Starting phenix.real_space_refine (version: 1.21rc1) on Thu May 11 18:48:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmn_13539/05_2023/7pmn_13539_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmn_13539/05_2023/7pmn_13539.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/7pmn_13539/05_2023/7pmn_13539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmn_13539/05_2023/7pmn_13539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmn_13539/05_2023/7pmn_13539_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmn_13539/05_2023/7pmn_13539_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.038 sd= 1.533 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 7 6.06 5 P 73 5.49 5 Mg 2 5.21 5 S 328 5.16 5 C 47367 2.51 5 N 12777 2.21 5 O 14086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 74640 Number of models: 1 Model: "" Number of chains: 28 Chain: "2" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5183 Classifications: {'peptide': 656} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 26, 'TRANS': 629} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "3" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4834 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 586} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4731 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 571} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5231 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 634} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5042 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 617} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "7" Number of atoms: 4936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4936 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 602} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1609 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4569 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 548} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 742 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "J" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 629 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "K" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1120 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain breaks: 2 Chain: "L" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3921 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 2 Chain: "Q" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6203 Classifications: {'peptide': 766} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 737} Chain breaks: 12 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4427 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 520} Chain breaks: 3 Chain: "X" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5410 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 20, 'TRANS': 644} Chain breaks: 7 Chain: "Y" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1347 SG CYS 2 341 107.908 140.322 86.410 1.00143.32 S ATOM 1370 SG CYS 2 344 111.059 140.921 84.015 1.00149.77 S ATOM 1528 SG CYS 2 364 110.663 142.376 87.400 1.00142.22 S ATOM 1549 SG CYS 2 367 108.958 143.768 84.286 1.00146.93 S ATOM 11468 SG CYS 4 349 90.861 173.714 95.654 1.00114.31 S ATOM 11489 SG CYS 4 352 91.092 177.303 96.374 1.00121.63 S ATOM 11636 SG CYS 4 371 88.509 175.930 93.917 1.00119.95 S ATOM 11678 SG CYS 4 376 92.244 176.202 92.923 1.00126.45 S ATOM 15885 SG CYS 5 183 93.362 128.528 73.048 1.00 91.04 S ATOM 15910 SG CYS 5 186 94.574 128.123 69.603 1.00 80.50 S ATOM 16057 SG CYS 5 211 96.898 129.556 72.331 1.00100.68 S ATOM 16085 SG CYS 5 236 93.975 131.512 70.941 1.00103.86 S ATOM 21348 SG CYS 6 311 108.005 157.400 94.334 1.00115.71 S ATOM 21370 SG CYS 6 314 110.913 159.718 93.933 1.00110.76 S ATOM 21527 SG CYS 6 333 107.446 161.298 94.176 1.00116.54 S ATOM 21561 SG CYS 6 338 108.469 159.450 91.116 1.00121.25 S ATOM 26550 SG CYS 7 262 67.373 164.824 79.803 1.00117.01 S ATOM 26573 SG CYS 7 265 65.492 166.196 76.997 1.00124.96 S ATOM 26723 SG CYS 7 284 67.329 162.491 77.122 1.00125.97 S ATOM 26760 SG CYS 7 289 69.185 165.724 76.511 1.00142.98 S ATOM 63018 SG CYS Q2108 93.416 51.536 184.180 1.00 74.93 S ATOM 63045 SG CYS Q2111 91.653 53.648 186.791 1.00 72.48 S ATOM 63194 SG CYS Q2130 94.605 55.012 184.848 1.00 70.26 S ATOM 63218 SG CYS Q2133 95.041 52.219 187.547 1.00 71.37 S ATOM 63481 SG CYS Q2164 80.823 73.945 144.454 1.00 65.02 S ATOM 63504 SG CYS Q2167 77.765 75.526 146.039 1.00 78.18 S ATOM 63605 SG CYS Q2179 77.435 72.833 143.161 1.00 68.73 S ATOM 63618 SG CYS Q2181 78.850 76.455 142.829 1.00 78.12 S Time building chain proxies: 27.49, per 1000 atoms: 0.37 Number of scatterers: 74640 At special positions: 0 Unit cell: (234.26, 231.08, 218.36, 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 7 29.99 S 328 16.00 P 73 15.00 Mg 2 11.99 O 14086 8.00 N 12777 7.00 C 47367 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.74 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21502 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 341 " pdb=" ZN 41001 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 376 " pdb=" ZN 51502 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 186 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " pdb=" ZN Q2301 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2108 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2111 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2133 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2130 " pdb=" ZN Q2302 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2181 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2164 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2167 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2179 " Number of angles added : 42 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17452 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 372 helices and 88 sheets defined 42.7% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 236 Processing helix chain '2' and resid 246 through 251 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 3.652A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 306 through 308 No H-bonds generated for 'chain '2' and resid 306 through 308' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 488 Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 568 through 570 No H-bonds generated for 'chain '2' and resid 568 through 570' Processing helix chain '2' and resid 573 through 576 No H-bonds generated for 'chain '2' and resid 573 through 576' Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 625 removed outlier: 5.017A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS 2 621 " --> pdb=" O ARG 2 617 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU 2 622 " --> pdb=" O THR 2 618 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA 2 623 " --> pdb=" O SER 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 705 removed outlier: 3.597A pdb=" N ARG 2 694 " --> pdb=" O GLU 2 690 " (cutoff:3.500A) Processing helix chain '2' and resid 740 through 753 Processing helix chain '2' and resid 760 through 773 removed outlier: 3.692A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 798 Processing helix chain '2' and resid 807 through 823 Processing helix chain '2' and resid 831 through 846 Processing helix chain '2' and resid 851 through 865 removed outlier: 4.590A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 34 removed outlier: 4.632A pdb=" N GLY 3 22 " --> pdb=" O ASP 3 18 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP 3 23 " --> pdb=" O ALA 3 19 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 54 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 135 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 354 Processing helix chain '3' and resid 358 through 366 removed outlier: 4.788A pdb=" N LEU 3 363 " --> pdb=" O PHE 3 360 " (cutoff:3.500A) Processing helix chain '3' and resid 375 through 385 Processing helix chain '3' and resid 394 through 396 No H-bonds generated for 'chain '3' and resid 394 through 396' Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 492 removed outlier: 3.768A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 532 No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 537 through 542 removed outlier: 5.109A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 586 through 589 No H-bonds generated for 'chain '3' and resid 586 