Starting phenix.real_space_refine on Fri Feb 16 23:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfo_13375/02_2024/7pfo_13375_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfo_13375/02_2024/7pfo_13375.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/7pfo_13375/02_2024/7pfo_13375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfo_13375/02_2024/7pfo_13375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfo_13375/02_2024/7pfo_13375_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfo_13375/02_2024/7pfo_13375_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 6 6.06 5 P 63 5.49 5 Mg 3 5.21 5 S 404 5.16 5 C 42845 2.51 5 N 11921 2.21 5 O 12844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 1398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68086 Number of models: 1 Model: "" Number of chains: 29 Chain: "B" Number of atoms: 6061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 6061 Classifications: {'peptide': 759} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 729} Chain breaks: 13 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4199 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 487} Chain: "4" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4929 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 28, 'TRANS': 590} Chain breaks: 3 Chain: "6" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5014 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 23, 'TRANS': 608} Chain breaks: 3 Chain: "7" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4722 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain breaks: 4 Chain: "3" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4858 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 23, 'TRANS': 596} Chain breaks: 2 Chain: "2" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5580 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 29, 'TRANS': 673} Chain breaks: 2 Chain: "5" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4735 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 579} Chain breaks: 3 Chain: "D" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1606 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "E" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1431 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 163} Chain: "F" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1679 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "C" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4347 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 520} Chain breaks: 1 Chain: "K" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5215 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "L" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 735 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain: "M" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 662 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "H" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} bond proxies already assigned to first conformer: 3234 Chain: "I" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} bond proxies already assigned to first conformer: 3234 Chain: "J" Number of atoms: 3183 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} bond proxies already assigned to first conformer: 3228 Chain: "N" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 438 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "Q" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 683 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} 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: "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: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5586 SG CYS B2221 87.165 77.217 130.112 1.00 92.50 S ATOM 5609 SG CYS B2224 84.305 76.966 132.424 1.00 93.52 S ATOM 5702 SG CYS B2236 84.493 74.859 129.013 1.00 93.58 S ATOM 5714 SG CYS B2238 83.393 78.408 129.204 1.00 93.49 S ATOM 11497 SG CYS 4 306 83.486 179.724 86.837 1.00 30.34 S ATOM 11519 SG CYS 4 309 83.909 183.448 87.607 1.00 39.08 S ATOM 11665 SG CYS 4 328 81.296 182.287 85.129 1.00 38.63 S ATOM 11686 SG CYS 4 331 85.071 181.990 84.323 1.00 45.61 S ATOM 16456 SG CYS 6 158 98.632 170.348 85.288 1.00 42.32 S ATOM 16478 SG CYS 6 161 101.311 173.001 85.079 1.00 48.89 S ATOM 16639 SG CYS 6 180 97.894 173.828 86.080 1.00 45.70 S ATOM 16678 SG CYS 6 185 98.615 172.985 82.349 1.00 58.29 S ATOM 21533 SG CYS 7 184 60.165 171.599 68.687 1.00 36.53 S ATOM 21556 SG CYS 7 187 58.784 172.254 65.292 1.00 44.58 S ATOM 21702 SG CYS 7 206 60.997 169.072 66.054 1.00 41.60 S ATOM 21739 SG CYS 7 211 62.429 172.641 65.920 1.00 55.47 S ATOM 31118 SG CYS 2 332 107.122 144.866 69.900 1.00147.97 S ATOM 31291 SG CYS 2 355 105.796 148.974 69.162 1.00143.54 S ATOM 36593 SG CYS 5 172 87.733 138.297 60.224 1.00107.04 S ATOM 36616 SG CYS 5 175 88.120 138.292 56.545 1.00116.31 S ATOM 36787 SG CYS 5 197 91.007 139.446 58.531 1.00114.99 S ATOM 36793 SG CYS 5 207 87.934 141.665 58.702 1.00115.50 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN H 810 " occ=0.53 ... (16 atoms not shown) pdb=" NE2BGLN H 810 " occ=0.47 residue: pdb=" N AGLN I 810 " occ=0.53 ... (16 atoms not shown) pdb=" NE2BGLN I 810 " occ=0.47 residue: pdb=" N AGLN J 810 " occ=0.53 ... (16 atoms not shown) pdb=" NE2BGLN J 810 " occ=0.47 Time building chain proxies: 30.82, per 1000 atoms: 0.45 Number of scatterers: 68086 At special positions: 0 Unit cell: (248.24, 254.66, 195.81, 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 6 29.99 S 404 16.00 P 63 15.00 Mg 3 11.99 O 12844 8.00 N 11921 7.00 C 42845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B2158 " - pdb=" SG CYS B2161 " distance=2.04 Simple disulfide: pdb=" SG CYS B2158 " - pdb=" SG CYS B2190 " distance=2.02 Simple disulfide: pdb=" SG CYS B2161 " - pdb=" SG CYS B2190 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 329 " - pdb=" SG CYS 2 352 " distance=2.04 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: 22.72 Conformation dependent library (CDL) restraints added in 11.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21001 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 332 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 197 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 207 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 185 " pdb=" ZN 71000 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 206 " pdb=" ZN B2301 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2224 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2238 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2236 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2221 " Number of angles added : 30 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 323 helices and 85 sheets defined 42.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.11 Creating SS restraints... Processing helix chain 'B' and resid 1392 through 1394 No H-bonds generated for 'chain 'B' and resid 1392 through 1394' Processing helix chain 'B' and resid 1455 through 1462 Processing helix chain 'B' and resid 1483 through 1489 removed outlier: 4.900A pdb=" N TYR B1488 " --> pdb=" O ILE B1484 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B1489 " --> pdb=" O ARG B1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1517 No H-bonds generated for 'chain 'B' and resid 1515 through 1517' Processing helix chain 'B' and resid 1574 through 1598 Proline residue: B1582 - end of helix removed outlier: 3.799A pdb=" N VAL B1587 " --> pdb=" O THR B1583 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TRP B1591 " --> pdb=" O VAL B1587 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU B1592 " --> pdb=" O GLN B1588 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B1597 " --> pdb=" O LEU B1593 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N SER B1598 " --> pdb=" O LYS B1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 1619 through 1634 removed outlier: 4.379A pdb=" N ARG B1626 " --> pdb=" O LEU B1622 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1652 No H-bonds generated for 'chain 'B' and resid 1649 through 1652' Processing helix chain 'B' and resid 1657 through 1659 No H-bonds generated for 'chain 'B' and resid 1657 through 1659' Processing helix chain 'B' and resid 1683 through 1689 Proline residue: B1688 - end of helix Processing helix chain 'B' and resid 1693 through 1704 Processing helix chain 'B' and resid 1716 through 1732 removed outlier: 3.530A pdb=" N LEU B1731 " --> pdb=" O GLU B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1750 through 1753 Processing helix chain 'B' and resid 1757 through 1764 Processing helix chain 'B' and resid 1791 through 1793 No H-bonds generated for 'chain 'B' and resid 1791 through 1793' Processing helix chain 'B' and resid 1836 through 1853 removed outlier: 4.111A pdb=" N THR B1840 " --> pdb=" O ALA B1836 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B1841 " --> pdb=" O LEU B1837 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B1851 " --> pdb=" O LYS B1847 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B1852 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1857 through 1871 removed outlier: 5.736A pdb=" N SER B1862 " --> pdb=" O ARG B1858 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL B1863 " --> pdb=" O LEU B1859 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B1864 " --> pdb=" O GLY B1860 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B1865 " --> pdb=" O SER B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1880 through 1903 removed outlier: 4.111A pdb=" N ILE B1884 " --> pdb=" O VAL B1880 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B1896 " --> pdb=" O SER B1892 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B1897 " --> pdb=" O SER B1893 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B1899 " --> pdb=" O HIS B1895 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1939 removed outlier: 3.740A pdb=" N ARG B1932 " --> pdb=" O VAL B1929 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS B1934 " --> pdb=" O SER B1931 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS B1935 " --> pdb=" O ARG B1932 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1945 No H-bonds generated for 'chain 'B' and resid 1943 through 1945' Processing helix chain 'B' and resid 1990 through 1994 Processing helix chain 'B' and resid 1997 through 2024 Proline residue: B2020 - end of helix removed outlier: 3.787A pdb=" N THR B2023 " --> pdb=" O ALA B2019 " (cutoff:3.500A) Proline residue: B2024 - end of helix Processing helix chain 'B' and resid 2049 through 2077 removed outlier: 4.935A pdb=" N TYR B2054 " --> pdb=" O SER B2051 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B2060 " --> pdb=" O ASN B2057 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B2063 " --> pdb=" O THR B2060 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B2066 " --> pdb=" O PHE B2063 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B2071 " --> pdb=" O GLN B2068 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B2074 " --> pdb=" O GLN B2071 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B2075 " --> pdb=" O LYS B2072 " (cutoff:3.500A) Processing helix chain 'B' and resid 2083 through 2085 No H-bonds generated for 'chain 'B' and resid 2083 through 2085' Processing helix chain 'B' and resid 2101 through 2114 removed outlier: 3.543A pdb=" N LEU B2114 " --> pdb=" O LYS B2110 " (cutoff:3.500A) Processing helix chain 'B' and resid 2120 through 2133 Processing helix chain 'B' and resid 2196 through 2215 Processing helix chain 'B' and resid 2248 through 2265 removed outlier: 3.739A pdb=" N GLN B2254 " --> pdb=" O VAL B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2270 through 2279 Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.706A pdb=" N ALA A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.839A pdb=" N GLU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 383 through 392 removed outlier: 5.828A pdb=" N GLU A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.670A pdb=" N TYR A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 149 No H-bonds generated for 'chain '4' and resid 147 through 149' Processing helix chain '4' and resid 159 through 172 Processing helix chain '4' and resid 192 through 203 removed outlier: 4.035A pdb=" N ASN 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL 4 202 " --> pdb=" O GLY 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 230 through 247 Proline residue: 4 235 - end of helix removed outlier: 3.896A pdb=" N PHE 4 246 " --> pdb=" O ASN 4 242 " (cutoff:3.500A) Processing helix chain '4' and resid 271 through 273 