Starting phenix.real_space_refine on Tue Oct 15 06:47:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/10_2024/7pt6_13619.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/10_2024/7pt6_13619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/10_2024/7pt6_13619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/10_2024/7pt6_13619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/10_2024/7pt6_13619.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/10_2024/7pt6_13619.cif" } resolution = 3.2 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= -0.000 sd= 0.009 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 14 6.06 5 P 44 5.49 5 Mg 14 5.21 5 S 348 5.16 5 C 46800 2.51 5 N 12922 2.21 5 O 14216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 74358 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4989 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 25, 'TRANS': 603} Chain breaks: 3 Chain: "C" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5000 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 31, 'TRANS': 605} Chain breaks: 6 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5323 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 24, 'TRANS': 643} Chain breaks: 1 Chain: "E" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5037 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 28, 'TRANS': 615} Chain breaks: 3 Chain: "F" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5048 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 22, 'TRANS': 614} Chain breaks: 3 Chain: "G" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5370 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 30, 'TRANS': 652} Chain breaks: 3 Chain: "H" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3292 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 3 Chain: "I" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2846 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 4 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 2, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38276 SG CYS B 341 108.239 119.330 82.035 1.00 60.30 S ATOM 38299 SG CYS B 344 104.865 117.329 81.772 1.00 70.03 S ATOM 38457 SG CYS B 364 106.767 117.685 85.188 1.00 66.27 S ATOM 38478 SG CYS B 367 107.177 115.368 82.128 1.00 80.44 S ATOM 48370 SG CYS D 349 150.067 109.690 99.731 1.00 32.18 S ATOM 48391 SG CYS D 352 151.963 107.783 102.291 1.00 37.99 S ATOM 48538 SG CYS D 371 152.555 107.175 98.437 1.00 49.73 S ATOM 48580 SG CYS D 376 149.692 105.721 100.412 1.00 61.15 S ATOM 53543 SG CYS E 183 115.426 114.103 59.306 1.00 8.16 S ATOM 53568 SG CYS E 186 113.748 110.814 58.055 1.00 15.58 S ATOM 53758 SG CYS E 211 112.356 112.739 61.072 1.00 8.02 S ATOM 53793 SG CYS E 236 115.535 110.784 61.259 1.00 25.49 S ATOM 58562 SG CYS F 311 130.842 113.153 98.619 1.00 81.58 S ATOM 58584 SG CYS F 314 130.099 111.672 101.984 1.00 86.40 S ATOM 58741 SG CYS F 333 133.589 111.137 100.425 1.00 74.61 S ATOM 58775 SG CYS F 338 130.537 109.439 98.938 1.00 90.37 S ATOM 64097 SG CYS G 262 160.469 106.319 73.340 1.00 6.57 S ATOM 64120 SG CYS G 265 161.269 103.703 70.656 1.00 7.29 S ATOM 64274 SG CYS G 284 158.295 106.042 70.206 1.00 7.12 S ATOM 64311 SG CYS G 289 158.232 103.236 72.724 1.00 18.98 S ATOM 69288 SG CYS H 223 53.744 126.028 110.192 1.00 94.06 S ATOM 69301 SG CYS H 225 55.327 124.088 108.518 1.00 92.69 S ATOM 69663 SG CYS H 293 52.868 124.502 106.372 1.00 65.25 S ATOM 73518 SG CYS I 661 40.286 110.831 81.482 1.00 51.12 S ATOM 73541 SG CYS I 664 39.890 107.063 80.475 1.00 48.86 S Restraints were copied for chains: 3, 4, 5, 6, 1, 7, 9, 8, 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN 61104 " occ=0.50 residue: pdb="ZN ZN F1104 " occ=0.50 Time building chain proxies: 43.60, per 1000 atoms: 0.59 Number of scatterers: 74358 At special positions: 0 Unit cell: (248.04, 224.72, 154.76, 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 14 29.99 S 348 16.00 P 44 15.00 Mg 14 11.99 O 14216 8.00 N 12922 7.00 C 46800 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.68 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 367 " pdb=" ZN 41002 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 349 " pdb=" ZN 51002 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 183 " pdb=" ZN 61104 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 904 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 262 " pdb=" ZN 81003 " pdb="ZN ZN 81003 " - pdb=" SG CYS 8 293 " pdb="ZN ZN 81003 " - pdb=" ND1 HIS 8 348 " pdb="ZN ZN 81003 " - pdb=" SG CYS 8 223 " pdb="ZN ZN 81003 " - pdb=" SG CYS 8 225 " pdb=" ZN 91101 " pdb="ZN ZN 91101 " - pdb=" NE2 HIS 9 674 " pdb="ZN ZN 91101 " - pdb=" ND1 HIS 9 680 " pdb="ZN ZN 91101 " - pdb=" SG CYS 9 664 " pdb="ZN ZN 91101 " - pdb=" SG CYS 9 661 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 344 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 364 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 341 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 367 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 352 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 376 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 371 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 349 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 236 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 211 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 186 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 183 " pdb=" ZN F1104 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 338 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 311 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 314 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 333 " pdb=" ZN G 904 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 265 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 289 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 284 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 262 " pdb=" ZN H1003 " pdb="ZN ZN H1003 " - pdb=" SG CYS H 293 " pdb="ZN ZN H1003 " - pdb=" ND1 HIS H 348 " pdb="ZN ZN H1003 " - pdb=" SG CYS H 223 " pdb="ZN ZN H1003 " - pdb=" SG CYS H 225 " pdb=" ZN I1101 " pdb="ZN ZN I1101 " - pdb=" NE2 HIS I 674 " pdb="ZN ZN I1101 " - pdb=" ND1 HIS I 680 " pdb="ZN ZN I1101 " - pdb=" SG CYS I 664 " pdb="ZN ZN I1101 " - pdb=" SG CYS I 661 " Number of angles added : 68 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17656 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 102 sheets defined 43.