through 589' Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 686 Processing helix chain '3' and resid 690 through 694 Processing helix chain '3' and resid 699 through 715 Processing helix chain '3' and resid 723 through 738 removed outlier: 3.529A pdb=" N ASN 3 731 " --> pdb=" O LYS 3 727 " (cutoff:3.500A) Processing helix chain '4' and resid 187 through 198 removed outlier: 3.881A pdb=" N PHE 4 197 " --> pdb=" O ASN 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 213 through 215 No H-bonds generated for 'chain '4' and resid 213 through 215' Processing helix chain '4' and resid 218 through 221 No H-bonds generated for 'chain '4' and resid 218 through 221' Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 252 through 263 removed outlier: 3.775A pdb=" N GLU 4 255 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP 4 256 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN 4 263 " --> pdb=" O GLN 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 314 through 316 No H-bonds generated for 'chain '4' and resid 314 through 316' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 386 through 388 No H-bonds generated for 'chain '4' and resid 386 through 388' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 506 through 514 removed outlier: 3.783A pdb=" N ALA 4 514 " --> pdb=" O ARG 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 526 removed outlier: 3.648A pdb=" N ILE 4 526 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 573 through 584 Processing helix chain '4' and resid 620 through 624 Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 639 through 651 removed outlier: 4.183A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 Processing helix chain '4' and resid 714 through 728 removed outlier: 4.074A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 Processing helix chain '4' and resid 764 through 779 removed outlier: 4.095A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS 4 779 " --> pdb=" O VAL 4 775 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 813 removed outlier: 4.101A pdb=" N MET 4 811 " --> pdb=" O ALA 4 807 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 833 Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 102 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 262 through 264 No H-bonds generated for 'chain '5' and resid 262 through 264' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 353 through 362 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 removed outlier: 3.928A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) Processing helix chain '5' and resid 441 through 443 No H-bonds generated for 'chain '5' and resid 441 through 443' Processing helix chain '5' and resid 446 through 449 No H-bonds generated for 'chain '5' and resid 446 through 449' Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 482 through 484 No H-bonds generated for 'chain '5' and resid 482 through 484' Processing helix chain '5' and resid 487 through 497 removed outlier: 3.808A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 removed outlier: 3.749A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 579 through 589 Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 639 Processing helix chain '5' and resid 650 through 666 Processing helix chain '5' and resid 674 through 692 removed outlier: 4.444A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 711 through 721 removed outlier: 4.021A pdb=" N GLN 5 716 " --> pdb=" O ARG 5 712 " (cutoff:3.500A) Processing helix chain '5' and resid 730 through 738 Processing helix chain '5' and resid 746 through 757 Processing helix chain '6' and resid 99 through 101 No H-bonds generated for 'chain '6' and resid 99 through 101' Processing helix chain '6' and resid 106 through 121 Processing helix chain '6' and resid 135 through 145 Processing helix chain '6' and resid 155 through 172 removed outlier: 5.328A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 197 Processing helix chain '6' and resid 276 through 278 No H-bonds generated for 'chain '6' and resid 276 through 278' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 441 through 443 No H-bonds generated for 'chain '6' and resid 441 through 443' Processing helix chain '6' and resid 501 through 507 removed outlier: 4.634A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 521 Processing helix chain '6' and resid 525 through 532 removed outlier: 3.561A pdb=" N VAL 6 530 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 580 through 591 removed outlier: 3.521A pdb=" N LYS 6 586 " --> pdb=" O GLN 6 583 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 6 589 " --> pdb=" O LYS 6 586 " (cutoff:3.500A) Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 646 through 649 No H-bonds generated for 'chain '6' and resid 646 through 649' Processing helix chain '6' and resid 653 through 657 removed outlier: 3.614A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 653 through 657' Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 706 No H-bonds generated for 'chain '6' and resid 703 through 706' Processing helix chain '6' and resid 721 through 734 Processing helix chain '6' and resid 748 through 760 removed outlier: 3.749A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 783 removed outlier: 3.904A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR 6 772 " --> pdb=" O GLU 6 768 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 834 removed outlier: 4.500A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 27 Processing helix chain '7' and resid 31 through 33 No H-bonds generated for 'chain '7' and resid 31 through 33' Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 94 Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 110 through 124 removed outlier: 3.762A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 136 No H-bonds generated for 'chain '7' and resid 134 through 136' Processing helix chain '7' and resid 138 through 154 Processing helix chain '7' and resid 194 through 197 No H-bonds generated for 'chain '7' and resid 194 through 197' Processing helix chain '7' and resid 220 through 222 No H-bonds generated for 'chain '7' and resid 220 through 222' Processing helix chain '7' and resid 227 through 229 No H-bonds generated for 'chain '7' and resid 227 through 229' Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 290 No H-bonds generated for 'chain '7' and resid 287 through 290' Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 397 through 407 removed outlier: 4.678A pdb=" N MET 7 402 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 416 Processing helix chain '7' and resid 426 through 437 removed outlier: 3.640A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU 7 436 " --> pdb=" O LEU 7 432 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 543 Processing helix chain '7' and resid 580 through 582 No H-bonds generated for 'chain '7' and resid 580 through 582' Processing helix chain '7' and resid 588 through 593 removed outlier: 3.786A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 606 through 622 Processing helix chain '7' and resid 635 through 647 removed outlier: 3.538A pdb=" N GLU 7 640 " --> pdb=" O SER 7 636 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR 7 641 " --> pdb=" O LYS 7 637 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 670 removed outlier: 3.719A pdb=" N ASP 7 670 " --> pdb=" O ARG 7 666 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 727 Processing helix chain 'A' and resid 4 through 22 Processing helix chain 'A' and resid 34 through 59 removed outlier: 4.286A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 103 removed outlier: 3.530A pdb=" N MET A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.653A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 138 through 162 removed outlier: 4.099A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.457A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.704A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 removed outlier: 4.263A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 192 Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 56 through 72 Processing helix chain 'D' and resid 81 through 106 Processing helix chain 'D' and resid 124 through 153 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 64 through 72 Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 100 through 103 No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 