No H-bonds generated for 'chain '4' and resid 271 through 273' Processing helix chain '4' and resid 276 through 278 No H-bonds generated for 'chain '4' and resid 276 through 278' Processing helix chain '4' and resid 358 through 360 No H-bonds generated for 'chain '4' and resid 358 through 360' Processing helix chain '4' and resid 443 through 454 removed outlier: 3.671A pdb=" N ARG 4 454 " --> pdb=" O LYS 4 450 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 465 Processing helix chain '4' and resid 474 through 485 Processing helix chain '4' and resid 515 through 526 removed outlier: 4.851A pdb=" N ASN 4 525 " --> pdb=" O GLN 4 521 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 4 526 " --> pdb=" O TYR 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 562 through 565 No H-bonds generated for 'chain '4' and resid 562 through 565' Processing helix chain '4' and resid 576 through 578 No H-bonds generated for 'chain '4' and resid 576 through 578' Processing helix chain '4' and resid 581 through 593 Processing helix chain '4' and resid 630 through 634 Processing helix chain '4' and resid 638 through 643 removed outlier: 4.596A pdb=" N ARG 4 643 " --> pdb=" O THR 4 639 " (cutoff:3.500A) Processing helix chain '4' and resid 656 through 670 Processing helix chain '4' and resid 674 through 697 Processing helix chain '4' and resid 704 through 722 removed outlier: 3.590A pdb=" N ILE 4 720 " --> pdb=" O ASP 4 716 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY 4 721 " --> pdb=" O MET 4 717 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER 4 722 " --> pdb=" O ARG 4 718 " (cutoff:3.500A) Processing helix chain '4' and resid 731 through 747 Processing helix chain '4' and resid 755 through 772 removed outlier: 3.589A pdb=" N GLU 4 760 " --> pdb=" O ILE 4 756 " (cutoff:3.500A) Processing helix chain '4' and resid 782 through 786 Processing helix chain '4' and resid 791 through 796 removed outlier: 5.180A pdb=" N LYS 4 796 " --> pdb=" O ALA 4 792 " (cutoff:3.500A) Processing helix chain '6' and resid 21 through 36 Processing helix chain '6' and resid 45 through 54 removed outlier: 4.312A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU 6 53 " --> pdb=" O LEU 6 49 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE 6 54 " --> pdb=" O ALA 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 71 Processing helix chain '6' and resid 73 through 81 Processing helix chain '6' and resid 83 through 101 Proline residue: 6 88 - end of helix removed outlier: 4.573A pdb=" N ASP 6 100 " --> pdb=" O THR 6 96 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG 6 101 " --> pdb=" O PHE 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 123 through 125 No H-bonds generated for 'chain '6' and resid 123 through 125' Processing helix chain '6' and resid 128 through 130 No H-bonds generated for 'chain '6' and resid 128 through 130' Processing helix chain '6' and resid 230 through 232 No H-bonds generated for 'chain '6' and resid 230 through 232' Processing helix chain '6' and resid 254 through 256 No H-bonds generated for 'chain '6' and resid 254 through 256' Processing helix chain '6' and resid 322 through 328 Processing helix chain '6' and resid 331 through 341 Processing helix chain '6' and resid 346 through 354 Processing helix chain '6' and resid 362 through 373 Processing helix chain '6' and resid 402 through 412 removed outlier: 3.587A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 448 through 451 No H-bonds generated for 'chain '6' and resid 448 through 451' Processing helix chain '6' and resid 462 through 464 No H-bonds generated for 'chain '6' and resid 462 through 464' Processing helix chain '6' and resid 467 through 478 removed outlier: 3.976A pdb=" N HIS 6 474 " --> pdb=" O GLN 6 470 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU 6 475 " --> pdb=" O VAL 6 471 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU 6 478 " --> pdb=" O HIS 6 474 " (cutoff:3.500A) Processing helix chain '6' and resid 516 through 519 No H-bonds generated for 'chain '6' and resid 516 through 519' Processing helix chain '6' and resid 524 through 529 removed outlier: 3.594A pdb=" N ARG 6 529 " --> pdb=" O PRO 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 558 removed outlier: 3.599A pdb=" N LEU 6 555 " --> pdb=" O ARG 6 551 " (cutoff:3.500A) Processing helix chain '6' and resid 569 through 581 removed outlier: 3.892A pdb=" N GLN 6 581 " --> pdb=" O LEU 6 577 " (cutoff:3.500A) Processing helix chain '6' and resid 588 through 606 Processing helix chain '6' and resid 618 through 634 Processing helix chain '6' and resid 642 through 660 Processing helix chain '7' and resid 6 through 19 Processing helix chain '7' and resid 24 through 27 No H-bonds generated for 'chain '7' and resid 24 through 27' Processing helix chain '7' and resid 32 through 41 Processing helix chain '7' and resid 52 through 57 removed outlier: 3.762A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 68 Processing helix chain '7' and resid 70 through 88 Proline residue: 7 86 - end of helix Processing helix chain '7' and resid 101 through 113 Processing helix chain '7' and resid 128 through 131 No H-bonds generated for 'chain '7' and resid 128 through 131' Processing helix chain '7' and resid 149 through 151 No H-bonds generated for 'chain '7' and resid 149 through 151' Processing helix chain '7' and resid 154 through 156 No H-bonds generated for 'chain '7' and resid 154 through 156' Processing helix chain '7' and resid 209 through 212 No H-bonds generated for 'chain '7' and resid 209 through 212' Processing helix chain '7' and resid 241 through 243 No H-bonds generated for 'chain '7' and resid 241 through 243' Processing helix chain '7' and resid 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain '7' and resid 284 through 290 Processing helix chain '7' and resid 343 through 350 removed outlier: 4.402A pdb=" N VAL 7 350 " --> pdb=" O GLY 7 346 " (cutoff:3.500A) Processing helix chain '7' and resid 356 through 365 removed outlier: 3.975A pdb=" N GLY 7 360 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY 7 361 " --> pdb=" O LEU 7 357 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN 7 364 " --> pdb=" O GLY 7 360 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER 7 365 " --> pdb=" O GLY 7 361 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 397 removed outlier: 3.711A pdb=" N SER 7 392 " --> pdb=" O SER 7 388 " (cutoff:3.500A) Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 447 through 449 No H-bonds generated for 'chain '7' and resid 447 through 449' Processing helix chain '7' and resid 452 through 464 Processing helix chain '7' and resid 501 through 505 Processing helix chain '7' and resid 509 through 512 No H-bonds generated for 'chain '7' and resid 509 through 512' Processing helix chain '7' and resid 527 through 543 Processing helix chain '7' and resid 556 through 567 Processing helix chain '7' and resid 575 through 594 Processing helix chain '7' and resid 603 through 619 Processing helix chain '7' and resid 627 through 644 Processing helix chain '3' and resid 11 through 23 Processing helix chain '3' and resid 25 through 27 No H-bonds generated for 'chain '3' and resid 25 through 27' Processing helix chain '3' and resid 31 through 41 Processing helix chain '3' and resid 51 through 57 Processing helix chain '3' and resid 59 through 67 Processing helix chain '3' and resid 69 through 87 Processing helix chain '3' and resid 89 through 93 removed outlier: 3.515A pdb=" N LYS 3 93 " --> pdb=" O ALA 3 89 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 89 through 93' Processing helix chain '3' and resid 107 through 109 No H-bonds generated for 'chain '3' and resid 107 through 109' Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 205 through 207 No H-bonds generated for 'chain '3' and resid 205 through 207' Processing helix chain '3' and resid 223 through 225 No H-bonds generated for 'chain '3' and resid 223 through 225' Processing helix chain '3' and resid 282 through 291 removed outlier: 4.170A pdb=" N THR 3 290 " --> pdb=" O LYS 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 301 Processing helix chain '3' and resid 311 through 322 Processing helix chain '3' and resid 351 through 361 Processing helix chain '3' and resid 375 through 379 removed outlier: 3.590A pdb=" N THR 3 379 " --> pdb=" O GLY 3 375 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 375 through 379' Processing helix chain '3' and resid 397 through 400 No H-bonds generated for 'chain '3' and resid 397 through 400' Processing helix chain '3' and resid 411 through 413 No H-bonds generated for 'chain '3' and resid 411 through 413' Processing helix chain '3' and resid 416 through 428 removed outlier: 4.178A pdb=" N ALA 3 421 " --> pdb=" O MET 3 417 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE 3 422 " --> pdb=" O ASP 3 418 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 465 through 468 No H-bonds generated for 'chain '3' and resid 465 through 468' Processing helix chain '3' and resid 473 through 478 removed outlier: 4.102A pdb=" N ARG 3 478 " --> pdb=" O SER 3 474 " (cutoff:3.500A) Processing helix chain '3' and resid 491 through 506 Processing helix chain '3' and resid 565 through 577 removed outlier: 4.844A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 584 through 602 removed outlier: 3.818A pdb=" N SER 3 602 " --> pdb=" O ARG 3 598 " (cutoff:3.500A) Processing helix chain '3' and resid 615 through 632 Processing helix chain '3' and resid 639 through 654 Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 189 through 205 Processing helix chain '2' and resid 214 through 223 Processing helix chain '2' and resid 234 through 240 removed outlier: 4.022A pdb=" N ALA 2 239 " --> pdb=" O GLU 2 235 " (cutoff:3.500A) Processing helix chain '2' and resid 242 through 248 Processing helix chain '2' and resid 252 through 270 removed outlier: 3.775A pdb=" N ALA 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 274 through 276 No H-bonds generated for 'chain '2' and resid 274 through 276' Processing helix chain '2' and resid 294 through 296 No H-bonds generated for 'chain '2' and resid 294 through 296' Processing helix chain '2' and resid 299 through 301 No H-bonds generated for 'chain '2' and resid 299 through 301' Processing helix chain '2' and resid 400 through 402 No H-bonds generated for 'chain '2' and resid 400 through 402' Processing helix chain '2' and resid 424 through 430 Processing helix chain '2' and resid 453 through 455 No H-bonds generated for 'chain '2' and resid 453 through 455' Processing helix chain '2' and resid 458 through 469 removed outlier: 4.020A pdb=" N LYS 2 469 " --> pdb=" O THR 2 465 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 480 Processing helix chain '2' and resid 489 through 500 Processing helix chain '2' and resid 507 through 509 No H-bonds generated for 'chain '2' and resid 507 through 509' Processing helix chain '2' and resid 529 through 539 Processing helix chain '2' and resid 553 through 557 Processing helix chain '2' and resid 575 through 578 No H-bonds generated for 'chain '2' and resid 575 through 578' Processing helix chain '2' and resid 589 through 591 No H-bonds generated for 'chain '2' and resid 589 through 591' Processing helix chain '2' and resid 594 through 605 removed outlier: 4.032A pdb=" N SER 2 599 " --> pdb=" O GLN 2 595 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE 2 600 " --> pdb=" O ASP 2 596 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS 2 601 " --> pdb=" O ARG 2 597 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA 2 603 " --> pdb=" O SER 2 599 " (cutoff:3.500A) Processing helix chain '2' and resid 643 through 646 No H-bonds generated for 'chain '2' and resid 643 through 646' Processing helix chain '2' and resid 651 through 654 No H-bonds generated for 'chain '2' and resid 651 through 654' Processing helix chain '2' and resid 669 through 685 Processing helix chain '2' and resid 717 through 727 removed outlier: 3.600A pdb=" N LYS 2 722 " --> pdb=" O GLU 2 718 " (cutoff:3.500A) Processing helix chain '2' and resid 740 through 756 removed outlier: 3.845A pdb=" N ALA 2 756 " --> pdb=" O LYS 2 752 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 780 Processing helix chain '2' and resid 788 through 804 Processing helix chain '2' and resid 811 through 819 Processing helix chain '2' and resid 829 through 847 removed outlier: 4.032A pdb=" N ILE 2 835 " --> pdb=" O LEU 2 832 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS 2 837 " --> pdb=" O PHE 2 834 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU 2 