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 removed outlier: 4.137A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 Processing helix chain '2' and resid 200 through 218 removed outlier: 3.803A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 245 through 253 removed outlier: 3.940A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 269 through 283 removed outlier: 3.655A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 477 through 489 removed outlier: 3.780A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 613 through 627 Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 677 removed outlier: 3.780A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 759 through 774 Processing helix chain '2' and resid 779 through 781 No H-bonds generated for 'chain '2' and resid 779 through 781' Processing helix chain '2' and resid 782 through 801 removed outlier: 4.346A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.985A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 848 Processing helix chain '2' and resid 854 through 859 removed outlier: 3.978A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '2' and resid 860 through 864 removed outlier: 4.385A pdb=" N ILE 2 863 " --> pdb=" O SER 2 860 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 36 through 56 Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 343 through 355 Processing helix chain '3' and resid 358 through 366 Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 479 through 493 removed outlier: 3.792A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 3.846A pdb=" N ALA 3 534 " --> pdb=" O HIS 3 530 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 543 removed outlier: 3.738A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 570 Processing helix chain '3' and resid 652 through 667 Processing helix chain '3' and resid 672 through 689 removed outlier: 4.126A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 3.846A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 739 Processing helix chain '4' and resid 186 through 200 Processing helix chain '4' and resid 202 through 210 removed outlier: 4.146A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 216 Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 244 through 251 removed outlier: 3.994A pdb=" N LEU 4 248 " --> pdb=" O ASP 4 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 4.049A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 287 removed outlier: 3.604A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 318 through 322 Processing helix chain '4' and resid 386 through 389 Processing helix chain '4' and resid 477 through 480 Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 502 through 514 Processing helix chain '4' and resid 517 through 526 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 644 through 651 removed outlier: 3.806A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 677 through 681 removed outlier: 4.237A pdb=" N ARG 4 681 " --> pdb=" O ILE 4 678 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 713 through 727 removed outlier: 3.617A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) Processing helix chain '4' and resid 743 through 758 removed outlier: 3.512A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 778 Processing helix chain '4' and resid 795 through 812 removed outlier: 3.609A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 833 removed outlier: 3.660A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '4' and resid 834 through 838 Processing helix chain '4' and resid 846 through 850 removed outlier: 3.500A pdb=" N VAL 4 850 " --> pdb=" O MET 4 847 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 Processing helix chain '5' and resid 82 through 107 Proline residue: 5 88 - end of helix removed outlier: 4.270A pdb=" N ALA 5 107 " --> pdb=" O ILE 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 removed outlier: 3.881A pdb=" N LEU 5 151 " --> pdb=" O LEU 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 152 through 156 removed outlier: 3.623A pdb=" N HIS 5 155 " --> pdb=" O ASP 5 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL 5 156 " --> pdb=" O SER 5 153 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 152 through 156' Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 362 Processing helix chain '5' and resid 365 through 372 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 499 removed outlier: 3.565A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 545 through 550 removed outlier: 3.837A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 545 through 550' Processing helix chain '5' and resid 561 through 576 Processing helix chain '5' and resid 579 through 589 removed outlier: 3.521A pdb=" N MET 5 583 " --> pdb=" O ASN 5 579 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 640 removed outlier: 3.772A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER 5 640 " --> pdb=" O ASN 5 636 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.503A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 687 Processing helix chain '6' and resid 105 through 122 removed outlier: 3.513A pdb=" N PHE 6 122 " --> pdb=" O PHE 6 118 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 146 Processing helix chain '6' and resid 155 through 161 removed outlier: 3.991A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 173 removed outlier: 3.617A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 193 through 197 removed outlier: 3.567A pdb=" N LEU 6 196 " --> pdb=" O ALA 6 193 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU 6 197 " --> pdb=" O PRO 6 194 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 193 through 197' Processing helix chain '6' and resid 280 through 284 removed outlier: 3.719A pdb=" N ILE 6 284 " --> pdb=" O SER 6 281 " (cutoff:3.500A) Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 407 through 410 Processing helix chain '6' and resid 500 through 507 removed outlier: 3.563A pdb=" N PHE 6 504 " --> pdb=" O ASP 6 500 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 522 Processing helix chain '6' and resid 524 through 532 Processing helix chain '6' and resid 540 through 553 removed outlier: 3.530A pdb=" N LYS 6 544 " --> pdb=" O HIS 6 540 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 589 removed outlier: 3.655A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 645 through 659 removed outlier: 3.519A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) Processing helix chain '6' and resid 684 through 688 removed outlier: 4.173A pdb=" N ARG 6 688 " --> pdb=" O VAL 6 685 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 708 removed outlier: 4.081A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 737 Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 784 removed outlier: 3.617A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.741A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.640A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 28 Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 95 Processing helix chain '7' and resid 101 through 109 Processing helix chain '7' and resid 109 through 124 removed outlier: 4.143A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 Processing helix chain '7' and resid 178 through 189 Processing helix chain '7' and resid 286 through 292 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 363 through 367 Processing helix chain '7' and resid 387 through 391 removed outlier: 3.680A pdb=" N PHE 7 391 " --> pdb=" O PHE 7 388 " (cutoff:3.500A) Processing helix chain '7' and resid 394 through 406 Processing helix chain '7' and resid 409 through 417 Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.891A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 544 Processing helix chain '7' and resid 569 through 573 removed outlier: 4.124A pdb=" N ARG 7 573 " --> pdb=" O LEU 7 570 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 584 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.602A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 606 through 622 Processing helix chain '7' and resid 634 through 647 removed outlier: 