224 through 240 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 280 removed outlier: 4.018A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing helix chain 'E' and resid 382 through 393 removed outlier: 5.412A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 462 through 484 removed outlier: 3.514A pdb=" N ARG E 472 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 515 removed outlier: 3.748A pdb=" N VAL E 489 " --> pdb=" O ASP E 486 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU E 490 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 514 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 515 " --> pdb=" O ALA E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 538 No H-bonds generated for 'chain 'E' and resid 536 through 538' Processing helix chain 'E' and resid 542 through 557 removed outlier: 3.520A pdb=" N CYS E 555 " --> pdb=" O TRP E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 615 removed outlier: 3.867A pdb=" N GLN E 610 " --> pdb=" O SER E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 646 removed outlier: 4.619A pdb=" N SER E 638 " --> pdb=" O GLU E 635 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 713 through 715 No H-bonds generated for 'chain 'F' and resid 713 through 715' Processing helix chain 'F' and resid 724 through 731 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 819 through 843 Processing helix chain 'F' and resid 851 through 875 removed outlier: 3.600A pdb=" N SER F 872 " --> pdb=" O ARG F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 888 removed outlier: 3.684A pdb=" N GLU F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 892 through 904 removed outlier: 3.950A pdb=" N ALA F 897 " --> pdb=" O ARG F 893 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 898 " --> pdb=" O ALA F 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 899 " --> pdb=" O LEU F 895 " (cutoff:3.500A) Processing helix chain 'F' and resid 908 through 921 Processing helix chain 'G' and resid 671 through 677 removed outlier: 3.890A pdb=" N TYR G 676 " --> pdb=" O ALA G 672 " (cutoff:3.500A) Processing helix chain 'G' and resid 724 through 731 Processing helix chain 'G' and resid 783 through 789 Processing helix chain 'G' and resid 819 through 844 Processing helix chain 'G' and resid 851 through 875 Processing helix chain 'G' and resid 879 through 888 Processing helix chain 'G' and resid 892 through 904 Processing helix chain 'G' and resid 908 through 922 Processing helix chain 'H' and resid 507 through 509 No H-bonds generated for 'chain 'H' and resid 507 through 509' Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 713 through 715 No H-bonds generated for 'chain 'H' and resid 713 through 715' Processing helix chain 'H' and resid 724 through 731 Processing helix chain 'H' and resid 783 through 789 removed outlier: 4.382A pdb=" N GLU H 788 " --> pdb=" O SER H 784 " (cutoff:3.500A) Processing helix chain 'H' and resid 819 through 843 Processing helix chain 'H' and resid 851 through 876 removed outlier: 4.063A pdb=" N ASP H 876 " --> pdb=" O SER H 872 " (cutoff:3.500A) Processing helix chain 'H' and resid 879 through 888 Processing helix chain 'H' and resid 892 through 904 Processing helix chain 'H' and resid 908 through 922 Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 29 through 32 No H-bonds generated for 'chain 'K' and resid 29 through 32' Processing helix chain 'K' and resid 84 through 99 removed outlier: 5.115A pdb=" N ASP K 99 " --> pdb=" O GLU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 123 removed outlier: 3.506A pdb=" N GLU K 122 " --> pdb=" O SER K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 144 through 158 removed outlier: 4.016A pdb=" N ALA K 149 " --> pdb=" O PRO K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 169 Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 189 through 191 No H-bonds generated for 'chain 'K' and resid 189 through 191' Processing helix chain 'L' and resid 212 through 221 Proline residue: L 216 - end of helix removed outlier: 4.342A pdb=" N ARG L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 232 removed outlier: 4.506A pdb=" N LEU L 232 " --> pdb=" O VAL L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 243 Processing helix chain 'L' and resid 245 through 247 No H-bonds generated for 'chain 'L' and resid 245 through 247' Processing helix chain 'L' and resid 258 through 270 Processing helix chain 'L' and resid 291 through 304 removed outlier: 4.216A pdb=" N LEU L 295 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG L 296 " --> pdb=" O SER L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 333 Processing helix chain 'L' and resid 336 through 339 Processing helix chain 'L' and resid 356 through 363 removed outlier: 4.298A pdb=" N LEU L 361 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 443 through 448 Processing helix chain 'L' and resid 469 through 472 No H-bonds generated for 'chain 'L' and resid 469 through 472' Processing helix chain 'L' and resid 476 through 479 Processing helix chain 'L' and resid 496 through 505 Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'L' and resid 565 through 573 Processing helix chain 'L' and resid 603 through 605 No H-bonds generated for 'chain 'L' and resid 603 through 605' Processing helix chain 'L' and resid 609 through 615 Processing helix chain 'L' and resid 632 through 640 removed outlier: 3.572A pdb=" N LYS L 636 " --> pdb=" O ASP L 632 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE L 638 " --> pdb=" O THR L 634 " (cutoff:3.500A) Processing helix chain 'L' and resid 642 through 644 No H-bonds generated for 'chain 'L' and resid 642 through 644' Processing helix chain 'L' and resid 661 through 673 removed outlier: 3.547A pdb=" N MET L 673 " --> pdb=" O LYS L 669 " (cutoff:3.500A) Processing helix chain 'L' and resid 697 through 705 Processing helix chain 'Q' and resid 1404 through 1411 Processing helix chain 'Q' and resid 1428 through 1430 No H-bonds generated for 'chain 'Q' and resid 1428 through 1430' Processing helix chain 'Q' and resid 1433 through 1440 removed outlier: 3.775A pdb=" N MET Q1439 " --> pdb=" O GLN Q1435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1524 through 1538 Processing helix chain 'Q' and resid 1540 through 1546 removed outlier: 3.859A pdb=" N TYR Q1546 " --> pdb=" O LYS Q1542 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1569 through 1583 Processing helix chain 'Q' and resid 1599 through 1605 Processing helix chain 'Q' and resid 1633 through 1656 removed outlier: 4.982A pdb=" N GLY Q1643 " --> pdb=" O VAL Q1639 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER Q1644 " --> pdb=" O LEU Q1640 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1668 through 1682 Processing helix chain 'Q' and resid 1700 through 1703 Processing helix chain 'Q' and resid 1707 through 1714 Processing helix chain 'Q' and resid 1739 through 1745 Processing helix chain 'Q' and resid 1785 through 1803 Processing helix chain 'Q' and resid 1807 through 1819 removed outlier: 4.677A pdb=" N ALA Q1817 " --> pdb=" O VAL Q1813 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER Q1818 " --> pdb=" O ASN Q1814 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1830 through 1853 Processing helix chain 'Q' and resid 1875 through 1890 removed outlier: 6.054A pdb=" N ALA Q1880 " --> pdb=" O GLU Q1876 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR Q1881 " --> pdb=" O ASN Q1877 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN Q1883 " --> pdb=" O TYR Q1879 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1893 through 1895 No H-bonds generated for 'chain 'Q' and resid 1893 through 1895' Processing helix chain 'Q' and resid 1940 through 1944 removed outlier: 3.867A pdb=" N PHE Q1944 " --> pdb=" O GLN Q1940 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1940 through 1944' Processing helix chain 'Q' and resid 1947 through 1974 Proline residue: Q1951 - end of helix Processing helix chain 'Q' and resid 2003 through 2006 Processing helix chain 'Q' and resid 2008 through 2025 Processing helix chain 'Q' and resid 2032 through 2035 No H-bonds generated for 'chain 'Q' and resid 2032 through 2035' Processing helix chain 'Q' and resid 2050 through 2064 Processing helix chain 'Q' and resid 2069 through 2083 removed outlier: 4.116A pdb=" N ILE Q2082 " --> pdb=" O GLU Q2078 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE Q2083 " --> pdb=" O LEU Q2079 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2090 through 2092 No H-bonds generated for 'chain 'Q' and resid 2090 through 2092' Processing helix chain 'Q' and resid 2124 through 2128 Processing helix chain 'Q' and resid 2139 through 2158 Processing helix chain 'Q' and resid 2191 through 2208 Processing helix chain 'Q' and resid 2211 through 2221 removed outlier: 3.780A pdb=" N THR Q2221 " --> pdb=" O ILE Q2217 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 29 Proline residue: R 19 - end of helix removed outlier: 4.305A pdb=" N ARG R 27 " --> pdb=" O ARG R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 49 Processing helix chain 'R' and resid 56 through 73 removed outlier: 3.704A pdb=" N THR R 59 " --> pdb=" O GLY R 56 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS R 61 " --> pdb=" O ALA R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 Processing helix chain 'R' and resid 166 through 168 No H-bonds generated for 'chain 'R' and resid 166 through 168' Processing helix chain 'R' and resid 196 through 199 Processing helix chain 'R' and resid 201 through 203 No H-bonds generated for 'chain 'R' and resid 201 through 203' Processing helix chain 'R' and resid 211 through 215 Processing helix chain 'R' and resid 217 through 231 Processing helix chain 'R' and resid 271 through 274 Processing helix chain 'R' and resid 352 through 358 Processing helix chain 'R' and resid 381 through 393 Processing helix chain 'R' and resid 411 through 426 removed outlier: 4.361A pdb=" N ASP R 426 " --> pdb=" O GLN R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 471 removed outlier: 3.989A pdb=" N ARG R 471 " --> pdb=" O THR R 467 " (cutoff:3.500A) Processing helix chain 'R' and resid 473 through 478 Processing helix chain 'R' and resid 490 through 496 removed outlier: 4.326A pdb=" N VAL R 495 " --> pdb=" O TRP R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 519 removed outlier: 3.503A pdb=" N VAL R 519 " --> pdb=" O LYS R 515 " (cutoff:3.500A) Processing helix chain 'R' and resid 546 through 553 Processing helix chain 'R' and resid 594 through 609 Processing helix chain 'R' and resid 624 through 630 removed outlier: 3.647A pdb=" N ASP R 627 " --> pdb=" O TRP R 624 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS R 628 " --> pdb=" O ASP R 625 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 31 Processing helix chain 'X' and resid 51 through 69 removed outlier: 3.655A pdb=" N ASP X 67 " --> pdb=" O LYS X 63 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 80 removed outlier: 3.932A pdb=" N ALA X 79 " --> pdb=" O ALA X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 86 No H-bonds generated for 'chain 'X' and resid 83 through 86' Processing helix chain 'X' and resid 88 through 104 Processing helix chain 'X' and resid 118 through 135 removed outlier: 4.490A pdb=" N LYS X 123 " --> pdb=" O ALA X 119 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE X 124 " --> pdb=" O TYR X 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 169 removed outlier: 5.107A pdb=" N GLY X 154 " --> pdb=" O ILE X 150 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU X 155 " --> pdb=" O THR X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 187 removed outlier: 3.985A pdb=" N VAL X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 214 Processing helix chain 'X' and resid 245 through 248 No H-bonds generated for 'chain 'X' and resid 245 through 248' Processing helix chain 'X' and resid 250 through 259 Processing helix chain 'X' and resid 262 through 271 Processing helix chain 'X' and resid 283 through 294 removed outlier: 3.631A pdb=" N MET X 290 " --> pdb=" O LEU X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 302 Processing helix chain 'X' and resid 330 through 351 removed outlier: 3.729A pdb=" N MET X 345 " --> pdb=" O LYS X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 360 No H-bonds generated for 'chain 'X' and resid 358 through 360' Processing helix chain 'X' and resid 381 through 383 No H-bonds generated for 'chain 'X' and resid 381 through 383' Processing helix chain 'X' and resid 385 through 394 Processing helix chain 'X' and resid 431 through 447 Processing helix chain 'X' and resid 449 through 460 Processing helix chain 'X' and resid 469 through 492 Processing helix chain 'X' and resid 498 through 504 removed outlier: 5.794A pdb=" N GLU X 503 " --> pdb=" O GLN X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 507 through 522 Processing helix chain 'X' and resid 526 through 549 Processing helix chain 'X' and resid 557 through 564 Processing helix chain 'X' and resid 568 through 582 Proline residue: X 577 - end of helix removed outlier: 4.883A pdb=" N SER X 581 " --> pdb=" O PRO X 577 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS X 582 " --> pdb=" O LYS X 578 " (cutoff:3.500A) Processing helix chain 'X' and resid 585 through 605 Processing helix chain 'X' and resid 659 through 666 removed outlier: 3.755A pdb=" N ASN X 665 " --> pdb=" O LYS X 661 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR X 666 " --> pdb=" O VAL X 662 " (cutoff:3.500A) Processing helix chain 'X' and resid 669 through 681 removed outlier: 4.307A pdb=" N ARG X 681 " --> pdb=" O ASN X 677 " (cutoff:3.500A) Processing helix chain 'X' and resid 687 through 702 Processing helix chain 'X' and resid 707 through 710 Processing helix chain 'X' and resid 713 through 723 Processing helix chain 'X' and resid 733 through 755 Processing helix chain 'X' and resid 757 through 764 removed outlier: 4.218A pdb=" N LEU X 763 " --> pdb=" O PHE X 760 " (cutoff:3.500A) Processing helix chain 'X' and resid 771 through 779 removed outlier: 4.925A pdb=" N TYR X 776 " --> pdb=" O GLU X 772 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 59 No H-bonds generated for 'chain 'Y' and resid 56 through 59' Processing helix chain 'Y' and resid 65 through 75 removed outlier: 5.342A pdb=" N HIS Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 102 removed outlier: 4.202A pdb=" N PHE Y 94 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 121 Processing helix chain 'Y' and resid 123 through 138 Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.513A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 422 through 429 removed outlier: 4.111A pdb=" N GLU 2 422 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER 2 455 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 339 through 341 Processing sheet with id= D, first strand: chain '2' and resid 525 through 527 Processing sheet with id= E, first strand: chain '2' and resid 679 through 683 removed outlier: 3.718A pdb=" N VAL 2 564 " --> pdb=" O VAL 2 603 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 578 through 582 Processing sheet with id= G, first strand: chain '2' and resid 628 through 633 Processing sheet with id= H, first strand: chain '2' and resid 331 through 337 removed outlier: 6.729A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 95 through 99 removed outlier: 6.734A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 165 through 167 removed outlier: 8.124A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 185 through 187 Processing sheet with id= L, first strand: chain '3' and resid 209 through 213 Processing sheet with id= M, first strand: chain '3' and resid 545 through 549 Processing sheet with id= N, first strand: chain '3' and resid 444 through 447 Processing sheet with id= O, first strand: chain '3' and resid 494 through 497 removed outlier: 3.535A pdb=" N THR 3 504 " --> pdb=" O ILE 3 497 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '3' and resid 193 through 198 removed outlier: 6.713A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 240 through 244 removed outlier: 6.699A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '4' and resid 414 through 420 removed outlier: 3.750A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4' and resid 355 through 359 Processing sheet with id= T, first strand: chain '4' and resid 704 through 706 removed outlier: 6.296A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '4' and resid 653 through 658 Processing sheet with id= V, first strand: chain '4' and resid 339 through 344 removed outlier: 6.751A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 60 through 64 removed outlier: 6.649A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain '5' and