842 " --> pdb=" O LEU 2 839 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL 2 844 " --> pdb=" O ALA 2 841 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR 2 846 " --> pdb=" O GLN 2 843 " (cutoff:3.500A) Processing helix chain '2' and resid 861 through 871 removed outlier: 4.064A pdb=" N LYS 2 868 " --> pdb=" O ASP 2 864 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 2 869 " --> pdb=" O LEU 2 865 " (cutoff:3.500A) Processing helix chain '2' and resid 878 through 882 Processing helix chain '2' and resid 885 through 888 No H-bonds generated for 'chain '2' and resid 885 through 888' Processing helix chain '5' and resid 22 through 41 Processing helix chain '5' and resid 54 through 65 Processing helix chain '5' and resid 74 through 80 Processing helix chain '5' and resid 82 through 90 Processing helix chain '5' and resid 92 through 111 removed outlier: 4.354A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU 5 98 " --> pdb=" O GLU 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 142 through 144 No H-bonds generated for 'chain '5' and resid 142 through 144' Processing helix chain '5' and resid 251 through 253 No H-bonds generated for 'chain '5' and resid 251 through 253' Processing helix chain '5' and resid 316 through 327 removed outlier: 3.589A pdb=" N GLU 5 321 " --> pdb=" O GLN 5 317 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 338 Processing helix chain '5' and resid 347 through 358 Processing helix chain '5' and resid 387 through 397 removed outlier: 3.597A pdb=" N LYS 5 396 " --> pdb=" O LYS 5 392 " (cutoff:3.500A) Processing helix chain '5' and resid 411 through 414 No H-bonds generated for 'chain '5' and resid 411 through 414' Processing helix chain '5' and resid 433 through 436 No H-bonds generated for 'chain '5' and resid 433 through 436' Processing helix chain '5' and resid 447 through 449 No H-bonds generated for 'chain '5' and resid 447 through 449' Processing helix chain '5' and resid 452 through 463 removed outlier: 3.768A pdb=" N ALA 5 457 " --> pdb=" O ASP 5 453 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE 5 458 " --> pdb=" O ASP 5 454 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA 5 461 " --> pdb=" O ALA 5 457 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU 5 463 " --> pdb=" O HIS 5 459 " (cutoff:3.500A) Processing helix chain '5' and resid 500 through 503 Processing helix chain '5' and resid 508 through 511 No H-bonds generated for 'chain '5' and resid 508 through 511' Processing helix chain '5' and resid 526 through 544 removed outlier: 3.731A pdb=" N ALA 5 543 " --> pdb=" O LEU 5 539 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU 5 544 " --> pdb=" O HIS 5 540 " (cutoff:3.500A) Processing helix chain '5' and resid 556 through 569 removed outlier: 3.558A pdb=" N VAL 5 568 " --> pdb=" O ALA 5 564 " (cutoff:3.500A) Processing helix chain '5' and resid 576 through 600 Processing helix chain '5' and resid 610 through 626 Processing helix chain '5' and resid 634 through 651 removed outlier: 4.432A pdb=" N ALA 5 651 " --> pdb=" O SER 5 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 14 removed outlier: 3.755A pdb=" N LEU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 53 Processing helix chain 'D' and resid 57 through 93 Proline residue: D 60 - end of helix removed outlier: 3.525A pdb=" N VAL D 77 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.481A pdb=" N HIS D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 128 removed outlier: 3.631A pdb=" N LEU D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 5.196A pdb=" N GLN D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.871A pdb=" N LYS E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 92 through 103 Processing helix chain 'E' and resid 110 through 138 Processing helix chain 'E' and resid 150 through 172 removed outlier: 3.908A pdb=" N SER E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 28 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 70 through 76 Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'F' and resid 94 through 102 Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.695A pdb=" N LEU F 124 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 155 removed outlier: 4.524A pdb=" N ARG F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 165 No H-bonds generated for 'chain 'F' and resid 162 through 165' Processing helix chain 'F' and resid 170 through 190 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'G' and resid 23 through 39 Processing helix chain 'G' and resid 48 through 67 Processing helix chain 'G' and resid 73 through 102 Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 124 through 144 Processing helix chain 'G' and resid 158 through 161 No H-bonds generated for 'chain 'G' and resid 158 through 161' Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 212 through 217 Processing helix chain 'C' and resid 6 through 9 No H-bonds generated for 'chain 'C' and resid 6 through 9' Processing helix chain 'C' and resid 11 through 16 removed outlier: 4.506A pdb=" N SER C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 42 Processing helix chain 'C' and resid 55 through 65 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 169 through 189 removed outlier: 3.592A pdb=" N ASP C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 Processing helix chain 'C' and resid 214 through 229 removed outlier: 3.602A pdb=" N GLN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.946A pdb=" N ARG C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 292 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 307 through 318 Processing helix chain 'C' and resid 322 through 325 No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 334 through 350 removed outlier: 5.002A pdb=" N ASN C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.703A pdb=" N LEU C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 436 removed outlier: 3.782A pdb=" N LEU C 409 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 424 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 434 " --> pdb=" O ALA C 431 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 435 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR C 436 " --> pdb=" O CYS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 460 Processing helix chain 'C' and resid 463 through 480 removed outlier: 3.632A pdb=" N LEU C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 471 " --> pdb=" O SER C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 551 through 565 removed outlier: 4.533A pdb=" N SER C 555 " --> pdb=" O GLU C 552 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 556 " --> pdb=" O ASP C 553 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 565 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 15 Processing helix chain 'K' and resid 31 through 43 Processing helix chain 'K' and resid 50 through 58 Processing helix chain 'K' and resid 60 through 71 removed outlier: 4.778A pdb=" N LEU K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Proline residue: K 67 - end of helix Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.728A pdb=" N ALA K 81 " --> pdb=" O PRO K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 97 Processing helix chain 'K' and resid 104 through 124 Processing helix chain 'K' and resid 127 through 143 removed outlier: 3.560A pdb=" N GLU K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 167 Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 198 through 207 Processing helix chain 'K' and resid 212 through 225 removed outlier: 4.378A pdb=" N LEU K 216 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 236 removed outlier: 3.956A pdb=" N GLY K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 270 removed outlier: 3.625A pdb=" N SER K 247 " --> pdb=" O ALA K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 304 No H-bonds generated for 'chain 'K' and resid 301 through 304' Processing helix chain 'K' and resid 320 through 322 No H-bonds generated for 'chain 'K' and resid 320 through 322' Processing helix chain 'K' and resid 336 through 352 Processing helix chain 'K' and resid 354 through 367 Processing helix chain 'K' and resid 374 through 390 removed outlier: 3.509A pdb=" N LEU K 382 " --> pdb=" O MET K 379 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE K 385 " --> pdb=" O LEU K 382 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET K 386 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 403 removed outlier: 3.612A pdb=" N SER K 400 " --> pdb=" O GLY K 397 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU K 401 " --> pdb=" O LEU K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 426 through 454 removed outlier: 5.821A pdb=" N ALA K 430 " --> pdb=" O LYS K 427 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 450 " --> pdb=" O LEU K 447 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET K 453 " --> pdb=" O VAL K 450 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP K 454 " --> pdb=" O ASN K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 474 Processing helix chain 'K' and resid 476 through 478 No H-bonds generated for 'chain 'K' and resid 476 through 478' Processing helix chain 'K' and resid 481 through 487 Processing helix chain 'K' and resid 496 through 519 Processing helix chain 'K' and resid 691 through 697 removed outlier: 3.784A pdb=" N ARG K 697 " --> pdb=" O ASP K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 701 through 713 removed outlier: 4.536A pdb=" N SER K 713 " --> pdb=" O LEU K 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 719 through 734 Processing helix chain 'K' and resid 739 through 742 No H-bonds generated for 'chain 'K' and resid 739 through 742' Processing helix chain 'K' and resid 745 through 756 Processing helix chain 'K' and resid 760 through 762 No H-bonds generated for 'chain 'K' and resid 760 through 762' Processing helix chain 'K' and resid 764 through 783 Processing helix chain 'K' and resid 785 through 792 removed outlier: 3.575A pdb=" N LEU K 791 " --> pdb=" O PHE K 788 " (cutoff:3.500A) Processing helix chain 'K' and resid 797 through 800 Processing helix chain 'L' and resid 69 through 72 No H-bonds generated for 'chain 'L' and resid 69 through 72' Processing helix chain 'L' and resid 78 through 81 No H-bonds generated for 'chain 'L' and resid 78 through 81' Processing helix chain 'L' and resid 96 through 114 Processing helix chain 'L' and resid 120 through 132 removed outlier: 3.675A pdb=" N TYR L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 143 Processing helix chain 'H' and resid 664 through 670 removed outlier: 6.198A pdb=" N CYS H 668 " --> pdb=" O ARG H 665 " (cutoff:3.500A) Processing helix chain 'H' and resid 721 through 736 Processing helix chain 'H' and resid 738 through 744 Processing helix chain 'H' and resid 751 through 774 Processing helix chain 'H' and resid 778 through 787 removed outlier: 3.803A pdb=" N LEU H 787 " --> pdb=" O GLU H 783 " (cutoff:3.500A) Processing helix chain 'H' and resid 790 through 802 Processing helix chain 'H' and resid 806 through 822 Processing helix chain 'I' and resid 652 through 654 No H-bonds generated for 'chain 'I' and resid 652 through 654' Processing helix chain 'I' and resid 664 through 667 Processing helix chain 'I' and resid 721 through 744 removed outlier: 5.242A pdb=" N HIS I 738 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU I 739 " --> pdb=" O PHE I 735 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP I 740 " --> pdb=" O HIS I 736 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 775 Processing helix chain 'I' and resid 778 through 787 removed outlier: 4.374A pdb=" N LEU I 787 " --> pdb=" O GLU I 783 " (cutoff:3.500A) Processing helix chain 'I' and resid 790 through 804 removed outlier: 4.115A pdb=" N LEU I 795 " --> pdb=" O ASN I 791 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA I 796 " --> pdb=" O ALA I 792 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER I 803 " --> pdb=" O TYR I 799 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG I 804 " --> pdb=" O ALA I 800 " (cutoff:3.500A) Processing helix chain 'I' and resid 806 through 822 Processing helix chain 'J' and resid 664 through 667 Processing helix chain 'J' and resid 721 through 745 removed outlier: 4.977A pdb=" N HIS J 738 " --> pdb=" O ILE J 734 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU J 739 " --> pdb=" O PHE J 735 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP J 740 " --> pdb=" O HIS J 736 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 774 Processing helix chain 'J' and resid 778 through 787 Processing helix chain 'J' and resid 790 through 804 removed outlier: 5.174A pdb=" N SER J 803 " --> pdb=" O TYR J 799 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG J 804 " --> pdb=" O ALA J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 806 through 820 Processing helix chain 'Q' and resid 285 through 299 Processing helix chain 'Q' and resid 314 through 318 Processing helix chain 'Q' and resid 526 through 538 Processing helix chain 'Q' and resid 594 through 617 removed outlier: 4.037A pdb=" N ALA Q 604 " --> pdb=" O LYS Q 600 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 1385 through 1387 Processing sheet with id= B, first strand: chain 'B' and resid 1406 through 1410 Processing sheet with id= C, first strand: chain 'B' and resid 1638 through 1640 removed outlier: 6.494A pdb=" N GLU B1533 " --> pdb=" O LEU B1639 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 1781 through 1785 removed outlier: 3.837A pdb=" N MET B1917 " --> pdb=" O CYS B1910 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B1908 " --> pdb=" O PRO B1919 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1966 through 1969 removed outlier: 4.189A pdb=" N GLN B1988 " --> pdb=" O ALA B1967 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 2156 through 2158 Processing sheet with id= G, first strand: chain 'B' and resid 2219 through 2221 Processing sheet with id= H, first strand: chain 'B' and resid 1955 through 1958 removed outlier: 4.249A pdb=" N ASP B1955 " --> pdb=" O VAL B1972 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER B1970 " --> pdb=" O GLU B1957 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.332A pdb=" N LEU A 477 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE A 415 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 479 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 495 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 480 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 97 through 100 Processing sheet with id= K, first strand: chain 'A' and resid 223 through 228 removed outlier: 6.805A pdb=" N GLU A 227 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 240 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 225 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 518 through 522 removed outlier: 6.582A pdb=" N CYS A 318 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU A 290 " --> pdb=" O CYS A 318 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 320 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A 360 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 321 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 362 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 207 through 211 removed outlier: 6.594A pdb=" N GLN 4 259 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL 4 210 " --> pdb=" O GLN 4 259 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG 4 261 " --> pdb=" O VAL 4 210 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain '4' and resid 387 through 393 removed outlier: 6.756A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET 4 351 " --> pdb=" O THR 4 292 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR 4 414 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N HIS 4 375 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS 4 420 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 312 through 316 Processing sheet with id= P, first strand: chain '4' and resid 646 through 649 removed outlier: 6.725A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 546 through 550 removed outlier: 3.925A pdb=" N GLN 4 555 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 595 through 598 Processing sheet with id= S, first strand: chain '4' and resid 296 through 301 removed outlier: 6.613A pdb=" N LEU 4 345 " --> pdb=" O GLN 4 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '6' and resid 60 through 64 removed outlier: 6.457A pdb=" N TYR 6 111 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL 6 63 " --> pdb=" O TYR 6 111 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA 6 113 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '6' and resid 241 through 247 removed outlier: 6.625A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 14.215A pdb=" N SER 6 223 " --> pdb=" O TYR 6 294 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU 6 296 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU 6 225 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG 6 229 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N CYS 6 302 " --> pdb=" O ARG 6 229 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL 6 303 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP 6 243 " --> pdb=" O VAL 6 303 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '6' and resid 156 through 158 Processing sheet with id= W, first strand: chain '6' and resid 532 through 536 removed outlier: 6.314A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '6' and resid 432 through 436 Processing sheet with id= Y, first strand: chain '6' and resid 481 through 486 Processing sheet with id= Z, first strand: chain '6' and resid 148 through 153 removed outlier: 7.205A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '7' and resid 47 through 51 removed outlier: 6.817A pdb=" N GLU 7 135 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL 7 50 " --> pdb=" O GLU 7 135 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR 7 137 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain '7' and resid 270 through 276 removed outlier: 6.768A pdb=" N LYS 7 236 " --> pdb=" O THR 7 168 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL 7 170 " --> pdb=" O GLU 7 234 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU 7 234 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR 7 296 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR 7 254 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU 7 258 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ARG 7 302 " --> pdb=" O GLU 7 258 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE 7 303 " --> pdb=" O SER 7 272 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '7' and resid 190 through 194 Processing sheet with id= AD, first strand: chain '7' and resid 517 through 521 removed outlier: 3.692A pdb=" N ALA 7 488 " --> pdb=" O LEU 7 379 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '7' and resid 417 through 419 Processing sheet with id= AF, first strand: chain '7' and resid 466 through 470 Processing sheet with id= AG, first strand: chain '7' and resid 174 through 179 removed outlier: 6.727A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '3' and resid 46 through 50 removed outlier: 6.805A pdb=" N TYR 3 99 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL 3 49 " --> pdb=" O TYR 3 99 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY 3 101 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain '3' and resid 110 through 112 removed outlier: 7.948A pdb=" N VAL 3 111 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N CYS 3 126 " --> pdb=" O VAL 3 111 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR 3 240 " --> pdb=" O ALA 3 262 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA 3 262 " --> pdb=" O THR 3 240 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG 3 242 " --> pdb=" O LEU 3 260 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU 3 260 " --> pdb=" O ARG 3 242 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU 3 244 " --> pdb=" O THR 3 258 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N THR 3 258 " --> pdb=" O LEU 3 244 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N SER 3 216 " --> pdb=" O THR 3 258 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N LEU 3 260 " --> pdb=" O SER 3 216 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP 3 218 " --> pdb=" O LEU 3 260 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ALA 3 262 " --> pdb=" O ASP 3 218 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE 3 220 " --> pdb=" O ALA 3 262 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASN 3 264 " --> pdb=" O ILE 3 220 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASP 3 222 " --> pdb=" O ASN 3 264 " (cutoff:3.500A) removed outlier: 12.081A pdb=" N LYS 3 266 " --> pdb=" O ASP 3 222 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS 3 133 " --> pdb=" O THR 3 200 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN 3 202 " --> pdb=" O VAL 3 131 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL 3 131 " --> pdb=" O GLN 3 202 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '3' and resid 153 through 158 removed outlier: 3.527A pdb=" N LYS 3 153 " --> pdb=" O CYS 3 148 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL 3 145 " --> pdb=" O GLU 3 187 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '3' and resid 481 through 485 removed outlier: 6.655A pdb=" N GLY 3 404 " --> pdb=" O SER 3 447 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU 3 449 " --> pdb=" O GLY 3 404 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '3' and resid 380 through 384 Processing sheet with id= AM, first strand: chain '3' and resid 430 through 434 Processing sheet with id= AN, first strand: chain '3' and resid 138 through 143 removed outlier: 7.014A pdb=" N VAL 3 192 " --> pdb=" O VAL 3 142 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '2' and resid 229 through 233 removed outlier: 6.333A pdb=" N HIS 2 282 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL 2 232 " --> pdb=" O HIS 2 282 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG 2 284 " --> pdb=" O VAL 2 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain '2' and resid 393 through 399 removed outlier: 6.548A pdb=" N GLN 2 379 " --> pdb=" O VAL 2 312 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL 2 312 " --> pdb=" O GLN 2 379 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE 2 417 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA 2 441 " --> pdb=" O ILE 2 417 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS 2 419 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE 2 439 " --> pdb=" O HIS 2 419 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN 2 421 " --> pdb=" O THR 2 437 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR 2 437 " --> pdb=" O ASN 2 421 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '2' and resid 659 through 663 removed outlier: 6.631A pdb=" N ILE 2 544 " --> pdb=" O LEU 2 585 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP 2 587 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '2' and resid 558 through 562 Processing sheet with id= AS, first strand: chain '2' and resid 608 through 613 Processing sheet with id= AT, first strand: chain '2' and resid 319 through 324 removed outlier: 6.866A pdb=" N ILE 2 369 " --> pdb=" O SER 2 323 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '5' and resid 44 through 46 Processing sheet with id= AV, first strand: chain '5' and resid 69 through 73 removed outlier: 6.255A pdb=" N GLN 5 125 " --> pdb=" O ILE 5 70 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL 5 72 " --> pdb=" O GLN 5 125 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N MET 5 127 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain '5' and resid 244 through 250 removed outlier: 3.818A pdb=" N ALA 5 157 " --> pdb=" O LYS 5 228 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN 5 230 " --> pdb=" O ILE 5 155 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE 5 155 " --> pdb=" O GLN 5 230 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE 5 268 " --> pdb=" O VAL 5 296 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL 5 296 " --> pdb=" O ILE 5 268 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER 5 270 " --> pdb=" O ILE 5 294 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE 5 294 " --> pdb=" O SER 5 270 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '5' and resid 170 through 172 Processing sheet with id= AY, first strand: chain '5' and resid 516 through 520 Processing sheet with id= AZ, first strand: chain '5' and resid 416 through 420 Processing sheet with id= BA, first strand: chain '5' and resid 466 through 471 Processing sheet with id= BB, first strand: chain '5' and resid 162 through 168 removed outlier: 6.867A pdb=" N LYS 5 220 " --> pdb=" O THR 5 166 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'D' and resid 174 through 178 removed outlier: 4.572A pdb=" N GLU D 149 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'D' and resid 158 through 162 removed outlier: 6.977A pdb=" N THR D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'E' and resid 41 through 45 Processing sheet with id= BF, first