3.581A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 674 removed outlier: 4.207A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 703 removed outlier: 3.589A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 723 Processing helix chain '7' and resid 724 through 728 removed outlier: 3.633A pdb=" N LEU 7 727 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 26 removed outlier: 3.909A pdb=" N LYS 8 16 " --> pdb=" O PRO 8 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU 8 17 " --> pdb=" O PRO 8 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU 8 18 " --> pdb=" O GLU 8 14 " (cutoff:3.500A) Processing helix chain '8' and resid 27 through 30 removed outlier: 4.097A pdb=" N GLU 8 30 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 83 through 97 removed outlier: 3.570A pdb=" N MET 8 97 " --> pdb=" O LEU 8 93 " (cutoff:3.500A) Processing helix chain '8' and resid 127 through 132 removed outlier: 3.708A pdb=" N PHE 8 131 " --> pdb=" O GLU 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 136 through 158 Processing helix chain '8' and resid 286 through 291 Processing helix chain '8' and resid 298 through 313 removed outlier: 3.792A pdb=" N ILE 8 302 " --> pdb=" O THR 8 298 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE 8 308 " --> pdb=" O SER 8 304 " (cutoff:3.500A) Processing helix chain '8' and resid 324 through 337 removed outlier: 3.630A pdb=" N ILE 8 335 " --> pdb=" O GLU 8 331 " (cutoff:3.500A) Processing helix chain '8' and resid 337 through 348 removed outlier: 3.743A pdb=" N LEU 8 347 " --> pdb=" O LYS 8 343 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS 8 348 " --> pdb=" O CYS 8 344 " (cutoff:3.500A) Processing helix chain '8' and resid 368 through 384 removed outlier: 3.641A pdb=" N PHE 8 372 " --> pdb=" O GLY 8 368 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU 8 380 " --> pdb=" O LEU 8 376 " (cutoff:3.500A) Processing helix chain '8' and resid 391 through 404 removed outlier: 3.954A pdb=" N THR 8 395 " --> pdb=" O VAL 8 391 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS 8 404 " --> pdb=" O GLN 8 400 " (cutoff:3.500A) Processing helix chain '8' and resid 426 through 450 Processing helix chain '8' and resid 459 through 465 Processing helix chain '8' and resid 466 through 470 removed outlier: 3.648A pdb=" N ASN 8 470 " --> pdb=" O PRO 8 467 " (cutoff:3.500A) Processing helix chain '9' and resid 112 through 116 removed outlier: 3.695A pdb=" N TRP 9 116 " --> pdb=" O TRP 9 112 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 112 through 116' Processing helix chain '9' and resid 137 through 157 Processing helix chain '9' and resid 189 through 197 Processing helix chain '9' and resid 204 through 214 Processing helix chain '9' and resid 233 through 243 removed outlier: 3.736A pdb=" N LEU 9 243 " --> pdb=" O HIS 9 239 " (cutoff:3.500A) Processing helix chain '9' and resid 284 through 289 Processing helix chain '9' and resid 319 through 333 removed outlier: 4.080A pdb=" N LYS 9 325 " --> pdb=" O LYS 9 321 " (cutoff:3.500A) Processing helix chain '9' and resid 333 through 344 removed outlier: 3.671A pdb=" N ALA 9 337 " --> pdb=" O ASN 9 333 " (cutoff:3.500A) Processing helix chain '9' and resid 349 through 353 removed outlier: 4.033A pdb=" N LEU 9 352 " --> pdb=" O ASP 9 349 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN 9 353 " --> pdb=" O THR 9 350 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 349 through 353' Processing helix chain '9' and resid 373 through 385 Processing helix chain '9' and resid 521 through 528 removed outlier: 3.500A pdb=" N SER 9 528 " --> pdb=" O MET 9 524 " (cutoff:3.500A) Processing helix chain '9' and resid 670 through 675 Processing helix chain '9' and resid 677 through 686 Processing helix chain '9' and resid 691 through 701 removed outlier: 3.764A pdb=" N LEU 9 696 " --> pdb=" O ALA 9 692 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU 9 698 " --> pdb=" O ASP 9 694 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG 9 701 " --> pdb=" O ILE 9 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 4.136A pdb=" N SER B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 218 removed outlier: 3.803A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 245 through 253 removed outlier: 3.940A pdb=" N LEU B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 269 through 283 removed outlier: 3.654A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.780A pdb=" N ARG B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 594 through 599 Processing helix chain 'B' and resid 613 through 627 Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.780A pdb=" N ARG B 676 " --> pdb=" O PRO B 672 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 677 " --> pdb=" O ILE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 Processing helix chain 'B' and resid 759 through 774 Processing helix chain 'B' and resid 779 through 781 No H-bonds generated for 'chain 'B' and resid 779 through 781' Processing helix chain 'B' and resid 782 through 801 removed outlier: 4.345A pdb=" N VAL B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 824 removed outlier: 3.985A pdb=" N LEU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 824 " --> pdb=" O PHE B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.977A pdb=" N ARG B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 864 removed outlier: 4.385A pdb=" N ILE B 863 " --> pdb=" O SER B 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 35 Processing helix chain 'C' and resid 36 through 56 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 117 through 137 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 414 through 426 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.792A pdb=" N ALA C 485 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 534 removed outlier: 3.846A pdb=" N ALA C 534 " --> pdb=" O HIS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.738A pdb=" N ARG C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 570 Processing helix chain 'C' and resid 652 through 667 Processing helix chain 'C' and resid 672 through 689 removed outlier: 4.126A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 716 removed outlier: 3.846A pdb=" N LEU C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 739 Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 202 through 210 removed outlier: 4.146A pdb=" N ARG D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 224 through 237 Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.993A pdb=" N LEU D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 4.050A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 287 removed outlier: 3.604A pdb=" N ASN D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 386 through 389 Processing helix chain 'D' and resid 477 through 480 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 502 through 514 Processing helix chain 'D' and resid 517 through 526 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 644 through 651 removed outlier: 3.807A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 681 removed outlier: 4.237A pdb=" N ARG D 681 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 693 Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 713 through 727 removed outlier: 3.617A pdb=" N LEU