resid 273 through 279 removed outlier: 3.727A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE 5 297 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE 5 330 " --> pdb=" O ILE 5 297 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER 5 299 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE 5 328 " --> pdb=" O SER 5 299 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR 5 301 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 189 through 193 removed outlier: 4.584A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 552 through 556 removed outlier: 6.750A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 451 through 456 removed outlier: 3.621A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '5' and resid 501 through 506 Processing sheet with id= AC, first strand: chain '5' and resid 727 through 729 Processing sheet with id= AD, first strand: chain '5' and resid 173 through 178 removed outlier: 6.617A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 150 through 154 removed outlier: 6.381A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain '6' and resid 287 through 293 removed outlier: 9.287A pdb=" N THR 6 376 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N PHE 6 454 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP 6 378 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG 6 296 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 309 through 311 Processing sheet with id= AH, first strand: chain '6' and resid 711 through 715 removed outlier: 6.795A pdb=" N GLY 6 634 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU 6 679 " --> pdb=" O GLY 6 634 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AJ, first strand: chain '6' and resid 660 through 665 Processing sheet with id= AK, first strand: chain '6' and resid 301 through 306 removed outlier: 6.885A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '6' and resid 394 through 398 removed outlier: 3.754A pdb=" N ARG 6 394 " --> pdb=" O GLY 6 463 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS 6 396 " --> pdb=" O SER 6 461 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER 6 461 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR 6 398 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL 6 459 " --> pdb=" O THR 6 398 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 77 through 81 removed outlier: 6.139A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain '7' and resid 224 through 226 removed outlier: 9.328A pdb=" N LEU 7 225 " --> pdb=" O LEU 7 238 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR 7 240 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N SER 7 330 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU 7 376 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA 7 378 " --> pdb=" O ASN 7 332 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS 7 334 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N PHE 7 380 " --> pdb=" O HIS 7 334 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ASN 7 336 " --> pdb=" O PHE 7 380 " (cutoff:3.500A) removed outlier: 13.876A pdb=" N ARG 7 382 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 269 through 272 removed outlier: 4.510A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 596 through 600 removed outlier: 6.802A pdb=" N GLY 7 519 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU 7 564 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 496 through 499 removed outlier: 3.964A pdb=" N ALA 7 496 " --> pdb=" O GLU 7 509 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU 7 509 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '7' and resid 545 through 550 Processing sheet with id= AS, first strand: chain '7' and resid 252 through 257 removed outlier: 6.776A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= AU, first strand: chain 'A' and resid 172 through 176 removed outlier: 3.830A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 68 through 72 Processing sheet with id= AW, first strand: chain 'C' and resid 43 through 47 Processing sheet with id= AX, first strand: chain 'D' and resid 274 through 278 Processing sheet with id= AY, first strand: chain 'D' and resid 255 through 260 Processing sheet with id= AZ, first strand: chain 'E' and resid 56 through 61 removed outlier: 6.728A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'E' and resid 316 through 322 Processing sheet with id= BB, first strand: chain 'E' and resid 526 through 530 Processing sheet with id= BC, first strand: chain 'F' and resid 526 through 530 removed outlier: 3.581A pdb=" N THR F 495 " --> pdb=" O VAL F 502 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS F 506 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG F 491 " --> pdb=" O LYS F 506 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 536 through 539 Processing sheet with id= BE, first strand: chain 'F' and resid 578 through 584 removed outlier: 7.039A pdb=" N GLY F 591 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL F 581 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE F 589 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA F 583 " --> pdb=" O ARG F 587 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG F 587 " --> pdb=" O ALA F 583 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'F' and resid 615 through 621 removed outlier: 6.844A pdb=" N VAL F 628 " --> pdb=" O VAL F 616 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU F 618 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE F 626 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA F 620 " --> pdb=" O ARG F 624 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG F 624 " --> pdb=" O ALA F 620 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU F 642 " --> pdb=" O TYR F 650 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR F 650 " --> pdb=" O GLU F 642 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.749A pdb=" N SER F 686 " --> pdb=" O PHE F 698 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU F 706 " --> pdb=" O PRO F 720 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER F 708 " --> pdb=" O TRP F 718 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP F 718 " --> pdb=" O SER F 708 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'F' and resid 772 through 775 removed outlier: 6.265A pdb=" N ILE F 755 " --> pdb=" O PRO F 744 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 757 " --> pdb=" O VAL F 742 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL F 742 " --> pdb=" O VAL F 757 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 526 through 530 removed outlier: 3.551A pdb=" N THR G 495 " --> pdb=" O VAL G 502 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR G 504 " --> pdb=" O TYR G 493 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR G 493 " --> pdb=" O THR G 504 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS G 506 " --> pdb=" O ARG G 491 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG G 491 " --> pdb=" O LYS G 506 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 536 through 539 Processing sheet with id= BK, first strand: chain 'G' and resid 578 through 583 removed outlier: 6.792A pdb=" N GLY G 591 " --> pdb=" O THR G 579 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL G 581 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 589 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA G 583 " --> pdb=" O ARG G 587 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG G 587 " --> pdb=" O ALA G 583 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR G 596 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN G 601 " --> pdb=" O PRO G 606 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'G' and resid 615 through 621 removed outlier: 6.557A pdb=" N VAL G 628 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU G 618 " --> pdb=" O PHE G 626 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE G 626 " --> pdb=" O LEU G 618 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA G 620 " --> pdb=" O ARG G 624 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG G 624 " --> pdb=" O ALA G 620 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'G' and resid 686 through 689 removed outlier: 3.577A pdb=" N SER G 686 " --> pdb=" O PHE G 698 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 722 " --> pdb=" O LEU G 704 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU G 706 " --> pdb=" O PRO G 720 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER G 708 " --> pdb=" O TRP G 718 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP G 718 " --> pdb=" O SER G 708 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'G' and resid 772 through 775 removed outlier: 6.388A pdb=" N ILE G 755 " --> pdb=" O PRO G 744 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL G 757 " --> pdb=" O VAL G 742 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL G 742 " --> pdb=" O VAL G 757 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 526 through 530 removed outlier: 3.742A pdb=" N THR H 495 " --> pdb=" O VAL H 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 536 through 539 Processing sheet with id= BQ, first strand: chain 'H' and resid 578 through 583 removed outlier: 6.941A pdb=" N GLY H 591 " --> pdb=" O THR H 579 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL H 581 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE H 589 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR H 596 " --> pdb=" O THR H 592 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'H' and resid 615 through 621 removed outlier: 6.687A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU H 642 " --> pdb=" O TYR H 650 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR H 650 " --> pdb=" O GLU H 642 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'H' and resid 686 through 689 removed outlier: 3.588A pdb=" N LEU H 722 " --> pdb=" O LEU H 704 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU H 706 " --> pdb=" O PRO H 720 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER H 708 " --> pdb=" O TRP H 718 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP H 718 " --> pdb=" O SER H 708 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'H' and resid 772 through 775 removed outlier: 6.038A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL H 757 " --> pdb=" O VAL H 742 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL H 742 " --> pdb=" O VAL H 757 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'K' and resid 15 through 19 Processing sheet with id= BV, first strand: chain 'L' and resid 250 through 252 removed outlier: 7.013A pdb=" N GLN L 283 " --> pdb=" O PHE L 251 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU L 343 " --> pdb=" O LEU L 314 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU L 316 " --> pdb=" O GLU L 343 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER L 345 " --> pdb=" O LEU L 316 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS L 369 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU L 346 " --> pdb=" O LYS L 369 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU L 371 " --> pdb=" O LEU L 346 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE L 348 " --> pdb=" O GLU L 371 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE L 373 " --> pdb=" O ILE L 348 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR L 350 " --> pdb=" O ILE L 373 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL L 375 " --> pdb=" O TYR L 350 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS L 427 " --> pdb=" O ILE L 370 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU L 372 " --> pdb=" O LYS L 427 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR L 429 " --> pdb=" O LEU L 372 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE L 374 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE L 431 " --> pdb=" O PHE L 374 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN L 376 " --> pdb=" O ILE L 431 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS L 456 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU L 430 " --> pdb=" O LYS L 456 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR L 458 " --> pdb=" O LEU L 430 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS L 432 " --> pdb=" O THR L 458 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR L 460 " --> pdb=" O CYS L 432 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU L 485 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE L 459 " --> pdb=" O GLU L 485 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 487 " --> pdb=" O ILE L 459 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS L 514 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE L 488 " --> pdb=" O LYS L 514 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR L 516 " --> pdb=" O ILE L 488 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS L 555 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE L 517 " --> pdb=" O LYS L 555 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP L 557 " --> pdb=" O PHE L 517 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER L 584 " --> pdb=" O LEU L 556 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU L 621 " --> pdb=" O LEU L 585 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG L 650 " --> pdb=" O ILE L 622 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR L 686 " --> pdb=" O LEU L 651 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN L 711 " --> pdb=" O LEU L 687 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'Q' and resid 1345 through 1352 removed outlier: 5.897A pdb=" N THR Q1341 " --> pdb=" O VAL Q1324 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL Q1324 " --> pdb=" O THR Q1341 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Q' and resid 1354 through 1360 removed outlier: 4.582A pdb=" N LEU Q1397 " --> pdb=" O SER Q1379 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'Q' and resid 1483 through 1486 Processing sheet with id= BZ, first strand: chain 'Q' and resid 1508 through 1511 removed outlier: 6.652A pdb=" N GLU Q1559 " --> pdb=" O ILE Q1509 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE Q1511 " --> pdb=" O GLU Q1559 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL Q1561 " --> pdb=" O ILE Q1511 " (cutoff:3.500A) No H-bonds generated for sheet with id= BZ Processing sheet with id= CA, first strand: chain 'Q' and resid 1725 through 1727 removed outlier: 4.038A pdb=" N TYR Q1905 " --> pdb=" O CYS Q1922 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU Q1920 " --> pdb=" O ASP Q1907 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU Q1909 " --> pdb=" O SER Q1918 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER Q1918 " --> pdb=" O LEU Q1909 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP Q1911 " --> pdb=" O ASN Q1916 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASN Q1916 " --> pdb=" O TRP Q1911 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'Q' and resid 1901 through 1906 removed outlier: 6.691A pdb=" N ASP Q1733 " --> pdb=" O LYS Q1903 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR Q1905 " --> pdb=" O VAL Q1731 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL Q1731 " --> pdb=" O TYR Q1905 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS Q1869 " --> pdb=" O ILE Q1858 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE Q1858 " --> pdb=" O LYS Q1869 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'Q' and resid 2106 through 2108 Processing sheet with id= CD, first strand: chain 'Q' and resid 2162 through 2164 Processing sheet with id= CE, first strand: chain 'R' and resid 171 through 173 removed outlier: 6.582A pdb=" N THR R 638 " --> pdb=" O VAL R 540 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N PHE R 542 " --> pdb=" O THR R 638 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL R 640 " --> pdb=" O PHE R 542 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS R 657 " --> pdb=" O MET R 639 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU R 641 " --> pdb=" O LYS R 657 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE R 659 " --> pdb=" O LEU R 641 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'R' and resid 180 through 184 removed outlier: 4.279A pdb=" N ARG R 180 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'R' and resid 325 through 332 removed outlier: 3.728A pdb=" N GLN R 280 " --> pdb=" O TYR R 332 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TRP R 296 " --> pdb=" O ILE R 307 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU R 329 " --> pdb=" O THR R 342 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N MET R 344 " --> pdb=" O LEU R 327 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU R 327 " --> pdb=" O MET R 344 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'R' and resid 681 through 688 removed outlier: 3.718A pdb=" N LYS R 681 " --> pdb=" O VAL R 676 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU R 431 " --> pdb=" O VAL R 400 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU R 402 " --> pdb=" O LEU R 431 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE R 433 " --> pdb=" O LEU R 402 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR R 480 " --> pdb=" O LEU R 432 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP R 434 " --> pdb=" O THR R 480 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE R 482 " --> pdb=" O TRP R 434 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'X' and resid 32 through 35 Processing sheet with id= CJ, first strand: chain 'X' and resid 364 through 367 2994 hydrogen bonds defined for protein. 8433 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: 33.04 Time building geometry restraints manager: 26.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23575 1.34 - 1.46: 17055 1.46 - 1.59: 34875 1.59 - 1.71: 133 1.71 - 1.84: 532 Bond restraints: 76170 Sorted by residual: bond pdb=" O3A ANP 21500 " pdb=" PB ANP 21500 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O3A ANP 51500 " pdb=" PB ANP 51500 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N3B ANP 51500 " pdb=" PG ANP 51500 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" N3B ANP 21500 " pdb=" PG ANP 21500 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O5' ANP 21500 " pdb=" PA ANP 21500 " ideal model delta sigma weight residual 1.655 1.569 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 76165 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.64: 1941 105.64 - 112.81: 38703 112.81 - 119.98: 29400 119.98 - 127.16: 32310 127.16 - 134.33: 902 Bond angle restraints: 103256 Sorted by residual: angle pdb=" N LYS L 278 " pdb=" CA LYS L 278 " pdb=" C LYS L 278 " ideal model delta sigma weight residual 111.03 116.18 -5.15 1.11e+00 8.12e-01 2.15e+01 angle pdb=" CA TYR 2 227 " pdb=" CB TYR 2 227 " pdb=" CG TYR 2 227 " ideal model delta sigma weight residual 113.90 105.81 8.09 1.80e+00 3.09e-01 2.02e+01 angle pdb=" C SER 7 605 " pdb=" N ARG 7 606 " pdb=" CA ARG 7 606 " ideal model delta sigma weight residual 120.82 127.18 -6.36 1.50e+00 4.44e-01 1.80e+01 angle pdb=" CA TYR G 922 " pdb=" CB TYR G 922 " pdb=" CG TYR G 922 " ideal model delta sigma weight residual 113.90 121.49 -7.59 1.80e+00 3.09e-01 1.78e+01 angle pdb=" CA TYR Q1486 " pdb=" CB TYR Q1486 " pdb=" CG TYR Q1486 " ideal model delta sigma weight residual 113.90 121.04 -7.14 1.80e+00 3.09e-01 1.57e+01 ... (remaining 103251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 42277 17.92 - 35.84: 2923 35.84 - 53.77: 706 53.77 - 71.69: 204 71.69 - 89.61: 87 Dihedral angle restraints: 46197 sinusoidal: 19380 harmonic: 26817 Sorted by residual: dihedral pdb=" CA ASP R 489 " pdb=" C ASP R 489 " pdb=" N LEU R 490 " pdb=" CA LEU R 490 " ideal model delta harmonic sigma weight residual 180.00 -131.85 -48.15 0 5.00e+00 4.00e-02 9.27e+01 dihedral pdb=" CA ASP 2 678 " pdb=" C ASP 2 678 " pdb=" N ILE 2 679 " pdb=" CA ILE 2 679 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA GLU H 509 " pdb=" C GLU H 509 " pdb=" N GLN H 510 " pdb=" CA GLN H 510 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 46194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 11034 0.100 - 0.201: 728 0.201 - 0.301: 7 0.301 - 0.402: 2 0.402 - 0.502: 2 Chirality restraints: 11773 Sorted by residual: chirality pdb=" P DT I 103 " pdb=" OP1 DT I 103 " pdb=" OP2 DT I 103 " pdb=" O5' DT I 103 " both_signs ideal model delta sigma weight residual True 2.35 2.85 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" P DC J 1 " pdb=" OP1 DC J 1 " pdb=" OP2 DC J 1 " pdb=" O5' DC J 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" P DG I 1 " pdb=" OP1 DG I 1 " pdb=" OP2 DG I 1 " pdb=" O5' DG I 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 11770 not shown) Planarity restraints: 12924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 5 " 0.043 2.00e-02 2.50e+03 1.76e-02 9.33e+00 pdb=" N9 DG I 5 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 5 " -0.029 2.00e-02 2.50e+03 pdb=" N7 DG I 5 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 5 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 5 " 0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 5 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DG I 5 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 5 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 5 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DG I 5 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 5 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 227 " 0.039 2.00e-02 2.50e+03 2.10e-02 8.81e+00 pdb=" CG TYR 2 227 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 227 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 227 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 227 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR 2 227 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 2 227 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR 6 609 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" C THR 6 609 " -0.051 2.00e-02 2.50e+03 pdb=" O THR 6 609 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA 6 610 " 0.018 2.00e-02 2.50e+03 ... (remaining 12921 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 151 2.57 - 3.15: 62150 3.15 - 3.73: 118508 3.73 - 4.32: 169036 4.32 - 4.90: 272177 Nonbonded interactions: 622022 Sorted by model distance: nonbonded pdb=" O2G ANP 51500 " pdb="MG MG 51501 " model vdw 1.984 2.170 nonbonded pdb=" O2G ANP 21500 " pdb="MG MG 21501 " model vdw 1.990 2.170 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 51501 " model vdw 1.994 2.170 nonbonded pdb=" O1B ANP 51500 " pdb="MG MG 51501 " model vdw 1.997 2.170 nonbonded pdb=" O1B ANP 21500 " pdb="MG MG 21501 " model vdw 2.004 2.170 ... (remaining 622017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 through 901 or (resid 902 and (name N \ or name CA or name C or name O or name CB )) or resid 903 through 909 or (resid \ 910 and (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.050 Extract box with map and model: 15.380 Check model and map are aligned: 0.810 Set scattering table: 0.490 Process input model: 158.740 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.007 0.154 76170 Z= 0.426 Angle : 0.938 11.341 103256 Z= 0.517 Chirality : 0.051 0.502 11773 Planarity : 0.007 0.116 12924 Dihedral : 14.255 89.612 28745 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 8947 helix: 0.13 (0.08), residues: 3945 sheet: -0.65 (0.13), residues: 1366 loop : -0.26 (0.10), residues: 3636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1136 time to evaluate : 6.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 8 residues processed: 1170 average time/residue: 0.7435 time to fit residues: 1475.7735 Evaluate side-chains 615 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 607 time to evaluate : 6.709 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6370 time to fit residues: 18.2742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 769 optimal weight: 4.9990 chunk 690 optimal weight: 7.9990 chunk 383 optimal weight: 0.0980 chunk 235 optimal weight: 8.9990 chunk 465 optimal weight: 2.9990 chunk 368 optimal weight: 0.0980 chunk 714 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 434 optimal weight: 0.0070 chunk 531 optimal weight: 4.9990 chunk 827 optimal weight: 1.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 657 ASN A 125 HIS D 247 GLN E 254 GLN ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 244 HIS L 355 GLN ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1714 ASN Q1729 ASN ** Q2046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 76170 Z= 0.189 Angle : 0.630 12.117 103256 Z= 0.328 Chirality : 0.043 0.231 11773 Planarity : 0.004 0.050 12924 Dihedral : 10.914 84.644 10555 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 8947 helix: 0.84 (0.08), residues: 3908 sheet: -0.54 (0.13), residues: 1452 loop : 0.01 (0.11), residues: 3587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 686 time to evaluate : 6.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 43 residues processed: 743 average time/residue: 0.7021 time to fit residues: 913.6668 Evaluate side-chains 599 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 556 time to evaluate : 6.843 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.6884 time to fit residues: 63.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 459 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 688 optimal weight: 9.9990 chunk 563 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 828 optimal weight: 3.9990 chunk 895 optimal weight: 6.9990 chunk 738 optimal weight: 7.9990 chunk 821 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 chunk 664 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN ** 2 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 94 HIS ** 3 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN 6 659 GLN A 57 GLN E 7 GLN E 254 GLN E 402 GLN E 461 ASN E 521 HIS E 531 GLN L 475 GLN ** L 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 352 HIS X 416 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 76170 Z= 0.264 Angle : 0.593 11.349 103256 Z= 0.307 Chirality : 0.042 0.187 11773 Planarity : 0.004 0.054 12924 Dihedral : 10.590 80.609 10555 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8947 helix: 1.11 (0.08), residues: 3949 sheet: -0.54 (0.13), residues: 1431 loop : 0.06 (0.11), residues: 3567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 605 time to evaluate : 6.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 49 residues processed: 691 average time/residue: 0.6804 time to fit residues: 831.4371 Evaluate side-chains 584 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 535 time to evaluate : 6.745 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5509 time to fit residues: 60.8285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 818 optimal weight: 2.9990 chunk 623 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 395 optimal weight: 0.0970 chunk 556 optimal weight: 0.5980 chunk 831 optimal weight: 0.8980 chunk 880 optimal weight: 9.9990 chunk 434 optimal weight: 0.4980 chunk 788 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 HIS ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 271 GLN ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** L 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2060 HIS R 611 HIS X 352 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 76170 Z= 0.151 Angle : 0.550 13.779 103256 Z= 0.279 Chirality : 0.041 0.213 11773 Planarity : 0.004 0.049 12924 Dihedral : 10.385 76.816 10555 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8947 helix: 1.31 (0.08), residues: 3926 sheet: -0.41 (0.13), residues: 1427 loop : 0.16 (0.11), residues: 3594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 619 time to evaluate : 6.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 25 residues processed: 665 average time/residue: 0.6761 time to fit residues: 801.2476 Evaluate side-chains 571 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 546 time to evaluate : 6.730 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5512 time to fit residues: 35.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 733 optimal weight: 7.9990 chunk 499 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 655 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 751 optimal weight: 0.9990 chunk 608 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 449 optimal weight: 0.5980 chunk 790 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 164 HIS ** 3 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 HIS ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** Q1708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 352 HIS ** Y 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 76170 Z= 0.193 Angle : 0.541 12.374 103256 Z= 0.275 Chirality : 0.041 0.172 11773 Planarity : 0.004 0.051 12924 Dihedral : 10.252 72.990 10555 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.09), residues: 8947 helix: 1.46 (0.08), residues: 3932 sheet: -0.32 (0.14), residues: 1377 loop : 0.19 (0.11), residues: 3638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 583 time to evaluate : 6.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 21 residues processed: 622 average time/residue: 0.6990 time to fit residues: 773.5855 Evaluate side-chains 545 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 524 time to evaluate : 6.965 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6383 time to fit residues: 35.4553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 911 random chunks: chunk 296 optimal weight: 6.9990 chunk 792 optimal weight: 0.0870 chunk 174 optimal weight: 0.8980 chunk 517 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 881 optimal weight: 10.0000 chunk 731 optimal weight: 6.9990 chunk 408 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 291 optimal weight: 0.4980 chunk 462 optimal weight: 4.9990 overall best weight: 1.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 290 HIS ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 210 HIS ** 3 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 465 HIS ** 5 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN ** Q1708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 76170 Z= 0.177 Angle : 0.536 14.901 103256 Z= 0.270 Chirality : 0.040 0.167 11773 Planarity : 0.003 0.050 12924 Dihedral : 10.162 70.785 10555 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 8947 helix: 1.53 (0.08), residues: 3923 sheet: -0.26 (0.14), residues: 1379 loop : 0.24 (0.11), residues: 3645 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17894 Ramachandran restraints generated. 8947 Oldfield, 0 Emsley, 8947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 576 time to evaluate : 6.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 17 residues processed: 604 average time/residue: 0.6910 time to fit residues: 742.3312 Evaluate side-chains 552 residues out of total 8234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 535 time to evaluate : 6.844 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5971 time to fit residues: 28.2157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5901 > 50: distance: 104 - 203: 15.802 distance: 107 - 200: 8.033 distance: 118 - 185: 24.554 distance: 121 - 182: 11.016 distance: 133 - 170: 25.495 distance: 136 - 167: 14.990 distance: 162 - 167: 11.788 distance: 167 - 168: 9.896 distance: 169 - 170: 23.402 distance: 169 - 171: 13.128 distance: 171 - 172: 9.483 distance: 172 - 173: 15.271 distance: 172 - 175: 10.489 distance: 173 - 174: 23.878 distance: 173 - 182: 10.093 distance: 175 - 176: 10.979 distance: 176 - 177: 17.475 distance: 176 - 178: 14.910 distance: 177 - 179: 10.384 distance: 178 - 180: 10.783 distance: 180 - 181: 5.421 distance: 182 - 183: 16.336 distance: 183 - 184: 13.516 distance: 183 - 186: 5.803 distance: 184 - 185: 17.119 distance: 184 - 189: 8.342 distance: 186 - 187: 14.925 distance: 186 - 188: 17.766 distance: 189 - 190: 5.701 distance: 189 - 255: 7.625 distance: 190 - 191: 13.993 distance: 190 - 193: 11.723 distance: 191 - 192: 12.373 distance: 191 - 200: 18.808 distance: 192 - 252: 19.985 distance: 193 - 194: 12.251 distance: 194 - 195: 16.185 distance: 195 - 196: 5.653 distance: 196 - 197: 13.494 distance: 197 - 198: 8.278 distance: 197 - 199: 9.503 distance: 200 - 201: 23.831 distance: 201 - 202: 23.467 distance: 201 - 204: 27.813 distance: 202 - 203: 10.569 distance: 202 - 207: 10.005 distance: 204 - 205: 15.935 distance: 204 - 206: 43.683 distance: 207 - 208: 18.476 distance: 208 - 209: 35.257 distance: 208 - 211: 20.762 distance: 209 - 210: 13.813 distance: 209 - 215: 39.038 distance: 211 - 212: 36.467 distance: 212 - 213: 21.001 distance: 212 - 214: 30.009 distance: 215 - 216: 22.309 distance: 216 - 217: 8.965 distance: 217 - 218: 16.765 distance: 217 - 219: 18.394 distance: 219 - 220: 9.253 distance: 220 - 221: 4.257 distance: 220 - 223: 15.127 distance: 221 - 222: 20.749 distance: 221 - 231: 15.833 distance: 223 - 224: 19.733 distance: 224 - 225: 20.485 distance: 224 - 226: 7.007 distance: 225 - 227: 13.583 distance: 226 - 228: 7.339 distance: 227 - 229: 10.133 distance: 228 - 229: 3.781 distance: 229 - 230: 13.091 distance: 231 - 232: 8.739 distance: 232 - 233: 28.566 distance: 232 - 235: 16.689 distance: 233 - 234: 46.123 distance: 233 - 242: 11.455 distance: 235 - 236: 10.801 distance: 236 - 237: 8.490 distance: 237 - 238: 11.841 distance: 238 - 239: 8.063 distance: 239 - 240: 6.431 distance: 239 - 241: 17.393 distance: 242 - 243: 5.211 distance: 243 - 244: 50.591 distance: 244 - 245: 26.783 distance: 244 - 246: 19.944