strand: chain 'F' and resid 65 through 69 Processing sheet with id= BG, first strand: chain 'G' and resid 203 through 207 Processing sheet with id= BH, first strand: chain 'G' and resid 182 through 184 Processing sheet with id= BI, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.527A pdb=" N VAL C 19 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 50 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 21 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 52 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL C 23 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR C 71 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE C 22 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE C 73 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA C 24 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE C 75 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 94 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU C 74 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE C 96 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'C' and resid 269 through 276 removed outlier: 3.596A pdb=" N HIS C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'C' and resid 445 through 449 removed outlier: 8.062A pdb=" N CYS C 448 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 492 " --> pdb=" O CYS C 448 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C 503 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'K' and resid 18 through 21 Processing sheet with id= BM, first strand: chain 'K' and resid 282 through 288 removed outlier: 4.121A pdb=" N LEU K 295 " --> pdb=" O VAL K 284 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'H' and resid 479 through 483 removed outlier: 6.383A pdb=" N CYS H 457 " --> pdb=" O PHE H 446 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE H 446 " --> pdb=" O CYS H 457 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN H 459 " --> pdb=" O HIS H 444 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS H 444 " --> pdb=" O ASN H 459 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 489 through 492 Processing sheet with id= BP, first strand: chain 'H' and resid 566 through 568 removed outlier: 3.899A pdb=" N LEU H 553 " --> pdb=" O THR H 549 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA H 537 " --> pdb=" O ALA H 548 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 610 through 612 removed outlier: 6.080A pdb=" N HIS H 588 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL H 573 " --> pdb=" O HIS H 588 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'H' and resid 627 through 632 removed outlier: 6.610A pdb=" N VAL H 641 " --> pdb=" O ALA H 628 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE H 630 " --> pdb=" O CYS H 639 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS H 639 " --> pdb=" O ILE H 630 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP H 642 " --> pdb=" O ILE H 646 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE H 646 " --> pdb=" O ASP H 642 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS H 662 " --> pdb=" O VAL H 647 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET H 649 " --> pdb=" O PRO H 660 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN H 651 " --> pdb=" O TRP H 658 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TRP H 658 " --> pdb=" O ASN H 651 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'H' and resid 706 through 709 removed outlier: 6.107A pdb=" N ILE H 690 " --> pdb=" O VAL H 677 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL H 677 " --> pdb=" O ILE H 690 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS H 692 " --> pdb=" O TYR H 675 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR H 675 " --> pdb=" O CYS H 692 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'H' and resid 600 through 603 removed outlier: 7.308A pdb=" N LEU H 603 " --> pdb=" O HIS H 615 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS H 615 " --> pdb=" O LEU H 603 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'I' and resid 479 through 482 removed outlier: 6.271A pdb=" N CYS I 457 " --> pdb=" O PHE I 446 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE I 446 " --> pdb=" O CYS I 457 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN I 459 " --> pdb=" O HIS I 444 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS I 444 " --> pdb=" O ASN I 459 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'I' and resid 489 through 492 Processing sheet with id= BW, first strand: chain 'I' and resid 566 through 568 removed outlier: 3.608A pdb=" N TRP I 544 " --> pdb=" O GLY I 541 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'I' and resid 573 through 579 removed outlier: 7.184A pdb=" N VAL I 586 " --> pdb=" O VAL I 574 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET I 576 " --> pdb=" O PHE I 584 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE I 584 " --> pdb=" O MET I 576 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY I 578 " --> pdb=" O GLN I 582 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN I 582 " --> pdb=" O GLY I 578 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU I 603 " --> pdb=" O HIS I 615 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS I 615 " --> pdb=" O LEU I 603 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'I' and resid 627 through 632 removed outlier: 6.568A pdb=" N VAL I 641 " --> pdb=" O ALA I 628 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE I 630 " --> pdb=" O CYS I 639 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N CYS I 639 " --> pdb=" O ILE I 630 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE I 646 " --> pdb=" O ASP I 642 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS I 662 " --> pdb=" O VAL I 647 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET I 649 " --> pdb=" O PRO I 660 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN I 651 " --> pdb=" O TRP I 658 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TRP I 658 " --> pdb=" O ASN I 651 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'I' and resid 707 through 709 removed outlier: 6.251A pdb=" N ILE I 690 " --> pdb=" O VAL I 677 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL I 677 " --> pdb=" O ILE I 690 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS I 692 " --> pdb=" O TYR I 675 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR I 675 " --> pdb=" O CYS I 692 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'J' and resid 479 through 482 removed outlier: 6.401A pdb=" N CYS J 457 " --> pdb=" O PHE J 446 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE J 446 " --> pdb=" O CYS J 457 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN J 459 " --> pdb=" O HIS J 444 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS J 444 " --> pdb=" O ASN J 459 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'J' and resid 524 through 528 removed outlier: 3.981A pdb=" N LYS J 510 " --> pdb=" O CYS J 501 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'J' and resid 566 through 568 removed outlier: 3.759A pdb=" N LEU J 553 " --> pdb=" O THR J 549 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'J' and resid 610 through 612 removed outlier: 5.770A pdb=" N HIS J 588 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL J 573 " --> pdb=" O HIS J 588 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'J' and resid 627 through 632 removed outlier: 6.559A pdb=" N VAL J 641 " --> pdb=" O ALA J 628 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE J 630 " --> pdb=" O CYS J 639 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N CYS J 639 " --> pdb=" O ILE J 630 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP J 642 " --> pdb=" O ILE J 646 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE J 646 " --> pdb=" O ASP J 642 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS J 662 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N MET J 649 " --> pdb=" O PRO J 660 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN J 651 " --> pdb=" O TRP J 658 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TRP J 658 " --> pdb=" O ASN J 651 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'J' and resid 707 through 709 removed outlier: 6.223A pdb=" N ILE J 690 " --> pdb=" O VAL J 677 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL J 677 " --> pdb=" O ILE J 690 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS J 692 " --> pdb=" O TYR J 675 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR J 675 " --> pdb=" O CYS J 692 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'J' and resid 600 through 603 removed outlier: 7.352A pdb=" N LEU J 603 " --> pdb=" O HIS J 615 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N HIS J 615 " --> pdb=" O LEU J 603 " (cutoff:3.500A) 2776 hydrogen bonds defined for protein. 7556 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: 29.26 Time building geometry restraints manager: 24.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 12413 1.32 - 1.45: 17272 1.45 - 1.57: 39068 1.57 - 1.70: 120 1.70 - 1.83: 626 Bond restraints: 69499 Sorted by residual: bond pdb=" O3A ANP 5 802 " pdb=" PB ANP 5 802 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" O3A ANP 31500 " pdb=" PB ANP 31500 " ideal model delta sigma weight residual 1.700 1.547 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" O3A ANP 21003 " pdb=" PB ANP 21003 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C SER 7 365 " pdb=" N PRO 7 366 " ideal model delta sigma weight residual 1.334 1.384 -0.051 8.40e-03 1.42e+04 3.62e+01 bond pdb=" N3B ANP 31500 " pdb=" PG ANP 31500 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 69494 not shown) Histogram of bond angle deviations from ideal: 96.35 - 104.64: 1345 104.64 - 112.93: 35709 112.93 - 121.22: 37076 121.22 - 129.50: 19488 129.50 - 137.79: 487 Bond angle restraints: 94105 Sorted by residual: angle pdb=" CA ILE Q 297 " pdb=" CB ILE Q 297 " pdb=" CG2 ILE Q 297 " ideal model delta sigma weight residual 110.50 120.08 -9.58 1.70e+00 3.46e-01 3.18e+01 angle pdb=" C GLU A 83 " pdb=" N HIS A 84 " pdb=" CA HIS A 84 " ideal model delta sigma weight residual 121.54 132.12 -10.58 1.91e+00 2.74e-01 3.07e+01 angle pdb=" C TYR B1530 " pdb=" N SER B1531 " pdb=" CA SER B1531 " ideal model delta sigma weight residual 121.54 131.91 -10.37 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C VAL K 405 " pdb=" N ARG K 406 " pdb=" CA ARG K 406 " ideal model delta sigma weight residual 120.38 127.11 -6.73 1.37e+00 5.33e-01 2.41e+01 angle pdb=" C SER 3 634 " pdb=" N LYS 3 635 " pdb=" CA LYS 3 635 " ideal model delta sigma weight residual 121.54 130.71 -9.17 1.91e+00 2.74e-01 2.30e+01 ... (remaining 94100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.42: 40907 30.42 - 60.84: 1365 60.84 - 91.26: 149 91.26 - 121.69: 0 121.69 - 152.11: 2 Dihedral angle restraints: 42423 sinusoidal: 17920 harmonic: 24503 Sorted by residual: dihedral pdb=" CB CYS B2158 " pdb=" SG CYS B2158 " pdb=" SG CYS B2190 " pdb=" CB CYS B2190 " ideal model delta sinusoidal sigma weight residual -86.00 -161.59 75.59 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS B2161 " pdb=" SG CYS B2161 " pdb=" SG CYS B2190 " pdb=" CB CYS B2190 " ideal model delta sinusoidal sigma weight residual -86.00 -13.92 -72.08 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS B2158 " pdb=" SG CYS B2158 " pdb=" SG CYS B2161 " pdb=" CB CYS B2161 " ideal model delta sinusoidal sigma weight residual 93.00 151.30 -58.30 1 1.00e+01 1.00e-02 4.55e+01 ... (remaining 42420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 8873 0.074 - 0.149: 1481 0.149 - 0.223: 136 0.223 - 0.297: 14 0.297 - 0.371: 6 Chirality restraints: 10510 Sorted by residual: chirality pdb=" CB ILE A 152 " pdb=" CA ILE A 152 " pdb=" CG1 ILE A 152 " pdb=" CG2 ILE A 152 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB ILE 3 48 " pdb=" CA ILE 3 48 " pdb=" CG1 ILE 3 48 " pdb=" CG2 ILE 3 48 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" P DT M 51 " pdb=" OP1 DT M 51 " pdb=" OP2 DT M 51 " pdb=" O5' DT M 51 " both_signs ideal model delta sigma weight residual True 2.35 2.69 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 10507 not shown) Planarity restraints: 11975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET 6 329 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C MET 6 329 " 0.067 2.00e-02 2.50e+03 pdb=" O MET 6 329 " -0.026 2.00e-02 2.50e+03 pdb=" N THR 6 330 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 357 " 0.037 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR 3 357 