Starting phenix.real_space_refine on Sun Nov 17 21:17:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bw1_44944/11_2024/9bw1_44944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bw1_44944/11_2024/9bw1_44944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bw1_44944/11_2024/9bw1_44944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bw1_44944/11_2024/9bw1_44944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bw1_44944/11_2024/9bw1_44944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bw1_44944/11_2024/9bw1_44944.cif" } resolution = 3.65 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 290 5.49 5 Mg 11 5.21 5 S 136 5.16 5 C 29151 2.51 5 N 8356 2.21 5 O 9337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47283 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 692 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "4" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "5" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1065 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "I" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1790 Classifications: {'DNA': 87} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 86} Chain: "J" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3707 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain: "M" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6349 Classifications: {'peptide': 779} Link IDs: {'PTRANS': 32, 'TRANS': 746} Chain breaks: 1 Chain: "N" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6349 Classifications: {'peptide': 779} Link IDs: {'PTRANS': 32, 'TRANS': 746} Chain breaks: 1 Chain: "O" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2788 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain: "P" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2788 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain: "Q" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2440 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "a" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "b" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "c" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "x" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 119 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "y" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 119 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6698 SG CYS J 139 113.771 100.177 204.450 1.00 87.21 S ATOM 6719 SG CYS J 142 116.816 98.286 203.136 1.00 75.34 S ATOM 6933 SG CYS J 167 117.042 100.463 206.324 1.00 99.09 S ATOM 7022 SG CYS J 178 98.953 96.902 203.975 1.00112.08 S ATOM 7045 SG CYS J 181 95.339 95.995 204.276 1.00114.07 S ATOM 7180 SG CYS J 197 98.077 93.216 204.247 1.00 94.44 S ATOM 7201 SG CYS J 200 97.286 95.137 201.095 1.00102.55 S Time building chain proxies: 26.90, per 1000 atoms: 0.57 Number of scatterers: 47283 At special positions: 0 Unit cell: (152.892, 163.578, 278.658, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 136 16.00 P 290 15.00 Mg 11 11.99 O 9337 8.00 N 8356 7.00 C 29151 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: 12.27 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" ND1 HIS J 170 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 139 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 167 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 142 " pdb=" ZN J 602 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 178 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 200 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 197 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 181 " Number of angles added : 9 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9708 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 36 sheets defined 55.4% alpha, 8.5% beta 113 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 16.97 Creating SS restraints... Processing helix chain 'J' and resid 40 through 53 Processing helix chain 'J' and resid 55 through 63 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 81 through 87 removed outlier: 3.592A pdb=" N PHE J 85 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 157 through 161 Processing helix chain 'J' and resid 219 through 244 removed outlier: 4.125A pdb=" N GLN J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 262 removed outlier: 3.568A pdb=" N ILE J 253 " --> pdb=" O SER J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 277 Processing helix chain 'J' and resid 279 through 289 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 308 through 314 Processing helix chain 'J' and resid 314 through 320 removed outlier: 3.888A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR J 320 " --> pdb=" O LYS J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 328 Processing helix chain 'J' and resid 345 through 359 Processing helix chain 'J' and resid 366 through 375 Processing helix chain 'J' and resid 377 through 383 removed outlier: 3.688A pdb=" N ILE J 381 " --> pdb=" O HIS J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 426 removed outlier: 3.544A pdb=" N CYS J 389 " --> pdb=" O PHE J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 437 removed outlier: 3.640A pdb=" N LEU J 437 " --> pdb=" O ARG J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 446 removed outlier: 3.520A pdb=" N ARG J 445 " --> pdb=" O GLY J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 461 Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 15 through 28 Processing helix chain 'M' and resid 62 through 72 Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'M' and resid 147 through 155 Processing helix chain 'M' and resid 169 through 184 removed outlier: 5.113A pdb=" N ASP M 181 " --> pdb=" O GLN M 177 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR M 182 " --> pdb=" O PHE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 205 Processing helix chain 'M' and resid 209 through 215 Processing helix chain 'M' and resid 221 through 231 removed outlier: 3.551A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 Processing helix chain 'M' and resid 343 through 352 removed outlier: 3.800A pdb=" N ALA M 352 " --> pdb=" O ARG M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 368 Processing helix chain 'M' and resid 382 through 400 Processing helix chain 'M' and resid 402 through 408 removed outlier: 3.763A pdb=" N ILE M 405 " --> pdb=" O CYS M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 410 through 414 Processing helix chain 'M' and resid 422 through 437 Processing helix chain 'M' and resid 444 through 460 Processing helix chain 'M' and resid 465 through 474 Processing helix chain 'M' and resid 478 through 486 Processing helix chain 'M' and resid 487 through 492 Processing helix chain 'M' and resid 493 through 495 No H-bonds generated for 'chain 'M' and resid 493 through 495' Processing helix chain 'M' and resid 563 through 578 Processing helix chain 'M' and resid 595 through 605 removed outlier: 3.960A pdb=" N GLU M 599 " --> pdb=" O SER M 595 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE M 605 " --> pdb=" O LEU M 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 619 removed outlier: 3.760A pdb=" N PHE M 619 " --> pdb=" O LYS M 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 616 through 619' Processing helix chain 'M' and resid 620 through 634 removed outlier: 3.701A pdb=" N ARG M 625 " --> pdb=" O SER M 621 " (cutoff:3.500A) Processing helix chain 'M' and resid 643 through 651 removed outlier: 3.831A pdb=" N VAL M 648 " --> pdb=" O THR M 645 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG M 649 " --> pdb=" O ARG M 646 " (cutoff:3.500A) Processing helix chain 'M' and resid 656 through 661 removed outlier: 3.622A pdb=" N ALA M 661 " --> pdb=" O LYS M 658 " (cutoff:3.500A) Processing helix chain 'M' and resid 664 through 683 removed outlier: 4.430A pdb=" N TYR M 680 " --> pdb=" O ALA M 676 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP M 681 " --> pdb=" O TYR M 677 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 703 Processing helix chain 'M' and resid 706 through 710 Processing helix chain 'M' and resid 714 through 722 Processing helix chain 'M' and resid 747 through 752 removed outlier: 3.536A pdb=" N ASP M 752 " --> pdb=" O SER M 749 " (cutoff:3.500A) Processing helix chain 'M' and resid 795 through 812 Processing helix chain 'M' and resid 820 through 831 Processing helix chain 'M' and resid 834 through 856 removed outlier: 3.530A pdb=" N GLY M 856 " --> pdb=" O ARG M 852 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 15 through 27 Processing helix chain 'N' and resid 61 through 72 removed outlier: 4.025A pdb=" N ILE N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 131 Processing helix chain 'N' and resid 146 through 155 Processing helix chain 'N' and resid 169 through 185 removed outlier: 5.115A pdb=" N ASP N 181 " --> pdb=" O GLN N 177 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR N 182 " --> pdb=" O PHE N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 205 removed outlier: 3.512A pdb=" N GLN N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 215 Processing helix chain 'N' and resid 221 through 231 Processing helix chain 'N' and resid 254 through 263 Processing helix chain 'N' and resid 343 through 351 Processing helix chain 'N' and resid 353 through 368 Processing helix chain 'N' and resid 369 through 372 Processing helix chain 'N' and resid 382 through 400 Processing helix chain 'N' and resid 403 through 408 removed outlier: 3.987A pdb=" N LEU N 408 " --> pdb=" O ILE N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 410 through 414 removed outlier: 3.681A pdb=" N VAL N 413 " --> pdb=" O HIS N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 437 removed outlier: 3.682A pdb=" N TYR N 437 " --> pdb=" O ILE N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 460 Processing helix chain 'N' and resid 465 through 474 Processing helix chain 'N' and resid 479 through 486 Processing helix chain 'N' and resid 489 through 493 removed outlier: 3.527A pdb=" N TYR N 492 " --> pdb=" O ARG N 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN N 493 " --> pdb=" O ALA N 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 489 through 493' Processing helix chain 'N' and resid 564 through 578 Processing helix chain 'N' and resid 595 through 606 removed outlier: 3.963A pdb=" N GLU N 599 " --> pdb=" O SER N 595 " (cutoff:3.500A) Processing helix chain 'N' and resid 617 through 619 No H-bonds generated for 'chain 'N' and resid 617 through 619' Processing helix chain 'N' and resid 620 through 634 removed outlier: 3.804A pdb=" N LEU N 626 " --> pdb=" O VAL N 622 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE N 627 " --> pdb=" O CYS N 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY N 628 " --> pdb=" O GLU N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 643 through 647 removed outlier: 3.543A pdb=" N ASN N 647 " --> pdb=" O ILE N 644 " (cutoff:3.500A) Processing helix chain 'N' and resid 656 through 661 removed outlier: 3.544A pdb=" N LEU N 660 " --> pdb=" O ASN N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 664 through 679 Processing helix chain 'N' and resid 691 through 703 Processing helix chain 'N' and resid 706 through 710 Processing helix chain 'N' and resid 714 through 722 removed outlier: 3.566A pdb=" N LEU N 722 " --> pdb=" O GLN N 718 " (cutoff:3.500A) Processing helix chain 'N' and resid 747 through 756 Proline residue: N 753 - end of helix Processing helix chain 'N' and resid 787 through 792 Processing helix chain 'N' and resid 795 through 812 Processing helix chain 'N' and resid 820 through 831 removed outlier: 3.717A pdb=" N LEU N 824 " --> pdb=" O SER N 820 " (cutoff:3.500A) Processing helix chain 'N' and resid 834 through 855 removed outlier: 3.755A pdb=" N GLU N 849 " --> pdb=" O ALA N 845 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 850 " --> pdb=" O GLU N 846 " (cutoff:3.500A) Processing helix chain 'O' and resid 564 through 579 removed outlier: 3.614A pdb=" N MET O 569 " --> pdb=" O ARG O 565 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL O 570 " --> pdb=" O SER O 566 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 605 Processing helix chain 'O' and resid 620 through 634 removed outlier: 3.699A pdb=" N GLU O 624 " --> pdb=" O GLY O 620 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG O 625 " --> pdb=" O SER O 621 " (cutoff:3.500A) Processing helix chain 'O' and resid 635 through 638 Processing helix chain 'O' and resid 643 through 651 removed outlier: 3.599A pdb=" N ARG O 646 " --> pdb=" O GLN O 643 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL O 648 " --> pdb=" O THR O 645 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG O 649 " --> pdb=" O ARG O 646 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 660 Processing helix chain 'O' and resid 664 through 678 Processing helix chain 'O' and resid 691 through 704 Processing helix chain 'O' and resid 706 through 710 Processing helix chain 'O' and resid 714 through 721 Processing helix chain 'O' and resid 747 through 756 Proline residue: O 753 - end of helix removed outlier: 3.673A pdb=" N GLU O 756 " --> pdb=" O PRO O 753 " (cutoff:3.500A) Processing helix chain 'O' and resid 788 through 792 Processing helix chain 'O' and resid 795 through 816 removed outlier: 3.965A pdb=" N LYS O 800 " --> pdb=" O GLU O 796 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU O 801 " --> pdb=" O LYS O 797 " (cutoff:3.500A) Processing helix chain 'O' and resid 816 through 842 Processing helix chain 'P' and resid 564 through 569 removed outlier: 3.639A pdb=" N MET P 569 " --> pdb=" O ARG P 565 " (cutoff:3.500A) Processing helix chain 'P' and resid 569 through 579 Processing helix chain 'P' and resid 596 through 605 removed outlier: 3.560A pdb=" N PHE P 605 " --> pdb=" O LEU P 601 " (cutoff:3.500A) Processing helix chain 'P' and resid 617 through 619 No H-bonds generated for 'chain 'P' and resid 617 through 619' Processing helix chain 'P' and resid 620 through 634 removed outlier: 3.827A pdb=" N LEU P 626 " --> pdb=" O VAL P 622 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE P 634 " --> pdb=" O SER P 630 " (cutoff:3.500A) Processing helix chain 'P' and resid 643 through 651 removed outlier: 3.573A pdb=" N ARG P 646 " --> pdb=" O GLN P 643 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL P 648 " --> pdb=" O THR P 645 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG P 649 " --> pdb=" O ARG P 646 " (cutoff:3.500A) Processing helix chain 'P' and resid 652 through 656 removed outlier: 3.711A pdb=" N ASN P 656 " --> pdb=" O LYS P 653 " (cutoff:3.500A) Processing helix chain 'P' and resid 664 through 678 Processing helix chain 'P' and resid 691 through 703 Processing helix chain 'P' and resid 706 through 710 Processing helix chain 'P' and resid 714 through 721 Processing helix chain 'P' and resid 747 through 752 removed outlier: 3.517A pdb=" N ASP P 752 " --> pdb=" O SER P 749 " (cutoff:3.500A) Processing helix chain 'P' and resid 788 through 792 Processing helix chain 'P' and resid 796 through 816 removed outlier: 3.949A pdb=" N LYS P 800 " --> pdb=" O GLU P 796 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU P 801 " --> pdb=" O LYS P 797 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR P 814 " --> pdb=" O TYR P 810 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN P 816 " --> pdb=" O ASN P 812 " (cutoff:3.500A) Processing helix chain 'P' and resid 816 through 842 Processing helix chain 'Q' and resid 15 through 26 removed outlier: 3.585A pdb=" N ARG Q 19 " --> pdb=" O PRO Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 79 Processing helix chain 'Q' and resid 80 through 82 No H-bonds generated for 'chain 'Q' and resid 80 through 82' Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 149 through 164 Processing helix chain 'Q' and resid 172 through 178 removed outlier: 4.110A pdb=" N LYS Q 178 " --> pdb=" O HIS Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 196 Processing helix chain 'Q' and resid 208 through 214 removed outlier: 3.574A pdb=" N PHE Q 214 " --> pdb=" O LEU Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 removed outlier: 3.521A pdb=" N VAL Q 241 " --> pdb=" O SER Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 266 through 273 removed outlier: 3.641A pdb=" N ARG Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 296 Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.650A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 331 removed outlier: 3.756A pdb=" N CYS Q 315 " --> pdb=" O SER Q 311 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 331 " --> pdb=" O ARG Q 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 13 removed outlier: 3.505A pdb=" N LEU R 11 " --> pdb=" O PRO R 8 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR R 13 " --> pdb=" O GLU R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 removed outlier: 3.700A pdb=" N ARG R 19 " --> pdb=" O PRO R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.741A pdb=" N GLU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 148 through 163 Processing helix chain 'R' and resid 172 through 178 Processing helix chain 'R' and resid 189 through 200 Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 254 removed outlier: 3.594A pdb=" N VAL R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 273 removed outlier: 3.617A pdb=" N ARG R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 295 removed outlier: 3.581A pdb=" N LEU R 281 " --> pdb=" O CYS R 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG R 295 " --> pdb=" O ASP R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.521A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 329 removed outlier: 4.319A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 343 removed outlier: 3.741A pdb=" N VAL R 336 " --> pdb=" O THR R 332 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 13 removed outlier: 3.646A pdb=" N THR S 13 " --> pdb=" O GLU S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.972A pdb=" N GLU S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 82 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 148 through 164 Processing helix chain 'S' and resid 172 through 178 removed outlier: 3.508A pdb=" N HIS S 175 " --> pdb=" O GLU S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 200 removed outlier: 3.742A pdb=" N GLN S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU S 192 " --> pdb=" O GLN S 188 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU S 195 " --> pdb=" O CYS S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 removed outlier: 3.766A pdb=" N THR S 213 " --> pdb=" O GLU S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 224 removed outlier: 3.974A pdb=" N ARG S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 254 removed outlier: 3.513A pdb=" N VAL S 241 " --> pdb=" O SER S 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS S 254 " --> pdb=" O THR S 250 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 273 Processing helix chain 'S' and resid 277 through 296 removed outlier: 3.608A pdb=" N LEU S 281 " --> pdb=" O CYS S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 308 removed outlier: 4.559A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 329 Processing helix chain 'S' and resid 332 through 344 removed outlier: 3.540A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 13 Processing helix chain 'T' and resid 15 through 25 Processing helix chain 'T' and resid 30 through 46 Processing helix chain 'T' and resid 62 through 75 Processing helix chain 'T' and resid 78 through 83 Processing helix chain 'T' and resid 105 through 118 Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 173 through 178 Processing helix chain 'T' and resid 184 through 200 removed outlier: 3.586A pdb=" N GLN T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 215 Processing helix chain 'T' and resid 218 through 224 Processing helix chain 'T' and resid 237 through 254 Processing helix chain 'T' and resid 266 through 275 Processing helix chain 'T' and resid 277 through 296 Processing helix chain 'T' and resid 301 through 307 Processing helix chain 'T' and resid 311 through 327 Processing helix chain 'T' and resid 332 through 344 Processing helix chain 'U' and resid 9 through 14 removed outlier: 3.991A pdb=" N THR U 13 " --> pdb=" O LEU U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 25 Processing helix chain 'U' and resid 30 through 46 Processing helix chain 'U' and resid 62 through 83 removed outlier: 3.528A pdb=" N GLN U 72 " --> pdb=" O LEU U 68 " (cutoff:3.500A) Proline residue: U 80 - end of helix Processing helix chain 'U' and resid 105 through 118 removed outlier: 3.503A pdb=" N TYR U 109 " --> pdb=" O ASN U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 186 through 200 removed outlier: 3.886A pdb=" N MET U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY U 200 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 214 Processing helix chain 'U' and resid 218 through 224 Processing helix chain 'U' and resid 237 through 255 Processing helix chain 'U' and resid 266 through 275 Processing helix chain 'U' and resid 277 through 296 Processing helix chain 'U' and resid 301 through 307 Processing helix chain 'U' and resid 311 through 329 removed outlier: 3.810A pdb=" N GLN U 328 " --> pdb=" O GLU U 324 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU U 329 " --> pdb=" O GLY U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 343 Processing helix chain 'V' and resid 8 through 13 Processing helix chain 'V' and resid 15 through 25 removed outlier: 3.645A pdb=" N ARG V 19 " --> pdb=" O PRO V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 46 removed outlier: 3.517A pdb=" N GLU V 46 " --> pdb=" O ARG V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 77 Processing helix chain 'V' and resid 78 through 85 Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 148 through 164 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.560A pdb=" N LYS V 178 " --> pdb=" O HIS V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 200 removed outlier: 3.639A pdb=" N GLN V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU V 192 " --> pdb=" O GLN V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 215 Processing helix chain 'V' and resid 219 through 224 Processing helix chain 'V' and resid 237 through 254 Processing helix chain 'V' and resid 263 through 265 No H-bonds generated for 'chain 'V' and resid 263 through 265' Processing helix chain 'V' and resid 266 through 274 Processing helix chain 'V' and resid 277 through 296 removed outlier: 4.000A pdb=" N LEU V 281 " --> pdb=" O CYS V 277 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 308 removed outlier: 3.577A pdb=" N LEU V 305 " --> pdb=" O THR V 301 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 329 removed outlier: 3.892A pdb=" N GLU V 324 " --> pdb=" O LYS V 320 " (cutoff:3.500A) Processing helix chain 'V' and resid 332 through 343 removed outlier: 3.670A pdb=" N VAL V 336 " --> pdb=" O THR V 332 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 24 Processing helix chain 'W' and resid 30 through 46 Processing helix chain 'W' and resid 64 through 79 Processing helix chain 'W' and resid 80 through 84 removed outlier: 3.804A pdb=" N GLU W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER W 84 " --> pdb=" O LYS W 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 80 through 84' Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 148 through 164 Processing helix chain 'W' and resid 172 through 178 removed outlier: 3.530A pdb=" N HIS W 175 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY W 177 " --> pdb=" O GLN W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 200 removed outlier: 3.769A pdb=" N GLN W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 214 Processing helix chain 'W' and resid 218 through 224 Processing helix chain 'W' and resid 237 through 254 Processing helix chain 'W' and resid 263 through 265 No H-bonds generated for 'chain 'W' and resid 263 through 265' Processing helix chain 'W' and resid 266 through 275 Processing helix chain 'W' and resid 277 through 295 Processing helix chain 'W' and resid 301 through 308 removed outlier: 3.504A pdb=" N ARG W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 330 Processing helix chain 'W' and resid 332 through 344 Processing sheet with id=AA1, first strand: chain 'J' and resid 166 through 167 removed outlier: 3.713A pdb=" N LYS J 172 " --> pdb=" O CYS J 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 52 through 56 removed outlier: 6.531A pdb=" N TRP M 540 " --> pdb=" O LEU M 557 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU M 557 " --> pdb=" O TRP M 540 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR M 542 " --> pdb=" O VAL M 555 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL M 555 " --> pdb=" O THR M 542 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU M 544 " --> pdb=" O LEU M 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 75 through 80 removed outlier: 6.851A pdb=" N ALA M 113 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG M 161 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TRP M 115 " --> pdb=" O ARG M 161 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS M 163 " --> pdb=" O TRP M 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU M 117 " --> pdb=" O HIS M 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 85 through 90 Processing sheet with id=AA5, first strand: chain 'M' and resid 135 through 138 Processing sheet with id=AA6, first strand: chain 'M' and resid 235 through 236 Processing sheet with id=AA7, first strand: chain 'M' and resid 729 through 731 removed outlier: 4.850A pdb=" N GLN M 761 " --> pdb=" O PHE M 775 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP M 765 " --> pdb=" O ILE M 771 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE M 771 " --> pdb=" O ASP M 765 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY M 770 " --> pdb=" O SER M 785 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 52 through 56 removed outlier: 6.669A pdb=" N ASP N 546 " --> pdb=" O LEU N 552 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU N 552 " --> pdb=" O ASP N 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 75 through 80 removed outlier: 6.695A pdb=" N ILE N 108 " --> pdb=" O LEU N 76 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE N 78 " --> pdb=" O PHE N 106 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE N 106 " --> pdb=" O PHE N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 85 through 90 Processing sheet with id=AB2, first strand: chain 'N' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'N' and resid 208 through 209 removed outlier: 3.522A pdb=" N ILE N 208 " --> pdb=" O ILE N 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 527 through 528 removed outlier: 6.219A pdb=" N LEU N 527 " --> pdb=" O LEU N 536 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 729 through 731 removed outlier: 4.329A pdb=" N GLN N 761 " --> pdb=" O PHE N 775 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 551 through 558 removed outlier: 6.332A pdb=" N LEU O 552 " --> pdb=" O ASP O 546 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP O 546 " --> pdb=" O LEU O 552 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA O 554 " --> pdb=" O LEU O 544 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL O 586 " --> pdb=" O GLY O 516 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE O 518 " --> pdb=" O VAL O 586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS O 610 " --> pdb=" O VAL O 585 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 527 through 528 removed outlier: 6.644A pdb=" N LEU O 527 " --> pdb=" O LEU O 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 729 through 731 removed outlier: 4.644A pdb=" N GLN O 761 " --> pdb=" O PHE O 775 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 738 through 740 Processing sheet with id=AC1, first strand: chain 'P' and resid 552 through 558 removed outlier: 6.488A pdb=" N LEU P 552 " --> pdb=" O ASP P 546 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP P 546 " --> pdb=" O LEU P 552 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA P 554 " --> pdb=" O LEU P 544 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 527 through 528 Processing sheet with id=AC3, first strand: chain 'P' and resid 729 through 731 removed outlier: 4.667A pdb=" N GLN P 761 " --> pdb=" O PHE P 775 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP P 765 " --> pdb=" O ILE P 771 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE P 771 " --> pdb=" O ASP P 765 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 738 through 740 Processing sheet with id=AC5, first strand: chain 'Q' and resid 55 through 56 Processing sheet with id=AC6, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.436A pdb=" N VAL Q 92 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP Q 171 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE Q 94 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 91 through 95 removed outlier: 6.792A pdb=" N VAL R 92 " --> pdb=" O PHE R 169 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP R 171 " --> pdb=" O VAL R 92 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE R 94 " --> pdb=" O ASP R 171 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE R 53 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLY R 207 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 55 " --> pdb=" O GLY R 207 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'S' and resid 92 through 95 removed outlier: 6.756A pdb=" N VAL S 92 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP S 171 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE S 94 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 133 through 134 Processing sheet with id=AD1, first strand: chain 'T' and resid 92 through 95 removed outlier: 6.873A pdb=" N VAL T 92 " --> pdb=" O PHE T 169 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP T 171 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE T 94 " --> pdb=" O ASP T 171 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 133 through 135 Processing sheet with id=AD3, first strand: chain 'U' and resid 92 through 95 removed outlier: 6.708A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE U 168 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU U 206 " --> pdb=" O PHE U 168 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL U 170 " --> pdb=" O LEU U 206 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY U 207 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY U 57 " --> pdb=" O GLY U 207 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 133 through 135 Processing sheet with id=AD5, first strand: chain 'V' and resid 91 through 95 removed outlier: 6.229A pdb=" N ILE V 53 " --> pdb=" O LEU V 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 133 through 134 removed outlier: 3.777A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 203 through 206 removed outlier: 6.893A pdb=" N PHE W 52 " --> pdb=" O VAL W 226 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE W 228 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE W 54 " --> pdb=" O ILE W 228 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE W 230 " --> pdb=" O PHE W 54 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR W 56 " --> pdb=" O PHE W 230 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 93 through 94 Processing sheet with id=AD9, first strand: chain 'W' and resid 134 through 135 2037 hydrogen bonds defined for protein. 5655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 554 hydrogen bond angles 0 basepair planarities 113 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 23.21 Time building geometry restraints manager: 14.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7954 1.32 - 1.45: 14189 1.45 - 1.57: 25971 1.57 - 1.69: 570 1.69 - 1.82: 185 Bond restraints: 48869 Sorted by residual: bond pdb=" CA TYR P 788 " pdb=" C TYR P 788 " ideal model delta sigma weight residual 1.524 1.435 0.089 7.00e-03 2.04e+04 1.62e+02 bond pdb=" CA ARG T 223 " pdb=" C ARG T 223 " ideal model delta sigma weight residual 1.524 1.421 0.102 1.26e-02 6.30e+03 6.61e+01 bond pdb=" CA SER P 811 " pdb=" C SER P 811 " ideal model delta sigma weight residual 1.526 1.441 0.085 1.07e-02 8.73e+03 6.31e+01 bond pdb=" CA THR U 65 " pdb=" C THR U 65 " ideal model delta sigma weight residual 1.523 1.432 0.092 1.30e-02 5.92e+03 4.96e+01 bond pdb=" CA ARG N 580 " pdb=" C ARG N 580 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.34e-02 5.57e+03 4.89e+01 ... (remaining 48864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 66549 2.45 - 4.89: 704 4.89 - 7.34: 101 7.34 - 9.79: 31 9.79 - 12.23: 4 Bond angle restraints: 67389 Sorted by residual: angle pdb=" N ALA N 591 " pdb=" CA ALA N 591 " pdb=" C ALA N 591 " ideal model delta sigma weight residual 113.88 101.65 12.23 1.23e+00 6.61e-01 9.89e+01 angle pdb=" N ARG T 223 " pdb=" CA ARG T 223 " pdb=" C ARG T 223 " ideal model delta sigma weight residual 111.14 101.41 9.73 1.08e+00 8.57e-01 8.12e+01 angle pdb=" N GLY M 43 " pdb=" CA GLY M 43 " pdb=" C GLY M 43 " ideal model delta sigma weight residual 110.38 120.14 -9.76 1.28e+00 6.10e-01 5.81e+01 angle pdb=" N THR W 64 " pdb=" CA THR W 64 " pdb=" C THR W 64 " ideal model delta sigma weight residual 113.88 105.38 8.50 1.23e+00 6.61e-01 4.78e+01 angle pdb=" N LEU J 357 " pdb=" CA LEU J 357 " pdb=" C LEU J 357 " ideal model delta sigma weight residual 111.28 104.06 7.22 1.09e+00 8.42e-01 4.39e+01 ... (remaining 67384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 26421 34.34 - 68.69: 2289 68.69 - 103.03: 97 103.03 - 137.37: 1 137.37 - 171.71: 3 Dihedral angle restraints: 28811 sinusoidal: 13766 harmonic: 15045 Sorted by residual: dihedral pdb=" C TYR P 788 " pdb=" N TYR P 788 " pdb=" CA TYR P 788 " pdb=" CB TYR P 788 " ideal model delta harmonic sigma weight residual -122.60 -111.05 -11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C4' DA 4 -20 " pdb=" C3' DA 4 -20 " pdb=" O3' DA 4 -20 " pdb=" P DA 4 -19 " ideal model delta sinusoidal sigma weight residual 220.00 48.29 171.71 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA MET J 438 " pdb=" C MET J 438 " pdb=" N PRO J 439 " pdb=" CA PRO J 439 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 28808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 6752 0.069 - 0.139: 646 0.139 - 0.208: 31 0.208 - 0.277: 6 0.277 - 0.347: 1 Chirality restraints: 7436 Sorted by residual: chirality pdb=" CG LEU V 221 " pdb=" CB LEU V 221 " pdb=" CD1 LEU V 221 " pdb=" CD2 LEU V 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA LEU S 114 " pdb=" N LEU S 114 " pdb=" C LEU S 114 " pdb=" CB LEU S 114 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR N 564 " pdb=" N TYR N 564 " pdb=" C TYR N 564 " pdb=" CB TYR N 564 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 7433 not shown) Planarity restraints: 7681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU S 119 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO S 120 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO S 120 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO S 120 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 46 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO Q 47 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO Q 47 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO Q 47 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 362 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO J 363 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO J 363 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO J 363 " 0.057 5.00e-02 4.00e+02 ... (remaining 7678 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 365 2.51 - 3.11: 33791 3.11 - 3.71: 78298 3.71 - 4.30: 108678 4.30 - 4.90: 173769 Nonbonded interactions: 394901 Sorted by model distance: nonbonded pdb=" O3B ATP W 600 " pdb="MG MG W 601 " model vdw 1.917 2.170 nonbonded pdb=" OG1 THR U 64 " pdb="MG MG U 601 " model vdw 1.923 2.170 nonbonded pdb=" O1G ATP V 600 " pdb="MG MG V 601 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR R 64 " pdb="MG MG R 601 " model vdw 1.951 2.170 nonbonded pdb=" OD1 ASP M 104 " pdb="MG MG M 901 " model vdw 1.960 2.170 ... (remaining 394896 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 '2' and (resid -3 through 25 or resid 28 through 29)) selection = (chain '5' and (resid -3 through 25 or resid 28 through 29)) } ncs_group { reference = (chain 'M' and resid 1 through 857) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'S' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'T' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'U' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'V' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'W' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'x' selection = chain 'y' } 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: 4.850 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: 0.060 Extract box with map and model: 2.020 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 124.600 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.004 0.102 48869 Z= 0.262 Angle : 0.649 12.235 67389 Z= 0.368 Chirality : 0.042 0.347 7436 Planarity : 0.005 0.133 7681 Dihedral : 21.267 171.714 19103 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.11 % Favored : 95.64 % Rotamer: Outliers : 1.28 % Allowed : 29.92 % Favored : 68.80 % Cbeta Deviations : 0.02 % 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: -0.53 (0.12), residues: 5088 helix: 0.30 (0.10), residues: 2589 sheet: -1.09 (0.22), residues: 538 loop : -0.86 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 284 HIS 0.015 0.001 HIS S 162 PHE 0.029 0.001 PHE W 23 TYR 0.022 0.001 TYR O 742 ARG 0.015 0.000 ARG M 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 882 time to evaluate : 4.835 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: J 144 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: M 67 TYR cc_start: 0.7341 (m-80) cc_final: 0.6541 (m-80) REVERT: M 143 GLN cc_start: 0.7486 (tp-100) cc_final: 0.7002 (tm-30) REVERT: M 479 TYR cc_start: 0.6710 (t80) cc_final: 0.6498 (t80) REVERT: N 70 GLU cc_start: 0.7208 (tp30) cc_final: 0.6813 (tp30) REVERT: P 786 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: Q 192 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7031 (mm) REVERT: S 124 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.5096 (p-80) REVERT: U 41 MET cc_start: 0.6520 (mmt) cc_final: 0.6247 (tmm) REVERT: V 41 MET cc_start: 0.6970 (mmm) cc_final: 0.6629 (mmm) outliers start: 57 outliers final: 29 residues processed: 909 average time/residue: 0.6933 time to fit residues: 1018.0168 Evaluate side-chains 905 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 872 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain M residue 388 HIS Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain N residue 165 ASP Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 568 LEU Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 576 LYS Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain P residue 809 HIS Chi-restraints excluded: chain P residue 811 SER Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 124 HIS Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 224 ARG Chi-restraints excluded: chain U residue 67 ARG Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 220 GLN Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain W residue 215 ARG Chi-restraints excluded: chain W residue 249 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 446 optimal weight: 0.9980 chunk 400 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 160 optimal weight: 0.0870 chunk 252 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 480 optimal weight: 2.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: