VAL Chi-restraints excluded: chain O residue 1082 ASP Chi-restraints excluded: chain O residue 1088 VAL Chi-restraints excluded: chain O residue 1127 VAL Chi-restraints excluded: chain O residue 1174 LEU Chi-restraints excluded: chain O residue 1309 VAL Chi-restraints excluded: chain O residue 1314 ILE Chi-restraints excluded: chain O residue 1336 SER Chi-restraints excluded: chain O residue 1343 ILE Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 95 PHE Chi-restraints excluded: chain P residue 112 LYS Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 178 ASN Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain P residue 377 HIS Chi-restraints excluded: chain P residue 382 GLU Chi-restraints excluded: chain P residue 436 VAL Chi-restraints excluded: chain P residue 524 LEU Chi-restraints excluded: chain P residue 526 THR Chi-restraints excluded: chain P residue 530 LEU Chi-restraints excluded: chain P residue 550 ILE Chi-restraints excluded: chain P residue 592 THR Chi-restraints excluded: chain P residue 602 VAL Chi-restraints excluded: chain P residue 706 VAL Chi-restraints excluded: chain P residue 723 LEU Chi-restraints excluded: chain P residue 732 ILE Chi-restraints excluded: chain P residue 756 THR Chi-restraints excluded: chain P residue 808 LEU Chi-restraints excluded: chain P residue 813 TYR Chi-restraints excluded: chain P residue 851 THR Chi-restraints excluded: chain P residue 885 SER Chi-restraints excluded: chain P residue 890 THR Chi-restraints excluded: chain P residue 1033 GLN Chi-restraints excluded: chain P residue 1124 PHE Chi-restraints excluded: chain P residue 1138 VAL Chi-restraints excluded: chain P residue 1178 GLN Chi-restraints excluded: chain P residue 1184 ILE Chi-restraints excluded: chain P residue 1192 ASP Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1262 THR Chi-restraints excluded: chain P residue 1292 ASN Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1364 GLU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 103 TYR Chi-restraints excluded: chain v residue 115 TYR Chi-restraints excluded: chain v residue 300 VAL Chi-restraints excluded: chain v residue 331 ILE Chi-restraints excluded: chain v residue 370 VAL Chi-restraints excluded: chain v residue 374 THR Chi-restraints excluded: chain v residue 397 VAL Chi-restraints excluded: chain v residue 424 HIS Chi-restraints excluded: chain v residue 469 SER Chi-restraints excluded: chain v residue 498 LEU Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 94 PHE Chi-restraints excluded: chain y residue 3123 VAL Chi-restraints excluded: chain y residue 3134 THR Chi-restraints excluded: chain y residue 3149 LEU Chi-restraints excluded: chain z residue 3144 LEU Chi-restraints excluded: chain Z residue 31 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 18 PHE Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain u residue 37 ASN Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain f residue 50 SER Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 205 THR Chi-restraints excluded: chain f residue 212 VAL Chi-restraints excluded: chain f residue 216 ILE Chi-restraints excluded: chain f residue 225 VAL Chi-restraints excluded: chain f residue 265 TYR Chi-restraints excluded: chain f residue 280 PHE Chi-restraints excluded: chain f residue 297 TYR Chi-restraints excluded: chain f residue 311 LEU Chi-restraints excluded: chain f residue 333 TRP Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain f residue 358 SER Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 45 GLU Chi-restraints excluded: chain h residue 46 HIS Chi-restraints excluded: chain h residue 68 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain h residue 133 ILE Chi-restraints excluded: chain h residue 171 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 224 THR Chi-restraints excluded: chain h residue 302 MET Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 169 MET Chi-restraints excluded: chain k residue 182 LEU Chi-restraints excluded: chain k residue 232 HIS Chi-restraints excluded: chain k residue 238 LEU Chi-restraints excluded: chain k residue 257 VAL Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 28 ILE Chi-restraints excluded: chain m residue 96 LYS Chi-restraints excluded: chain m residue 193 VAL Chi-restraints excluded: chain m residue 211 ILE Chi-restraints excluded: chain m residue 215 LEU Chi-restraints excluded: chain m residue 245 ASP Chi-restraints excluded: chain m residue 252 LEU Chi-restraints excluded: chain p residue 10 SER Chi-restraints excluded: chain p residue 60 MET Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 111 VAL Chi-restraints excluded: chain p residue 144 GLU Chi-restraints excluded: chain p residue 175 HIS Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 197 LEU Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 234 ASP Chi-restraints excluded: chain p residue 257 VAL Chi-restraints excluded: chain p residue 264 MET Chi-restraints excluded: chain p residue 297 THR Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 85 ILE Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain r residue 128 ASN Chi-restraints excluded: chain r residue 147 LEU Chi-restraints excluded: chain r residue 152 LEU Chi-restraints excluded: chain r residue 170 LEU Chi-restraints excluded: chain r residue 202 LEU Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 230 HIS Chi-restraints excluded: chain r residue 261 LEU Chi-restraints excluded: chain r residue 273 SER Chi-restraints excluded: chain r residue 293 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 931 random chunks: chunk 586 optimal weight: 30.0000 chunk 786 optimal weight: 8.9990 chunk 226 optimal weight: 20.0000 chunk 681 optimal weight: 40.0000 chunk 109 optimal weight: 3.9990 chunk 205 optimal weight: 30.0000 chunk 739 optimal weight: 5.9990 chunk 309 optimal weight: 0.0040 chunk 759 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN ** J 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 HIS ** J 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 964 HIS K 35 HIS K 415 ASN ** K 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 735 HIS ** K 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 804 HIS ** N 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 HIS ** O 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 984 ASN O1089 HIS ** O1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1296 GLN P1178 GLN ** P1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1292 ASN ** P1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS ** Z 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 HIS ** k 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 23 GLN ** p 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122102 restraints weight = 165425.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124308 restraints weight = 90800.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125732 restraints weight = 57754.928| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 1.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 75983 Z= 0.240 Angle : 0.766 15.595 103244 Z= 0.380 Chirality : 0.046 0.563 11614 Planarity : 0.005 0.087 13471 Dihedral : 5.531 58.962 10399 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 3.93 % Allowed : 29.77 % Favored : 66.30 % 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: -1.17 (0.08), residues: 9356 helix: 0.25 (0.09), residues: 3528 sheet: -0.48 (0.14), residues: 1298 loop : -1.71 (0.09), residues: 4530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP x 54 HIS 0.030 0.001 HIS h 46 PHE 0.079 0.002 PHE Z 50 TYR 0.043 0.002 TYR r 181 ARG 0.010 0.001 ARG N 557 =============================================================================== Job complete usr+sys time: 32212.44 seconds wall clock time: 556 minutes 26.70 seconds (33386.70 seconds total)