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 357 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 357 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 357 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 357 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR 3 357 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR 3 357 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B2091 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C PRO B2091 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO B2091 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B2092 " 0.018 2.00e-02 2.50e+03 ... (remaining 11972 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 374 2.62 - 3.19: 57745 3.19 - 3.76: 109972 3.76 - 4.33: 153262 4.33 - 4.90: 248067 Nonbonded interactions: 569420 Sorted by model distance: nonbonded pdb=" OG SER 5 388 " pdb="MG MG 5 803 " model vdw 2.051 2.170 nonbonded pdb=" OG SER 3 352 " pdb="MG MG 31501 " model vdw 2.059 2.170 nonbonded pdb=" O2G ANP 31500 " pdb="MG MG 31501 " model vdw 2.062 2.170 nonbonded pdb=" O2G ANP 5 802 " pdb="MG MG 5 803 " model vdw 2.068 2.170 nonbonded pdb=" OE2 GLU 5 446 " pdb="MG MG 5 803 " model vdw 2.069 2.170 ... (remaining 569415 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 'H' and (resid 423 through 466 or resid 468 through 809 or resid 811 thro \ ugh 823)) selection = (chain 'I' and (resid 423 through 466 or resid 468 through 809 or resid 811 thro \ ugh 823)) selection = (chain 'J' and (resid 423 through 466 or resid 468 through 809 or resid 811 thro \ ugh 823)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 19.100 Check model and map are aligned: 0.780 Set scattering table: 0.490 Process input model: 166.310 Find NCS groups from input model: 3.170 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 0.157 69499 Z= 0.438 Angle : 1.032 13.843 94105 Z= 0.567 Chirality : 0.056 0.371 10510 Planarity : 0.008 0.073 11975 Dihedral : 14.807 152.108 26485 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 1.37 % Allowed : 5.16 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.83 (0.09), residues: 8267 helix: -0.29 (0.08), residues: 3540 sheet: -0.44 (0.14), residues: 1219 loop : -0.68 (0.10), residues: 3508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP K 380 HIS 0.012 0.002 HIS 3 439 PHE 0.042 0.004 PHE B1553 TYR 0.045 0.004 TYR K 19 ARG 0.015 0.001 ARG 5 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 321 time to evaluate : 6.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1393 MET cc_start: 0.2148 (OUTLIER) cc_final: 0.1200 (ttm) REVERT: B 1470 MET cc_start: 0.5572 (tmm) cc_final: 0.4853 (mpp) REVERT: B 2086 MET cc_start: 0.4164 (ptt) cc_final: 0.3875 (ptt) REVERT: B 2232 MET cc_start: 0.7827 (mtp) cc_final: 0.7222 (mtp) REVERT: 4 633 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7798 (t0) REVERT: 7 396 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (tmm160) REVERT: 7 559 MET cc_start: 0.8531 (mtp) cc_final: 0.8071 (mtm) REVERT: 7 566 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7395 (p) REVERT: H 447 MET cc_start: 0.3805 (mmm) cc_final: 0.3348 (mmp) REVERT: H 682 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5588 (pm20) REVERT: J 576 MET cc_start: 0.5860 (ptm) cc_final: 0.5557 (ptm) outliers start: 101 outliers final: 22 residues processed: 408 average time/residue: 0.6735 time to fit residues: 483.1177 Evaluate side-chains 280 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 6.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1393 MET Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2125 LEU Chi-restraints excluded: chain B residue 2238 CYS Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 396 ARG Chi-restraints excluded: chain 7 residue 566 CYS Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain H residue 682 GLU Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain I residue 769 LEU Chi-restraints excluded: chain I residue 771 LEU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 593 LYS Chi-restraints excluded: chain Q residue 602 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 703 optimal weight: 5.9990 chunk 631 optimal weight: 8.9990 chunk 350 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 425 optimal weight: 0.9990 chunk 337 optimal weight: 10.0000 chunk 652 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 397 optimal weight: 3.9990 chunk 485 optimal weight: 5.9990 chunk 756 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1430 GLN 4 195 GLN 2 280 HIS 2 777 HIS 5 426 ASN D 48 ASN D 188 GLN C 364 HIS H 512 HIS H 736 HIS ** J 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 69499 Z= 0.255 Angle : 0.584 12.617 94105 Z= 0.305 Chirality : 0.041 0.184 10510 Planarity : 0.004 0.055 11975 Dihedral : 10.420 152.015 9861 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.01 % Allowed : 7.34 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.09), residues: 8267 helix: 0.87 (0.09), residues: 3536 sheet: -0.41 (0.14), residues: 1289 loop : -0.36 (0.10), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 676 HIS 0.012 0.001 HIS Q 290 PHE 0.021 0.001 PHE 7 332 TYR 0.028 0.002 TYR 3 357 ARG 0.005 0.000 ARG I 777 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 251 time to evaluate : 6.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1393 MET cc_start: 0.2529 (mpp) cc_final: 0.1632 (ttm) REVERT: B 1468 LEU cc_start: 0.2538 (OUTLIER) cc_final: 0.2113 (pp) REVERT: B 1470 MET cc_start: 0.5719 (tmm) cc_final: 0.4755 (mpp) REVERT: B 1754 MET cc_start: 0.0157 (ptt) cc_final: -0.0224 (mtm) REVERT: B 1917 MET cc_start: 0.7424 (ppp) cc_final: 0.7172 (ppp) REVERT: B 1918 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6228 (p0) REVERT: B 2086 MET cc_start: 0.4337 (ptt) cc_final: 0.4072 (ptm) REVERT: B 2232 MET cc_start: 0.7950 (mtp) cc_final: 0.7360 (mtp) REVERT: A 61 MET cc_start: 0.7089 (tpp) cc_final: 0.6644 (tpt) REVERT: A 177 LYS cc_start: 0.5135 (OUTLIER) cc_final: 0.4910 (tptt) REVERT: 4 633 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.7855 (t0) REVERT: 7 369 MET cc_start: 0.7516 (tmm) cc_final: 0.6282 (tmm) REVERT: 7 396 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7511 (tmm160) REVERT: 7 565 MET cc_start: 0.8232 (ppp) cc_final: 0.8017 (ppp) REVERT: 7 566 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7689 (p) REVERT: 2 888 MET cc_start: 0.8323 (pmm) cc_final: 0.7945 (pmm) REVERT: C 169 MET cc_start: 0.8334 (pmm) cc_final: 0.7726 (pmm) REVERT: H 447 MET cc_start: 0.4079 (mmm) cc_final: 0.3768 (mmp) REVERT: H 649 MET cc_start: 0.7481 (ppp) cc_final: 0.7093 (ppp) REVERT: H 682 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6049 (pp20) outliers start: 74 outliers final: 27 residues processed: 315 average time/residue: 0.6213 time to fit residues: 348.1970 Evaluate side-chains 277 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 6.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1918 ASP Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 288 MET Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 396 ARG Chi-restraints excluded: chain 7 residue 566 CYS Chi-restraints excluded: chain 3 residue 218 ASP Chi-restraints excluded: chain 3 residue 485 MET Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain H residue 682 GLU Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain I residue 769 LEU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 602 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 420 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 629 optimal weight: 4.9990 chunk 515 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 757 optimal weight: 5.9990 chunk 818 optimal weight: 20.0000 chunk 674 optimal weight: 6.9990 chunk 751 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 chunk 607 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1842 HIS ** 5 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 444 HIS H 674 HIS J 728 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 69499 Z= 0.236 Angle : 0.540 13.337 94105 Z= 0.280 Chirality : 0.040 0.172 10510 Planarity : 0.004 0.051 11975 Dihedral : 9.750 149.958 9839 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.33 % Allowed : 7.98 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 8267 helix: 1.26 (0.09), residues: 3548 sheet: -0.41 (0.14), residues: 1261 loop : -0.23 (0.11), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J 519 HIS 0.007 0.001 HIS L 106 PHE 0.018 0.001 PHE 6 338 TYR 0.020 0.001 TYR 6 347 ARG 0.004 0.000 ARG I 777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 251 time to evaluate : 6.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1393 MET cc_start: 0.2269 (mpp) cc_final: 0.1213 (ttm) REVERT: B 1468 LEU cc_start: 0.3038 (OUTLIER) cc_final: 0.2561 (pp) REVERT: B 1470 MET cc_start: 0.5623 (tmm) cc_final: 0.4764 (mpp) REVERT: B 1748 MET cc_start: -0.2007 (mmm) cc_final: -0.2275 (mmm) REVERT: B 1754 MET cc_start: 0.0337 (ptt) cc_final: -0.0574 (mtm) REVERT: B 1918 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6240 (p0) REVERT: B 2232 MET cc_start: 0.7985 (mtp) cc_final: 0.7443 (mtp) REVERT: A 177 LYS cc_start: 0.5196 (OUTLIER) cc_final: 0.4908 (tptt) REVERT: 4 633 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7864 (t0) REVERT: 4 726 MET cc_start: 0.5328 (ptt) cc_final: 0.5107 (ptt) REVERT: 6 171 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: 7 369 MET cc_start: 0.7146 (tmm) cc_final: 0.6462 (tmm) REVERT: 7 637 MET cc_start: 0.7305 (tmm) cc_final: 0.6952 (tmm) REVERT: 2 888 MET cc_start: 0.8450 (pmm) cc_final: 0.8188 (pmm) REVERT: E 142 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7695 (p-80) REVERT: C 169 MET cc_start: 0.8310 (pmm) cc_final: 0.7417 (pmm) REVERT: H 447 MET cc_start: 0.3994 (mmm) cc_final: 0.3679 (mmp) REVERT: H 649 MET cc_start: 0.7510 (ppp) cc_final: 0.6852 (ppp) outliers start: 98 outliers final: 42 residues processed: 333 average time/residue: 0.6546 time to fit residues: 389.9630 Evaluate side-chains 292 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1766 LEU Chi-restraints excluded: chain B residue 1918 ASP Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 171 GLN Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 3 residue 218 ASP Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 485 MET Chi-restraints excluded: chain 3 residue 518 MET Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain I residue 769 LEU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 602 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 748 optimal weight: 9.9990 chunk 569 optimal weight: 10.0000 chunk 393 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 chunk 508 optimal weight: 0.8980 chunk 760 optimal weight: 6.9990 chunk 805 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 720 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1659 ASN 3 353 GLN 2 781 HIS C 287 HIS ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 69499 Z= 0.328 Angle : 0.574 12.673 94105 Z= 0.294 Chirality : 0.041 0.222 10510 Planarity : 0.004 0.048 11975 Dihedral : 9.564 149.862 9825 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 8.72 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 8267 helix: 1.42 (0.09), residues: 3542 sheet: -0.40 (0.14), residues: 1301 loop : -0.24 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 519 HIS 0.006 0.001 HIS K 302 PHE 0.021 0.001 PHE 6 338 TYR 0.029 0.001 TYR 6 347 ARG 0.006 0.000 ARG B1382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 251 time to evaluate : 6.395 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: B 1468 LEU cc_start: 0.2746 (OUTLIER) cc_final: 0.2227 (pp) REVERT: B 1470 MET cc_start: 0.5877 (tmm) cc_final: 0.4992 (mpp) REVERT: B 1639 LEU cc_start: -0.2732 (OUTLIER) cc_final: -0.2985 (pt) REVERT: B 1649 MET cc_start: 0.5212 (mmm) cc_final: 0.4713 (mmp) REVERT: B 1748 MET cc_start: -0.2048 (mmm) cc_final: -0.2250 (mmm) REVERT: B 1754 MET cc_start: 0.0198 (ptt) cc_final: -0.0770 (mtm) REVERT: B 1918 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6188 (p0) REVERT: B 2232 MET cc_start: 0.8071 (mtp) cc_final: 0.7498 (mtp) REVERT: A 177 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4600 (tptt) REVERT: 4 194 MET cc_start: 0.7485 (mtt) cc_final: 0.7151 (mtt) REVERT: 4 633 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7869 (t0) REVERT: 7 369 MET cc_start: 0.7317 (tmm) cc_final: 0.6494 (tmm) REVERT: 7 618 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7569 (mmm-85) REVERT: 2 770 MET cc_start: 0.7017 (mmm) cc_final: 0.6585 (mmm) REVERT: 2 888 MET cc_start: 0.8431 (pmm) cc_final: 0.8205 (pmm) REVERT: E 142 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7631 (p-80) REVERT: C 169 MET cc_start: 0.8410 (pmm) cc_final: 0.7507 (pmm) REVERT: C 564 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8145 (tt) REVERT: K 738 MET cc_start: 0.8087 (mtp) cc_final: 0.7663 (mtp) REVERT: J 425 MET cc_start: 0.6782 (tpt) cc_final: 0.6260 (tpp) REVERT: J 788 MET cc_start: 0.4238 (OUTLIER) cc_final: 0.3838 (mmp) outliers start: 111 outliers final: 59 residues processed: 342 average time/residue: 0.6111 time to fit residues: 374.5583 Evaluate side-chains 316 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 248 time to evaluate : 6.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1875 THR Chi-restraints excluded: chain B residue 1918 ASP Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 780 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 588 MET Chi-restraints excluded: chain 7 residue 618 ARG Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 218 ASP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 485 MET Chi-restraints excluded: chain 3 residue 518 MET Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 144 MET Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain Q residue 315 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 670 optimal weight: 9.9990 chunk 457 optimal weight: 0.0670 chunk 11 optimal weight: 40.0000 chunk 599 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 687 optimal weight: 2.9990 chunk 556 optimal weight: 0.0770 chunk 0 optimal weight: 50.0000 chunk 411 optimal weight: 4.9990 chunk 722 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 270 HIS 2 372 ASN ** 5 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69499 Z= 0.202 Angle : 0.515 12.249 94105 Z= 0.263 Chirality : 0.039 0.158 10510 Planarity : 0.003 0.049 11975 Dihedral : 9.359 149.662 9820 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 1.39 % Allowed : 9.35 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8267 helix: 1.59 (0.09), residues: 3525 sheet: -0.39 (0.14), residues: 1313 loop : -0.16 (0.11), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 525 HIS 0.005 0.001 HIS H 515 PHE 0.015 0.001 PHE A 509 TYR 0.026 0.001 TYR 6 347 ARG 0.012 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 252 time to evaluate : 6.369 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: B 1393 MET cc_start: 0.6105 (mmm) cc_final: 0.3484 (ptp) REVERT: B 1468 LEU cc_start: 0.2955 (OUTLIER) cc_final: 0.2377 (pp) REVERT: B 1470 MET cc_start: 0.5877 (tmm) cc_final: 0.4926 (mpp) REVERT: B 1639 LEU cc_start: -0.2838 (OUTLIER) cc_final: -0.3080 (pt) REVERT: B 1649 MET cc_start: 0.5229 (mmm) cc_final: 0.4962 (mmm) REVERT: B 1653 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.5099 (m-80) REVERT: B 1754 MET cc_start: 0.0215 (ptt) cc_final: -0.0356 (mtm) REVERT: B 2086 MET cc_start: 0.4121 (ptm) cc_final: 0.3576 (ptt) REVERT: B 2232 MET cc_start: 0.8041 (mtp) cc_final: 0.7447 (mtp) REVERT: A 1 MET cc_start: 0.4921 (mmm) cc_final: 0.4557 (tpp) REVERT: A 177 LYS cc_start: 0.5049 (OUTLIER) cc_final: 0.4683 (tptt) REVERT: 4 194 MET cc_start: 0.7456 (mtt) cc_final: 0.7253 (mtt) REVERT: 4 633 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7901 (t0) REVERT: 4 726 MET cc_start: 0.5448 (ptt) cc_final: 0.5082 (ptt) REVERT: 7 369 MET cc_start: 0.6936 (tmm) cc_final: 0.6718 (tmm) REVERT: 2 888 MET cc_start: 0.8590 (pmm) cc_final: 0.8386 (pmm) REVERT: 5 297 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7796 (pp) REVERT: E 142 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7717 (p-80) REVERT: C 169 MET cc_start: 0.8394 (pmm) cc_final: 0.7494 (pmm) REVERT: C 564 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8028 (tt) REVERT: J 788 MET cc_start: 0.4216 (OUTLIER) cc_final: 0.3960 (mmp) outliers start: 102 outliers final: 61 residues processed: 339 average time/residue: 0.6144 time to fit residues: 371.3726 Evaluate side-chains 318 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 248 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1653 PHE Chi-restraints excluded: chain B residue 1794 ILE Chi-restraints excluded: chain B residue 1845 MET Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 518 MET Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 287 VAL Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 622 THR Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain Q residue 315 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 270 optimal weight: 8.9990 chunk 725 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 472 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 805 optimal weight: 20.0000 chunk 669 optimal weight: 10.0000 chunk 373 optimal weight: 0.8980 chunk 67 optimal weight: 40.0000 chunk 266 optimal weight: 0.9990 chunk 423 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 420 HIS G 32 GLN C 46 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 GLN Q 602 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69499 Z= 0.165 Angle : 0.500 11.946 94105 Z= 0.255 Chirality : 0.039 0.174 10510 Planarity : 0.003 0.046 11975 Dihedral : 9.253 149.743 9820 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 1.51 % Allowed : 9.54 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.10), residues: 8267 helix: 1.65 (0.09), residues: 3531 sheet: -0.37 (0.14), residues: 1364 loop : -0.08 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 525 HIS 0.005 0.001 HIS H 515 PHE 0.023 0.001 PHE C 314 TYR 0.022 0.001 TYR 6 347 ARG 0.007 0.000 ARG 2 825 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 255 time to evaluate : 6.340 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: B 1468 LEU cc_start: 0.3138 (OUTLIER) cc_final: 0.2580 (pp) REVERT: B 1470 MET cc_start: 0.5856 (tmm) cc_final: 0.4868 (mpp) REVERT: B 1653 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: B 1754 MET cc_start: 0.0207 (ptt) cc_final: -0.0152 (mtm) REVERT: B 2232 MET cc_start: 0.7985 (mtp) cc_final: 0.7403 (mtp) REVERT: A 177 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4588 (tptt) REVERT: 4 299 MET cc_start: 0.7756 (tpp) cc_final: 0.7470 (ttm) REVERT: 4 633 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7831 (t0) REVERT: 4 726 MET cc_start: 0.5506 (ptt) cc_final: 0.5144 (ptt) REVERT: 7 369 MET cc_start: 0.7027 (tmm) cc_final: 0.6633 (tmm) REVERT: 5 297 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7815 (pp) REVERT: E 142 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7717 (p-80) REVERT: C 169 MET cc_start: 0.8382 (pmm) cc_final: 0.7485 (pmm) REVERT: C 564 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7955 (tt) REVERT: H 447 MET cc_start: 0.3875 (mmm) cc_final: 0.3238 (mmm) outliers start: 111 outliers final: 67 residues processed: 351 average time/residue: 0.6129 time to fit residues: 385.8815 Evaluate side-chains 320 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 246 time to evaluate : 6.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1653 PHE Chi-restraints excluded: chain B residue 1845 MET Chi-restraints excluded: chain B residue 1875 THR Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 209 ASN Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 544 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 780 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 218 ASP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 333 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain H residue 630 ILE Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 622 THR Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 602 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 777 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 459 optimal weight: 10.0000 chunk 588 optimal weight: 0.9980 chunk 456 optimal weight: 6.9990 chunk 678 optimal weight: 9.9990 chunk 450 optimal weight: 3.9990 chunk 802 optimal weight: 0.0570 chunk 502 optimal weight: 8.9990 chunk 489 optimal weight: 3.9990 chunk 370 optimal weight: 8.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 14 GLN 7 243 GLN 2 321 GLN 2 343 GLN 2 371 GLN ** 5 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 602 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 69499 Z= 0.256 Angle : 0.536 16.309 94105 Z= 0.271 Chirality : 0.039 0.157 10510 Planarity : 0.003 0.045 11975 Dihedral : 9.257 149.435 9820 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.52 % Allowed : 9.74 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.10), residues: 8267 helix: 1.66 (0.09), residues: 3544 sheet: -0.40 (0.14), residues: 1373 loop : -0.08 (0.11), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 525 HIS 0.005 0.001 HIS 5 147 PHE 0.015 0.001 PHE 6 203 TYR 0.022 0.001 TYR 6 347 ARG 0.007 0.000 ARG 2 887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 253 time to evaluate : 7.340 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: B 1393 MET cc_start: 0.3523 (mpp) cc_final: 0.0566 (ptp) REVERT: B 1468 LEU cc_start: 0.3445 (OUTLIER) cc_final: 0.2772 (pp) REVERT: B 1470 MET cc_start: 0.5865 (tmm) cc_final: 0.4840 (mpp) REVERT: B 1639 LEU cc_start: -0.2940 (OUTLIER) cc_final: -0.3195 (pt) REVERT: B 1653 PHE cc_start: 0.5880 (OUTLIER) cc_final: 0.5377 (m-80) REVERT: B 1754 MET cc_start: 0.0195 (ptt) cc_final: -0.0139 (mtm) REVERT: B 2201 MET cc_start: 0.8510 (ppp) cc_final: 0.8249 (ppp) REVERT: B 2232 MET cc_start: 0.8074 (mtp) cc_final: 0.7469 (mtp) REVERT: A 1 MET cc_start: 0.5070 (mmm) cc_final: 0.4689 (tpp) REVERT: A 177 LYS cc_start: 0.4874 (OUTLIER) cc_final: 0.4507 (tptt) REVERT: 4 194 MET cc_start: 0.7507 (mtt) cc_final: 0.7302 (mtt) REVERT: 4 299 MET cc_start: 0.7755 (tpp) cc_final: 0.7477 (ttm) REVERT: 4 633 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7904 (t0) REVERT: 7 369 MET cc_start: 0.7124 (tmm) cc_final: 0.6677 (tmm) REVERT: 5 297 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7864 (pp) REVERT: C 169 MET cc_start: 0.8411 (pmm) cc_final: 0.7518 (pmm) REVERT: C 564 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7986 (tt) REVERT: H 447 MET cc_start: 0.3749 (mmm) cc_final: 0.3129 (mmm) outliers start: 112 outliers final: 77 residues processed: 348 average time/residue: 0.6246 time to fit residues: 391.2671 Evaluate side-chains 333 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 249 time to evaluate : 6.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1653 PHE Chi-restraints excluded: chain B residue 1845 MET Chi-restraints excluded: chain B residue 1875 THR Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain B residue 2158 CYS Chi-restraints excluded: chain B residue 2159 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 209 ASN Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 544 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 780 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 531 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 333 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 287 VAL Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain H residue 630 ILE Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 622 THR Chi-restraints excluded: chain Q residue 315 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 496 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 510 optimal weight: 1.9990 chunk 546 optimal weight: 0.7980 chunk 396 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 631 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 420 HIS 4 593 GLN C 46 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 602 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 69499 Z= 0.174 Angle : 0.506 14.232 94105 Z= 0.257 Chirality : 0.039 0.195 10510 Planarity : 0.003 0.045 11975 Dihedral : 9.163 149.452 9818 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.37 % Allowed : 10.14 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.10), residues: 8267 helix: 1.73 (0.09), residues: 3510 sheet: -0.34 (0.14), residues: 1373 loop : -0.04 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 676 HIS 0.005 0.001 HIS H 515 PHE 0.019 0.001 PHE C 314 TYR 0.019 0.001 TYR 6 347 ARG 0.005 0.000 ARG 4 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 252 time to evaluate : 8.187 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: B 1468 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.2747 (pp) REVERT: B 1470 MET cc_start: 0.5850 (tmm) cc_final: 0.4824 (mpp) REVERT: B 1639 LEU cc_start: -0.3039 (OUTLIER) cc_final: -0.3310 (pt) REVERT: B 1653 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: B 2232 MET cc_start: 0.8003 (mtp) cc_final: 0.7456 (mtp) REVERT: A 177 LYS cc_start: 0.4794 (OUTLIER) cc_final: 0.4431 (tptt) REVERT: 4 194 MET cc_start: 0.7545 (mtt) cc_final: 0.7173 (mtt) REVERT: 4 299 MET cc_start: 0.7783 (tpp) cc_final: 0.7535 (ttm) REVERT: 4 633 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7841 (t0) REVERT: 4 726 MET cc_start: 0.5579 (ptt) cc_final: 0.5190 (ptt) REVERT: 7 369 MET cc_start: 0.6974 (tmm) cc_final: 0.6580 (tmm) REVERT: 5 297 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7811 (pp) REVERT: C 169 MET cc_start: 0.8431 (pmm) cc_final: 0.7557 (pmm) REVERT: C 564 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7925 (tt) REVERT: H 447 MET cc_start: 0.3914 (mmm) cc_final: 0.3283 (mmm) outliers start: 101 outliers final: 75 residues processed: 338 average time/residue: 0.7029 time to fit residues: 428.5163 Evaluate side-chains 327 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 245 time to evaluate : 6.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1653 PHE Chi-restraints excluded: chain B residue 1845 MET Chi-restraints excluded: chain B residue 1875 THR Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain B residue 2102 LEU Chi-restraints excluded: chain B residue 2158 CYS Chi-restraints excluded: chain B residue 2159 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 209 ASN Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 544 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 780 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 3 residue 46 ARG Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 218 ASP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 531 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 287 VAL Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain H residue 630 ILE Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 622 THR Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 602 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 730 optimal weight: 8.9990 chunk 769 optimal weight: 0.9990 chunk 701 optimal weight: 20.0000 chunk 748 optimal weight: 9.9990 chunk 768 optimal weight: 5.9990 chunk 450 optimal weight: 0.8980 chunk 325 optimal weight: 0.6980 chunk 587 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 676 optimal weight: 6.9990 chunk 707 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1763 GLN ** 4 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 606 GLN 6 328 GLN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 602 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 69499 Z= 0.184 Angle : 0.512 16.074 94105 Z= 0.259 Chirality : 0.039 0.214 10510 Planarity : 0.003 0.043 11975 Dihedral : 9.124 149.425 9816 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer: Outliers : 1.26 % Allowed : 10.33 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 8267 helix: 1.78 (0.09), residues: 3509 sheet: -0.36 (0.14), residues: 1381 loop : -0.02 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 676 HIS 0.005 0.001 HIS H 515 PHE 0.014 0.001 PHE 6 203 TYR 0.034 0.001 TYR 6 347 ARG 0.004 0.000 ARG Q 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 249 time to evaluate : 6.361 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: B 1468 LEU cc_start: 0.3407 (OUTLIER) cc_final: 0.2699 (pp) REVERT: B 1470 MET cc_start: 0.5944 (tmm) cc_final: 0.4917 (mpp) REVERT: B 1639 LEU cc_start: -0.2992 (OUTLIER) cc_final: -0.3243 (pt) REVERT: B 1649 MET cc_start: 0.6138 (mmp) cc_final: 0.4915 (tmm) REVERT: B 1653 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: B 2232 MET cc_start: 0.7972 (mtp) cc_final: 0.7493 (mtp) REVERT: B 2267 MET cc_start: 0.2248 (mmm) cc_final: 0.1325 (mmm) REVERT: A 177 LYS cc_start: 0.4933 (OUTLIER) cc_final: 0.4510 (tptt) REVERT: 4 194 MET cc_start: 0.7510 (mtt) cc_final: 0.7144 (mtt) REVERT: 4 299 MET cc_start: 0.7792 (tpp) cc_final: 0.7548 (ttm) REVERT: 4 633 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7833 (t0) REVERT: 4 726 MET cc_start: 0.5626 (ptt) cc_final: 0.5223 (ptt) REVERT: 7 369 MET cc_start: 0.6944 (tmm) cc_final: 0.6530 (tmm) REVERT: 5 297 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7816 (pp) REVERT: D 7 MET cc_start: 0.6932 (mmm) cc_final: 0.6649 (mmm) REVERT: C 169 MET cc_start: 0.8377 (pmm) cc_final: 0.7507 (pmm) REVERT: C 564 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7882 (tt) REVERT: H 447 MET cc_start: 0.3893 (mmm) cc_final: 0.3280 (mmm) REVERT: H 649 MET cc_start: 0.7498 (ppp) cc_final: 0.7066 (ppp) outliers start: 93 outliers final: 76 residues processed: 330 average time/residue: 0.6238 time to fit residues: 369.2974 Evaluate side-chains 330 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 247 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1653 PHE Chi-restraints excluded: chain B residue 1875 THR Chi-restraints excluded: chain B residue 1959 ARG Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain B residue 2102 LEU Chi-restraints excluded: chain B residue 2158 CYS Chi-restraints excluded: chain B residue 2159 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 209 ASN Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 544 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 780 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 3 residue 46 ARG Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 531 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 333 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 670 VAL Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 287 VAL Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain H residue 630 ILE Chi-restraints excluded: chain H residue 725 MET Chi-restraints excluded: chain I residue 505 ASP Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 559 ILE Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 622 THR Chi-restraints excluded: chain Q residue 602 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 745 optimal weight: 5.9990 chunk 491 optimal weight: 4.9990 chunk 791 optimal weight: 7.9990 chunk 482 optimal weight: 1.9990 chunk 375 optimal weight: 0.6980 chunk 549 optimal weight: 6.9990 chunk 829 optimal weight: 5.9990 chunk 763 optimal weight: 20.0000 chunk 660 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 510 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1763 GLN ** 4 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 331 GLN ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 459 ASN Q 602 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 69499 Z= 0.234 Angle : 0.528 15.453 94105 Z= 0.267 Chirality : 0.039 0.228 10510 Planarity : 0.003 0.043 11975 Dihedral : 9.130 149.232 9814 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer: Outliers : 1.24 % Allowed : 10.29 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 0.96 (0.10), residues: 8267 helix: 1.78 (0.09), residues: 3509 sheet: -0.38 (0.14), residues: 1399 loop : -0.03 (0.11), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 676 HIS 0.018 0.001 HIS L 106 PHE 0.014 0.001 PHE 6 203 TYR 0.034 0.001 TYR 6 347 ARG 0.013 0.000 ARG Q 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16534 Ramachandran restraints generated. 8267 Oldfield, 0 Emsley, 8267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 250 time to evaluate : 6.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1468 LEU cc_start: 0.3498 (OUTLIER) cc_final: 0.2790 (pp) REVERT: B 1470 MET cc_start: 0.5842 (tmm) cc_final: 0.4819 (mpp) REVERT: B 1639 LEU cc_start: -0.2969 (OUTLIER) cc_final: -0.3204 (pt) REVERT: B 1649 MET cc_start: 0.6089 (mmp) cc_final: 0.4840 (tmm) REVERT: B 1653 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5274 (m-80) REVERT: B 1748 MET cc_start: -0.2422 (tpp) cc_final: -0.2652 (tpp) REVERT: B 2201 MET cc_start: 0.8520 (ppp) cc_final: 0.8160 (ppp) REVERT: B 2232 MET cc_start: 0.7977 (mtp) cc_final: 0.7548 (mtp) REVERT: B 2267 MET cc_start: 0.2234 (mmm) cc_final: 0.1323 (mmm) REVERT: A 177 LYS cc_start: 0.4864 (OUTLIER) cc_final: 0.4474 (tptt) REVERT: 4 194 MET cc_start: 0.7529 (mtt) cc_final: 0.7134 (mtt) REVERT: 4 299 MET cc_start: 0.7818 (tpp) cc_final: 0.7541 (ttm) REVERT: 4 633 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7843 (t0) REVERT: 4 699 MET cc_start: 0.8100 (ttp) cc_final: 0.7857 (tmm) REVERT: 4 726 MET cc_start: 0.5614 (ptt) cc_final: 0.5197 (ptt) REVERT: 7 369 MET cc_start: 0.7044 (tmm) cc_final: 0.6568 (tmm) REVERT: 7 559 MET cc_start: 0.8506 (mtp) cc_final: 0.8218 (mtp) REVERT: 5 297 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7858 (pp) REVERT: C 169 MET cc_start: 0.8357 (pmm) cc_final: 0.7493 (pmm) REVERT: C 564 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7911 (tt) REVERT: H 447 MET cc_start: 0.3870 (mmm) cc_final: 0.3264 (mmm) outliers start: 91 outliers final: 76 residues processed: 327 average time/residue: 0.6426 time to fit residues: 379.7941 Evaluate side-chains 330 residues out of total 7352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 247 time to evaluate : 6.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1394 VAL Chi-restraints excluded: chain B residue 1411 ILE Chi-restraints excluded: chain B residue 1468 LEU Chi-restraints excluded: chain B residue 1514 VAL Chi-restraints excluded: chain B residue 1537 LEU Chi-restraints excluded: chain B residue 1639 LEU Chi-restraints excluded: chain B residue 1653 PHE Chi-restraints excluded: chain B residue 1845 MET Chi-restraints excluded: chain B residue 1875 THR Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain B residue 2102 LEU Chi-restraints excluded: chain B residue 2159 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain 4 residue 209 ASN Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 249 TYR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 388 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 541 VAL Chi-restraints excluded: chain 4 residue 544 THR Chi-restraints excluded: chain 4 residue 633 ASN Chi-restraints excluded: chain 4 residue 634 ILE Chi-restraints excluded: chain 4 residue 780 ILE Chi-restraints excluded: chain 4 residue 788 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 245 THR Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 357 THR Chi-restraints excluded: chain 6 residue 434 VAL Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 7 residue 84 LEU Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 7 residue 333 TYR Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 391 LEU Chi-restraints excluded: chain 7 residue 418 VAL Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 3 residue 46 ARG Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 531 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 178 LYS Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2 residue 325 VAL Chi-restraints excluded: chain 2 residue 333 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 738 MET Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 287 VAL Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 349 MET Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain H residue 630 ILE Chi-restraints excluded: chain H residue 725 MET Chi-restraints excluded: chain I residue 505 ASP Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 601 VAL Chi-restraints excluded: chain I residue 682 GLU Chi-restraints excluded: chain J residue 622 THR Chi-restraints excluded: chain Q residue 612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 833 random chunks: chunk 405 optimal weight: 0.7980 chunk 524 optimal weight: 3.9990 chunk 703 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 609 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 661 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 679 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN 4 201 ASN ** 4 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN C 501 HIS ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN ** H 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 602 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.055885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035897 restraints weight = 627664.910| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.55 r_work: 0.2763 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 69499 Z= 0.294 Angle : 0.565 16.765 94105 Z= 0.285 Chirality : 0.040 0.169 10510 Planarity : 0.004 0.061 11975 Dihedral : 9.207 149.054 9814 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 1.22 % Allowed : 10.52 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 8267 helix: 1.67 (0.09), residues: 3545 sheet: -0.41 (0.14), residues: 1386 loop : -0.06 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 676 HIS 0.020 0.001 HIS L 106 PHE 0.014 0.001 PHE 6 203 TYR 0.034 0.001 TYR 6 347 ARG 0.014 0.000 ARG Q 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12140.96 seconds wall clock time: 217 minutes 24.02 seconds (13044.02 seconds total)