D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 758 removed outlier: 3.512A pdb=" N MET D 749 " --> pdb=" O GLU D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 778 Processing helix chain 'D' and resid 795 through 812 removed outlier: 3.608A pdb=" N GLU D 799 " --> pdb=" O THR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 833 removed outlier: 3.660A pdb=" N VAL D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 Processing helix chain 'D' and resid 846 through 850 removed outlier: 3.500A pdb=" N VAL D 850 " --> pdb=" O MET D 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 82 through 107 Proline residue: E 88 - end of helix removed outlier: 4.269A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.880A pdb=" N LEU E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.623A pdb=" N HIS E 155 " --> pdb=" O ASP E 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 152 through 156' Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 350 through 362 Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 486 through 499 removed outlier: 3.565A pdb=" N VAL E 491 " --> pdb=" O ASP E 487 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 498 " --> pdb=" O HIS E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 550 removed outlier: 3.837A pdb=" N ARG E 549 " --> pdb=" O THR E 545 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 550 " --> pdb=" O ILE E 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 545 through 550' Processing helix chain 'E' and resid 561 through 576 Processing helix chain 'E' and resid 579 through 589 removed outlier: 3.521A pdb=" N MET E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 610 Processing helix chain 'E' and resid 615 through 640 removed outlier: 3.773A pdb=" N GLU E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 667 removed outlier: 3.504A pdb=" N LEU E 653 " --> pdb=" O THR E 649 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU E 667 " --> pdb=" O LEU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 687 Processing helix chain 'F' and resid 105 through 122 removed outlier: 3.512A pdb=" N PHE F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 146 Processing helix chain 'F' and resid 155 through 161 removed outlier: 3.990A pdb=" N MET F 160 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG F 161 " --> pdb=" O HIS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.617A pdb=" N ALA F 169 " --> pdb=" O ALA F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 192 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 193 through 197 removed outlier: 3.567A pdb=" N LEU F 196 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU F 197 " --> pdb=" O PRO F 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 193 through 197' Processing helix chain 'F' and resid 280 through 284 removed outlier: 3.719A pdb=" N ILE F 284 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 407 through 410 Processing helix chain 'F' and resid 500 through 507 removed outlier: 3.563A pdb=" N PHE F 504 " --> pdb=" O ASP F 500 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 507 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 522 Processing helix chain 'F' and resid 524 through 532 Processing helix chain 'F' and resid 540 through 553 removed outlier: 3.531A pdb=" N LYS F 544 " --> pdb=" O HIS F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 589 removed outlier: 3.655A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 645 through 659 removed outlier: 3.520A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 688 removed outlier: 4.172A pdb=" N ARG F 688 " --> pdb=" O VAL F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 702 through 708 removed outlier: 4.081A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 737 Processing helix chain 'F' and resid 747 through 759 Processing helix chain 'F' and resid 766 through 784 removed outlier: 3.618A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 815 removed outlier: 3.741A pdb=" N LEU F 800 " --> pdb=" O THR F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 835 removed outlier: 3.640A pdb=" N ILE F 835 " --> pdb=" O LEU F 831 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 28 Processing helix chain 'G' and resid 61 through 72 Processing helix chain 'G' and resid 82 through 95 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 109 through 124 removed outlier: 4.144A pdb=" N PHE G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 363 through 367 Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.680A pdb=" N PHE G 391 " --> pdb=" O PHE G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 406 Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 438 Processing helix chain 'G' and resid 465 through 477 Processing helix chain 'G' and resid 511 through 516 Processing helix chain 'G' and resid 525 through 529 removed outlier: 3.892A pdb=" N MET G 529 " --> pdb=" O PHE G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 544 Processing helix chain 'G' and resid 569 through 573 removed outlier: 4.125A pdb=" N ARG G 573 " --> pdb=" O LEU G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 579 through 584 Processing helix chain 'G' and resid 587 through 594 removed outlier: 3.601A pdb=" N PHE G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 622 Processing helix chain 'G' and resid 634 through 647 removed outlier: 3.581A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 674 removed outlier: 4.207A pdb=" N TYR G 659 " --> pdb=" O ALA G 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 685 through 703 removed outlier: 3.589A pdb=" N LEU G 689 " --> pdb=" O THR G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 724 through 728 removed outlier: 3.633A pdb=" N LEU G 727 " --> pdb=" O LYS G 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 removed outlier: 3.908A pdb=" N LYS H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU H 17 " --> pdb=" O PRO H 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 30 removed outlier: 4.097A pdb=" N GLU H 30 " --> pdb=" O PRO H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 27 through 30' Processing helix chain 'H' and resid 83 through 97 removed outlier: 3.570A pdb=" N MET H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 removed outlier: 3.707A pdb=" N PHE H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 158 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 298 through 313 removed outlier: 3.793A pdb=" N ILE H 302 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 337 removed outlier: 3.630A pdb=" N ILE H 335 " --> pdb=" O GLU H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 removed outlier: 3.743A pdb=" N LEU H 347 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS H 348 " --> pdb=" O CYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 384 removed outlier: 3.641A pdb=" N PHE H 372 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU H 380 " --> pdb=" O LEU H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 404 removed outlier: 3.954A pdb=" N THR H 395 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS H 404 " --> pdb=" O GLN H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 450 Processing helix chain 'H' and resid 459 through 465 Processing helix chain 'H' and resid 466 through 470 removed outlier: 3.648A pdb=" N ASN H 470 " --> pdb=" O PRO H 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.695A pdb=" N TRP I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 112 through 116' Processing helix chain 'I' and resid 137 through 157 Processing helix chain 'I' and resid 189 through 197 Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 233 through 243 removed outlier: 3.736A pdb=" N LEU I 243 " --> pdb=" O HIS I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 289 Processing helix chain 'I' and resid 319 through 333 removed outlier: 4.081A pdb=" N LYS I 325 " --> pdb=" O LYS I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 344 removed outlier: 3.671A pdb=" N ALA I 337 " --> pdb=" O ASN I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 353 removed outlier: 4.033A pdb=" N LEU I 352 " --> pdb=" O ASP I 349 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN I 353 " --> pdb=" O THR I 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 349 through 353' Processing helix chain 'I' and resid 373 through 385 Processing helix chain 'I' and resid 521 through 528 Processing helix chain 'I' and resid 670 through 675 Processing helix chain 'I' and resid 677 through 686 Processing helix chain 'I' and resid 691 through 701 removed outlier: 3.764A pdb=" N LEU I 696 " --> pdb=" O ALA I 692 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU I 698 " --> pdb=" O ASP I 694 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG I 701 " --> pdb=" O ILE I 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 242 Processing sheet with id=AA2, first strand: chain '2' and resid 351 through 352 removed outlier: 6.663A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N HIS 2 405 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LEU 2 411 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 12.792A pdb=" N LYS 2 457 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 339 through 341 Processing sheet with id=AA4, first strand: chain '2' and resid 525 through 526 Processing sheet with id=AA5, first strand: chain '2' and resid 563 through 567 removed outlier: 6.165A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA7, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA8, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AA9, first strand: chain '3' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 179 through 189 current: chain '3' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 208 through 213 current: chain '3' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 279 current: chain '3' and resid 318 through 330 Processing sheet with id=AB1, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain '3' and resid 429 through 433 removed outlier: 5.848A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 445 through 446 Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 496 Processing sheet with id=AB5, first strand: chain '3' and resid 670 through 671 removed outlier: 6.916A pdb=" N GLN 3 670 " --> pdb=" O VAL 3 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 179 through 180 Processing sheet with id=AB7, first strand: chain '4' and resid 240 through 241 Processing sheet with id=AB8, first strand: chain '4' and resid 324 through 335 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 324 through 335 current: chain '4' and resid 357 through 359 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 357 through 359 current: chain '4' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 414 through 420 current: chain '4' and resid 458 through 467 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '4' and resid 364 through 367 Processing sheet with id=AC1, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AC2, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain '4' and resid 590 through 591 removed outlier: 6.391A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 604 through 607 Processing sheet with id=AC5, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC6, first strand: chain '4' and resid 761 through 762 removed outlier: 6.779A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '5' and resid 8 through 12 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 8 through 12 current: chain 'G' and resid 238 through 247 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 238 through 247 current: chain 'G' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 267 through 272 current: chain 'G' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 336 current: chain 'G' and resid 372 through 383 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 60 through 64 removed outlier: 6.096A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 189 through 193 removed outlier: 5.734A pdb=" N SER 5 174 " --> pdb=" O GLN 5 253 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN 5 253 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA 5 176 " --> pdb=" O ILE 5 251 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE 5 251 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER 5 180 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY 5 332 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AD2, first strand: chain '5' and resid 436 through 439 removed outlier: 6.806A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA 5 523 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU 5 414 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL 5 556 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '5' and resid 452 through 454 removed outlier: 6.706A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '5' and resid 501 through 505 Processing sheet with id=AD5, first strand: chain '5' and resid 613 through 614 removed outlier: 6.804A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '6' and resid 150 through 154 removed outlier: 6.500A pdb=" N ILE 6 151 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE 6 153 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '6' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 297 current: chain '6' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 317 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 461 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '6' and resid 595 through 599 removed outlier: 6.590A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS 6 572 " --> pdb=" O PHE 6 713 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE 6 715 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL 6 574 " --> pdb=" O ILE 6 715 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 611 through 613 Processing sheet with id=AE1, first strand: chain '6' and resid 660 through 662 Processing sheet with id=AE2, first strand: chain '6' and resid 764 through 765 removed outlier: 6.765A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AE4, first strand: chain '7' and resid 224 through 225 removed outlier: 5.892A pdb=" N LEU 7 225 " --> pdb=" O ARG 7 242 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ILE 7 244 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 247 current: chain '7' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 267 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 372 through 383 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain '7' and resid 442 through 443 removed outlier: 3.641A pdb=" N LYS 7 442 " --> pdb=" O ILE 7 450 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 480 through 484 removed outlier: 6.318A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '7' and resid 495 through 500 removed outlier: 4.378A pdb=" N GLU 7 505 " --> pdb=" O ASP 7 500 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 545 through 550 Processing sheet with id=AE9, first strand: chain '7' and resid 651 through 652 removed outlier: 7.074A pdb=" N VAL 7 651 " --> pdb=" O VAL 7 708 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain '8' and resid 34 through 41 removed outlier: 6.871A pdb=" N LYS 8 49 " --> pdb=" O ILE 8 36 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS 8 38 " --> pdb=" O VAL 8 47 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL 8 47 " --> pdb=" O LYS 8 38 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY 8 40 " --> pdb=" O SER 8 45 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N SER 8 45 " --> pdb=" O GLY 8 40 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL 8 116 " --> pdb=" O ILE 8 78 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '8' and resid 159 through 160 Processing sheet with id=AF3, first strand: chain '8' and resid 169 through 172 Processing sheet with id=AF4, first strand: chain '8' and resid 264 through 266 Processing sheet with id=AF5, first strand: chain '8' and resid 350 through 355 Processing sheet with id=AF6, first strand: chain '9' and resid 161 through 162 removed outlier: 3.807A pdb=" N ILE 9 172 " --> pdb=" O ARG 9 125 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE 9 174 " --> pdb=" O TYR 9 127 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '9' and resid 531 through 532 Processing sheet with id=AF8, first strand: chain '9' and resid 659 through 661 removed outlier: 3.744A pdb=" N VAL 9 666 " --> pdb=" O CYS 9 661 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AG1, first strand: chain 'B' and resid 351 through 352 removed outlier: 6.663A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N HIS B 405 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ILE B 451 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU B 407 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 453 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 409 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER B 455 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N LEU B 411 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 12.791A pdb=" N LYS B 457 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N THR B 449 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN B 433 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE B 451 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS B 431 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA B 453 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE B 429 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AG3, first strand: chain 'B' and resid 525 through 526 Processing sheet with id=AG4, first strand: chain 'B' and resid 563 through 567 removed outlier: 6.165A pdb=" N CYS B 604 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA B 649 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 606 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 539 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA B 650 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 541 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 540 " --> pdb=" O CYS B 681 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL B 683 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 542 " --> pdb=" O VAL B 683 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AG6, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AG7, first strand: chain 'C' and resid 95 through 99 Processing sheet with id=AG8, first strand: chain 'C' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 179 through 189 current: chain 'C' and resid 208 through 213 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 208 through 213 current: chain 'C' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 279 current: chain 'C' and resid 318 through 330 Processing sheet with id=AG9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AH1, first strand: chain 'C' and resid 429 through 433 removed outlier: 5.847A pdb=" N VAL C 470 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA C 515 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 472 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 405 " --> pdb=" O ALA C 514 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA C 516 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET C 407 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 406 " --> pdb=" O PHE C 547 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 549 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 408 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AH3, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AH4, first strand: chain 'C' and resid 670 through 671 removed outlier: 6.916A pdb=" N GLN C 670 " --> pdb=" O VAL C 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AH6, first strand: chain 'D' and resid 324 through 335 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 324 through 335 current: chain 'D' and resid 357 through 359 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 357 through 359 current: chain 'D' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 420 current: chain 'D' and resid 458 through 467 No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 364 through 367 Processing sheet with id=AH8, first strand: chain 'D' and resid 453 through 454 Processing sheet with id=AH9, first strand: chain 'D' and resid 550 through 551 Processing sheet with id=AI1, first strand: chain 'D' and resid 590 through 591 removed outlier: 6.392A pdb=" N ILE D 564 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA D 675 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU D 566 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 565 " --> pdb=" O TYR D 706 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL D 708 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS D 567 " --> pdb=" O VAL D 708 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 604 through 607 Processing sheet with id=AI3, first strand: chain 'D' and resid 653 through 658 Processing sheet with id=AI4, first strand: chain 'D' and resid 761 through 762 removed outlier: 6.780A pdb=" N ILE D 761 " --> pdb=" O VAL D 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.096A pdb=" N LEU E 61 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN E 140 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL E 63 " --> pdb=" O ASN E 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'E' and resid 189 through 193 removed outlier: 5.733A pdb=" N SER E 174 " --> pdb=" O GLN E 253 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN E 253 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA E 176 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE E 251 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER E 180 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER E 247 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N MET E 182 " --> pdb=" O HIS E 245 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N HIS E 245 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER E 335 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG E 291 " --> pdb=" O SER E 335 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS E 158 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 398 through 399 Processing sheet with id=AI8, first strand: chain 'E' and resid 436 through 439 removed outlier: 6.806A pdb=" N VAL E 437 " --> pdb=" O CYS E 478 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP E 480 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR E 439 " --> pdb=" O ASP E 480 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL E 477 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA E 522 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE E 479 " --> pdb=" O ALA E 522 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 412 " --> pdb=" O ALA E 521 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA E 523 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU E 414 " --> pdb=" O ALA E 523 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU E 413 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL E 556 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU E 415 " --> pdb=" O VAL E 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'E' and resid 452 through 454 removed outlier: 6.706A pdb=" N SER E 452 " --> pdb=" O GLU E 465 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 501 through 505 Processing sheet with id=AJ2, first strand: chain 'E' and resid 613 through 614 removed outlier: 6.804A pdb=" N ARG E 613 " --> pdb=" O ALA E 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.500A pdb=" N ILE F 151 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE F 268 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE F 153 " --> pdb=" O PHE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'F' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 287 through 297 current: chain 'F' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 317 through 322 current: chain 'F' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 376 through 382 current: chain 'F' and resid 450 through 461 No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'F' and resid 595 through 599 removed outlier: 6.590A pdb=" N VAL F 596 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP F 639 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR F 598 " --> pdb=" O ASP F 639 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE F 571 " --> pdb=" O ALA F 680 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS F 572 " --> pdb=" O PHE F 713 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE F 715 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 574 " --> pdb=" O ILE F 715 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 611 through 613 Processing sheet with id=AJ7, first strand: chain 'F' and resid 660 through 662 Processing sheet with id=AJ8, first strand: chain 'F' and resid 764 through 765 removed outlier: 6.765A pdb=" N ILE F 764 " --> pdb=" O ILE F 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 Processing sheet with id=AJ9, first strand: chain 'G' and resid 77 through 81 Processing sheet with id=AK1, first strand: chain 'G' and resid 442 through 443 removed outlier: 3.640A pdb=" N LYS G 442 " --> pdb=" O ILE G 450 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'G' and resid 480 through 484 removed outlier: 6.319A pdb=" N VAL G 481 " --> pdb=" O CYS G 522 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP G 524 " --> pdb=" O VAL G 481 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR G 483 " --> pdb=" O ASP G 524 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS G 521 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA G 566 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 523 " --> pdb=" O ALA G 566 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 495 through 500 removed outlier: 4.378A pdb=" N GLU G 505 " --> pdb=" O ASP G 500 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 545 through 550 Processing sheet with id=AK5, first strand: chain 'G' and resid 651 through 652 removed outlier: 7.074A pdb=" N VAL G 651 " --> pdb=" O VAL G 708 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'H' and resid 34 through 41 removed outlier: 6.871A pdb=" N LYS H 49 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS H 38 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY H 40 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N SER H 45 " --> pdb=" O GLY H 40 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL H 116 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'H' and resid 159 through 160 Processing sheet with id=AK8, first strand: chain 'H' and resid 169 through 172 Processing sheet with id=AK9, first strand: chain 'H' and resid 264 through 266 Processing sheet with id=AL1, first strand: chain 'H' and resid 350 through 351 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 350 through 351 current: chain 'I' and resid 265 through 270 Processing sheet with id=AL2, first strand: chain 'I' and resid 161 through 162 removed outlier: 3.807A pdb=" N ILE I 172 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE I 174 " --> pdb=" O TYR I 127 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'I' and resid 659 through 661 removed outlier: 3.744A pdb=" N VAL I 666 " --> pdb=" O CYS I 661 " (cutoff:3.500A) 2881 hydrogen bonds defined for protein. 8280 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: 30.07 Time building geometry restraints manager: 16.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 18773 1.33 - 1.48: 22791 1.48 - 1.64: 33508 1.64 - 1.79: 77 1.79 - 1.94: 471 Bond restraints: 75620 Sorted by residual: bond pdb=" N PRO F 336 " pdb=" CD PRO F 336 " ideal model delta sigma weight residual 1.473 1.334 0.139 1.40e-02 5.10e+03 9.84e+01 bond pdb=" N PRO 6 336 " pdb=" CD PRO 6 336 " ideal model delta sigma weight residual 1.473 1.334 0.139 1.40e-02 5.10e+03 9.82e+01 bond pdb=" CA ARG F 350 " pdb=" C ARG F 350 " ideal model delta sigma weight residual 1.522 1.630 -0.109 1.43e-02 4.89e+03 5.77e+01 bond pdb=" CA ARG 6 350 " pdb=" C ARG 6 350 " ideal model delta sigma weight residual 1.522 1.630 -0.108 1.43e-02 4.89e+03 5.75e+01 bond pdb=" N PRO 5 418 " pdb=" CD PRO 5 418 " ideal model delta sigma weight residual 1.473 1.577 -0.104 1.40e-02 5.10e+03 5.55e+01 ... (remaining 75615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 101514 4.88 - 9.76: 712 9.76 - 14.64: 60 14.64 - 19.53: 6 19.53 - 24.41: 2 Bond angle restraints: 102294 Sorted by residual: angle pdb=" N PRO H 224 " pdb=" CA PRO H 224 " pdb=" C PRO H 224 " ideal model delta sigma weight residual 114.80 90.39 24.41 1.42e+00 4.96e-01 2.95e+02 angle pdb=" N PRO 8 224 " pdb=" CA PRO 8 224 " pdb=" C PRO 8 224 " ideal model delta sigma weight residual 114.80 90.43 24.37 1.42e+00 4.96e-01 2.94e+02 angle pdb=" N SER 2 797 " pdb=" CA SER 2 797 " pdb=" C SER 2 797 " ideal model delta sigma weight residual 111.36 122.29 -10.93 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N SER B 797 " pdb=" CA SER B 797 " pdb=" C SER B 797 " ideal model delta sigma weight residual 111.36 122.25 -10.89 1.09e+00 8.42e-01 9.98e+01 angle pdb=" N SER 6 351 " pdb=" CA SER 6 351 " pdb=" C SER 6 351 " ideal model delta sigma weight residual 110.41 122.53 -12.12 1.23e+00 6.61e-01 9.72e+01 ... (remaining 102289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 45120 33.30 - 66.60: 1192 66.60 - 99.89: 120 99.89 - 133.19: 2 133.19 - 166.49: 6 Dihedral angle restraints: 46440 sinusoidal: 19238 harmonic: 27202 Sorted by residual: dihedral pdb=" CD ARG 9 176 " pdb=" NE ARG 9 176 " pdb=" CZ ARG 9 176 " pdb=" NH1 ARG 9 176 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG I 176 " pdb=" NE ARG I 176 " pdb=" CZ ARG I 176 " pdb=" NH1 ARG I 176 " ideal model delta sinusoidal sigma weight residual 0.00 -89.91 89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" C ARG 6 350 " pdb=" N ARG 6 350 " pdb=" CA ARG 6 350 " pdb=" CB ARG 6 350 " ideal model delta harmonic sigma weight residual -122.60 -137.46 14.86 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 46437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 10993 0.119 - 0.238: 595 0.238 - 0.357: 106 0.357 - 0.476: 16 0.476 - 0.595: 4 Chirality restraints: 11714 Sorted by residual: chirality pdb=" CA CYS 8 223 " pdb=" N CYS 8 223 " pdb=" C CYS 8 223 " pdb=" CB CYS 8 223 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA CYS H 223 " pdb=" N CYS H 223 " pdb=" C CYS H 223 " pdb=" CB CYS H 223 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA ARG 6 350 " pdb=" N ARG 6 350 " pdb=" C ARG 6 350 " pdb=" CB ARG 6 350 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 11711 not shown) Planarity restraints: 13096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 9 176 " 0.973 9.50e-02 1.11e+02 4.36e-01 1.18e+02 pdb=" NE ARG 9 176 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG 9 176 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG 9 176 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG 9 176 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 176 " -0.973 9.50e-02 1.11e+02 4.36e-01 1.18e+02 pdb=" NE ARG I 176 " 0.070 2.00e-02 2.50e+03 pdb=" CZ ARG I 176 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG I 176 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG I 176 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 9 324 " 0.041 2.00e-02 2.50e+03 8.20e-02 6.72e+01 pdb=" C VAL 9 324 " -0.142 2.00e-02 2.50e+03 pdb=" O VAL 9 324 " 0.054 2.00e-02 2.50e+03 pdb=" N LYS 9 325 " 0.047 2.00e-02 2.50e+03 ... (remaining 13093 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 191 2.35 - 2.99: 37979 2.99 - 3.63: 110694 3.63 - 4.26: 176673 4.26 - 4.90: 296115 Nonbonded interactions: 621652 Sorted by model distance: nonbonded pdb=" NE2 GLN 8 432 " pdb=" CZ2 TRP 8 436 " model vdw 1.718 3.420 nonbonded pdb=" NE2 GLN H 432 " pdb=" CZ2 TRP H 436 " model vdw 1.719 3.420 nonbonded pdb=" N LYS D 204 " pdb=" OD1 ASP D 221 " model vdw 1.757 3.120 nonbonded pdb=" N LYS 4 204 " pdb=" OD1 ASP 4 221 " model vdw 1.757 3.120 nonbonded pdb=" CE LYS 9 380 " pdb=" OE1 GLN 9 383 " model vdw 1.821 3.440 ... (remaining 621647 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 '1' selection = chain 'A' } ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = chain '4' selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } ncs_group { reference = chain '8' selection = chain 'H' } ncs_group { reference = chain '9' selection = chain 'I' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 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: 0.000 Extract box with map and model: 2.090 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 149.490 Find NCS groups from input model: 4.450 Set up NCS constraints: 0.320 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 75620 Z= 0.390 Angle : 1.065 24.406 102294 Z= 0.678 Chirality : 0.065 0.595 11714 Planarity : 0.009 0.436 13096 Dihedral : 15.098 166.490 28784 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.34 % Allowed : 1.90 % Favored : 97.76 % Cbeta Deviations : 0.34 % 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: -0.49 (0.09), residues: 9146 helix: 0.41 (0.09), residues: 3584 sheet: -0.92 (0.12), residues: 1592 loop : -0.60 (0.10), residues: 3970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP 9 381 HIS 0.014 0.001 HIS 7 615 PHE 0.050 0.002 PHE C 735 TYR 0.047 0.002 TYR G 659 ARG 0.049 0.001 ARG 6 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1139 time to evaluate : 6.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 835 ASP cc_start: 0.7807 (m-30) cc_final: 0.7459 (m-30) REVERT: 3 151 HIS cc_start: 0.7195 (m-70) cc_final: 0.6896 (m90) REVERT: 3 731 ASN cc_start: 0.8216 (m-40) cc_final: 0.7957 (t0) REVERT: 4 382 MET cc_start: 0.8076 (mmm) cc_final: 0.7517 (mmp) REVERT: 5 153 SER cc_start: 0.8642 (p) cc_final: 0.8415 (p) REVERT: 5 393 MET cc_start: 0.8656 (mmp) cc_final: 0.8190 (mmp) REVERT: 7 573 ARG cc_start: 0.7298 (tpt90) cc_final: 0.6833 (tpp-160) REVERT: 7 602 ASP cc_start: 0.6296 (t0) cc_final: 0.6082 (p0) REVERT: 8 56 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7664 (tppt) REVERT: 8 146 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7706 (mm-30) REVERT: 8 367 ASN cc_start: 0.7228 (m-40) cc_final: 0.6582 (t0) REVERT: 8 441 TRP cc_start: 0.8595 (m100) cc_final: 0.8153 (m100) REVERT: 9 165 PHE cc_start: 0.6338 (m-80) cc_final: 0.5838 (m-80) REVERT: 9 273 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6608 (mm110) REVERT: 9 531 MET cc_start: 0.8641 (mmm) cc_final: 0.8312 (mmm) REVERT: 9 535 LYS cc_start: 0.5194 (ptmt) cc_final: 0.4506 (mmmt) REVERT: B 544 ASP cc_start: 0.7881 (m-30) cc_final: 0.7679 (m-30) REVERT: B 586 THR cc_start: 0.7476 (m) cc_final: 0.7101 (m) REVERT: B 653 ASN cc_start: 0.7739 (t0) cc_final: 0.7502 (t0) REVERT: D 199 MET cc_start: 0.8588 (mmt) cc_final: 0.8219 (mmt) REVERT: D 273 ASP cc_start: 0.7793 (m-30) cc_final: 0.7500 (m-30) REVERT: D 749 MET cc_start: 0.8283 (ttp) cc_final: 0.8072 (ttm) REVERT: D 811 MET cc_start: 0.8506 (ttp) cc_final: 0.8290 (ttp) REVERT: E 485 MET cc_start: 0.8571 (ttp) cc_final: 0.8238 (ttm) REVERT: E 514 ASN cc_start: 0.7748 (m-40) cc_final: 0.7359 (m-40) REVERT: E 583 MET cc_start: 0.4341 (mtt) cc_final: 0.4137 (mtm) REVERT: F 313 MET cc_start: 0.5389 (tpp) cc_final: 0.5085 (tpt) REVERT: F 644 MET cc_start: 0.8830 (ttm) cc_final: 0.8606 (ttp) REVERT: G 125 MET cc_start: 0.8952 (tpt) cc_final: 0.8364 (tpt) REVERT: G 449 LYS cc_start: 0.8497 (mttt) cc_final: 0.8205 (tptp) REVERT: G 687 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8174 (mtt90) REVERT: H 319 MET cc_start: 0.6598 (tpp) cc_final: 0.5287 (tpp) REVERT: H 386 PHE cc_start: 0.7965 (m-80) cc_final: 0.7588 (m-10) REVERT: I 129 ASP cc_start: 0.5662 (t70) cc_final: 0.5446 (t0) REVERT: I 292 ASP cc_start: 0.7633 (t0) cc_final: 0.7311 (t0) outliers start: 28 outliers final: 4 residues processed: 1162 average time/residue: 0.7294 time to fit residues: 1418.6437 Evaluate side-chains 788 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 783 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 574 LYS Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain G residue 687 ARG Chi-restraints excluded: chain H residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 777 optimal weight: 9.9990 chunk 698 optimal weight: 0.9990 chunk 387 optimal weight: 0.0470 chunk 238 optimal weight: 1.9990 chunk 470 optimal weight: 0.8980 chunk 372 optimal weight: 0.9990 chunk 721 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 438 optimal weight: 0.3980 chunk 537 optimal weight: 0.9980 chunk 836 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: