Starting phenix.real_space_refine (version: dev) on Sat Apr 9 02:52:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqm_0948/04_2022/6lqm_0948_neut_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 139464 Number of models: 1 Model: "" Number of chains: 53 Chain: "0" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 555 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain breaks: 1 Chain: "2" Number of atoms: 75841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3532, 75841 Classifications: {'RNA': 3532} Modifications used: {'5*END': 1, 'rna3p': 69, 'rna2p_pyr': 224, 'rna3p_pur': 1531, 'rna2p': 15, 'rna3p_pyr': 1338, 'rna2p_pur': 340} Link IDs: {'rna3p': 2953, 'rna2p': 578} Chain breaks: 14 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 42 Chain: "3" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2043 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "5" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 5, 'rna3p_pyr': 54} Link IDs: {'rna3p': 108, 'rna2p': 11} Chain: "6" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1672 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 213} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'rna3p_pyr': 67, 'rna2p_pur': 14, 'rna3p_pur': 62, 'rna2p_pyr': 13, '5*END': 1} Link IDs: {'rna3p': 128, 'rna2p': 27} Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1708 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 3244 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3238 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 13, 'TRANS': 386, 'PCIS': 2} Conformer: "B" Number of residues, atoms: 402, 3238 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 13, 'TRANS': 386, 'PCIS': 2} bond proxies already assigned to first conformer: 3299 Chain: "C" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2850 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 18, 'TRANS': 339} Chain breaks: 1 Chain: "E" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "G" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1927 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "J" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1249 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Chain: "K" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "L" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "M" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "N" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1410 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "O" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "P" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Q" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1640 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 14, 'TRANS': 188} Chain: "R" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 387 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "S" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "T" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "V" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "W" Number of atoms: 842 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Conformer: "B" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} bond proxies already assigned to first conformer: 838 Chain: "X" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Y" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Z" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "a" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "b" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 163, 'PCIS': 1} Chain: "c" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "d" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 825 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "e" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 973 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "f" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 515 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "g" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "h" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1093 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "l" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "m" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "r" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2382 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "t" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "u" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "v" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1897 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'CIS': 1, 'TRANS': 219} Chain breaks: 1 Chain: "w" Number of atoms: 1878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Conformer: "B" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} bond proxies already assigned to first conformer: 1896 Chain: "2" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 245 Unusual residues: {' MG': 245} Classifications: {'undetermined': 245} Link IDs: {None: 244} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 59.30, per 1000 atoms: 0.43 Number of scatterers: 139464 At special positions: 0 Unit cell: (213.716, 240.166, 284.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 272 16.00 P 3805 15.00 Mg 251 11.99 O 36220 8.00 N 26099 7.00 C 72817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 3 308 " - pdb=" SG CYS 3 383 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 92 " distance=2.01 Simple disulfide: pdb=" SG CYS R 99 " - pdb=" SG CYS R 110 " 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 48.18 Conformation dependent library (CDL) restraints added in 7.2 seconds 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13278 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 252 helices and 71 sheets defined 41.7% alpha, 13.9% beta 1120 base pairs and 2095 stacking pairs defined. Time for finding SS restraints: 56.45 Creating SS restraints... Processing helix chain '0' and resid 396 through 403 removed outlier: 5.601A pdb=" N TYR 0 400 " --> pdb=" O LEU 0 396 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS 0 401 " --> pdb=" O MET 0 397 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG 0 403 " --> pdb=" O TYR 0 399 " (cutoff:3.500A) Processing helix chain '0' and resid 435 through 469 removed outlier: 4.414A pdb=" N LEU 0 439 " --> pdb=" O THR 0 435 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA 0 465 " --> pdb=" O MET 0 461 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN 0 468 " --> pdb=" O ASN 0 464 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET 0 469 " --> pdb=" O ALA 0 465 " (cutoff:3.500A) Processing helix chain '3' and resid 166 through 180 Processing helix chain '3' and resid 201 through 216 removed outlier: 3.746A pdb=" N ALA 3 205 " --> pdb=" O SER 3 201 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN 3 206 " --> pdb=" O LYS 3 202 " (cutoff:3.500A) Processing helix chain '3' and resid 258 through 266 removed outlier: 5.061A pdb=" N GLY 3 266 " --> pdb=" O ALA 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 303 removed outlier: 4.325A pdb=" N TRP 3 300 " --> pdb=" O GLY 3 296 " (cutoff:3.500A) Proline residue: 3 303 - end of helix Processing helix chain '3' and resid 309 through 314 removed outlier: 4.079A pdb=" N LEU 3 313 " --> pdb=" O HIS 3 309 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU 3 314 " --> pdb=" O PRO 3 310 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 309 through 314' Processing helix chain '3' and resid 365 through 370 removed outlier: 3.795A pdb=" N LEU 3 369 " --> pdb=" O LEU 3 365 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASN 3 370 " --> pdb=" O GLY 3 366 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 365 through 370' Processing helix chain '3' and resid 379 through 384 removed outlier: 6.045A pdb=" N CYS 3 383 " --> pdb=" O ASP 3 379 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN 3 384 " --> pdb=" O LEU 3 380 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 379 through 384' Processing helix chain '3' and resid 387 through 394 removed outlier: 5.457A pdb=" N ASN 3 394 " --> pdb=" O VAL 3 390 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 17 removed outlier: 4.624A pdb=" N PHE 6 16 " --> pdb=" O GLU 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 43 removed outlier: 4.033A pdb=" N TYR 6 35 " --> pdb=" O SER 6 31 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL 6 37 " --> pdb=" O ASN 6 33 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE 6 38 " --> pdb=" O PHE 6 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU 6 41 " --> pdb=" O VAL 6 37 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU 6 42 " --> pdb=" O PHE 6 38 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER 6 43 " --> pdb=" O GLU 6 39 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 63 removed outlier: 5.164A pdb=" N MET 6 62 " --> pdb=" O ILE 6 58 " (cutoff:3.500A) Processing helix chain '6' and resid 77 through 88 removed outlier: 3.647A pdb=" N ASN 6 86 " --> pdb=" O GLN 6 82 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 108 Processing helix chain '6' and resid 122 through 133 removed outlier: 3.918A pdb=" N GLU 6 126 " --> pdb=" O ASP 6 122 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 6 130 " --> pdb=" O GLU 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 147 through 152 removed outlier: 3.923A pdb=" N TYR 6 151 " --> pdb=" O LEU 6 147 " (cutoff:3.500A) Processing helix chain '6' and resid 166 through 178 removed outlier: 3.666A pdb=" N GLN 6 170 " --> pdb=" O SER 6 166 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP 6 171 " --> pdb=" O ILE 6 167 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU 6 172 " --> pdb=" O GLU 6 168 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 6 173 " --> pdb=" O ASP 6 169 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU 6 176 " --> pdb=" O GLU 6 172 " (cutoff:3.500A) Processing helix chain '6' and resid 192 through 197 removed outlier: 4.629A pdb=" N GLY 6 196 " --> pdb=" O VAL 6 192 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 222 removed outlier: 4.054A pdb=" N VAL 6 217 " --> pdb=" O THR 6 213 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL 6 218 " --> pdb=" O GLU 6 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 20 removed outlier: 4.317A pdb=" N GLU A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 4.071A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 4.219A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.809A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 4.641A pdb=" N ILE A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 127 through 132 removed outlier: 5.307A pdb=" N ALA A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 132' Processing helix chain 'A' and resid 143 through 155 removed outlier: 4.279A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 removed outlier: 4.148A pdb=" N LEU A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.220A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 4.105A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.923A pdb=" N GLN B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.693A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.610A pdb=" N GLU B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 4.018A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 4.301A pdb=" N LEU B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 361' Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 392 through 402 removed outlier: 3.509A pdb=" N ILE B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 5.671A pdb=" N ASN B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 302 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 4.340A pdb=" N TRP B 235 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 4.455A pdb=" N LYS C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 20 " --> pdb=" O TRP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 removed outlier: 3.596A pdb=" N PHE C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.818A pdb=" N ASN C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.584A pdb=" N HIS C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Proline residue: C 102 - end of helix Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.757A pdb=" N LEU C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 4.511A pdb=" N LYS D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 25 through 30' Processing helix chain 'D' and resid 33 through 49 removed outlier: 4.362A pdb=" N LYS D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 133 removed outlier: 4.048A pdb=" N ALA D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.610A pdb=" N SER D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 141 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 removed outlier: 4.539A pdb=" N GLY D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 156 through 161' Processing helix chain 'D' and resid 163 through 175 removed outlier: 4.302A pdb=" N LYS D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.995A pdb=" N ILE D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.707A pdb=" N ARG D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 Proline residue: D 242 - end of helix Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.923A pdb=" N LYS D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.778A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 334 through 361 removed outlier: 3.511A pdb=" N HIS D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 348 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 360 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 25 removed outlier: 4.201A pdb=" N ARG E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET E 22 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 41 removed outlier: 3.771A pdb=" N LYS E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'F' and resid 60 through 68 removed outlier: 3.728A pdb=" N LEU F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET F 65 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 60 through 68' Processing helix chain 'F' and resid 83 through 115 removed outlier: 4.089A pdb=" N GLU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.661A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 5.005A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.673A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 124 Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.725A pdb=" N THR G 145 " --> pdb=" O ASN G 141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 148 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 removed outlier: 5.767A pdb=" N PHE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.920A pdb=" N LEU G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 230 removed outlier: 4.555A pdb=" N ASP G 228 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG G 229 " --> pdb=" O ASN G 225 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 236 removed outlier: 4.413A pdb=" N ARG G 235 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 231 through 236' Processing helix chain 'G' and resid 243 through 266 removed outlier: 3.922A pdb=" N LYS G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU G 260 " --> pdb=" O ALA G 256 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU G 265 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY G 266 " --> pdb=" O ALA G 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.815A pdb=" N ARG H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY H 11 " --> pdb=" O ARG H 7 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 38 removed outlier: 4.203A pdb=" N LEU H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP H 23 " --> pdb=" O LYS H 19 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU H 24 " --> pdb=" O GLN H 20 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 37 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 74 removed outlier: 4.658A pdb=" N ARG H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 52 " --> pdb=" O ARG H 48 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS H 74 " --> pdb=" O ARG H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 Proline residue: H 85 - end of helix Processing helix chain 'H' and resid 88 through 95 removed outlier: 6.155A pdb=" N LEU H 95 " --> pdb=" O MET H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 102 Processing helix chain 'H' and resid 104 through 114 Processing helix chain 'I' and resid 63 through 86 removed outlier: 3.910A pdb=" N ALA I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS I 74 " --> pdb=" O VAL I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 166 removed outlier: 4.702A pdb=" N THR I 166 " --> pdb=" O GLN I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.979A pdb=" N PHE I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 171 through 176' Processing helix chain 'J' and resid 42 through 47 removed outlier: 6.158A pdb=" N PHE J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Proline residue: J 47 - end of helix No H-bonds generated for 'chain 'J' and resid 42 through 47' Processing helix chain 'J' and resid 61 through 80 removed outlier: 3.536A pdb=" N TYR J 75 " --> pdb=" O CYS J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.212A pdb=" N ILE J 149 " --> pdb=" O GLU J 145 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU J 150 " --> pdb=" O GLU J 146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA J 151 " --> pdb=" O HIS J 147 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS J 158 " --> pdb=" O ARG J 154 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Proline residue: J 160 - end of helix Processing helix chain 'J' and resid 177 through 188 removed outlier: 4.504A pdb=" N GLU J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP J 183 " --> pdb=" O ASP J 179 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 214 removed outlier: 4.186A pdb=" N LEU J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N HIS J 213 " --> pdb=" O TRP J 209 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER J 214 " --> pdb=" O ARG J 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 removed outlier: 3.922A pdb=" N ARG K 29 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG K 30 " --> pdb=" O HIS K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 30' Processing helix chain 'K' and resid 34 through 49 Processing helix chain 'K' and resid 51 through 64 removed outlier: 3.699A pdb=" N GLU K 59 " --> pdb=" O ARG K 55 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 Processing helix chain 'K' and resid 79 through 103 removed outlier: 3.610A pdb=" N ARG K 85 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 4.013A pdb=" N ARG L 6 " --> pdb=" O PRO L 2 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS L 7 " --> pdb=" O SER L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 7' Processing helix chain 'L' and resid 41 through 48 Processing helix chain 'L' and resid 64 through 69 removed outlier: 4.792A pdb=" N SER L 68 " --> pdb=" O LYS L 64 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE L 69 " --> pdb=" O ARG L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 64 through 69' Processing helix chain 'L' and resid 74 through 83 removed outlier: 4.064A pdb=" N LEU L 78 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N THR L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU L 81 " --> pdb=" O LYS L 77 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER L 83 " --> pdb=" O TRP L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 74 through 83' Processing helix chain 'L' and resid 84 through 93 removed outlier: 3.683A pdb=" N VAL L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN L 93 " --> pdb=" O ASN L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 107 removed outlier: 3.764A pdb=" N SER L 106 " --> pdb=" O ASP L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'M' and resid 4 through 11 removed outlier: 4.323A pdb=" N GLY M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS M 10 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG M 11 " --> pdb=" O SER M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 58 removed outlier: 3.626A pdb=" N LYS M 54 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG M 56 " --> pdb=" O LYS M 52 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.551A pdb=" N ILE M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG M 75 " --> pdb=" O TYR M 71 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 12 Proline residue: N 11 - end of helix No H-bonds generated for 'chain 'N' and resid 7 through 12' Processing helix chain 'N' and resid 30 through 44 removed outlier: 4.020A pdb=" N LYS N 38 " --> pdb=" O THR N 34 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL N 39 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU N 40 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU N 41 " --> pdb=" O ALA N 37 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU N 43 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 91 removed outlier: 3.925A pdb=" N GLU N 80 " --> pdb=" O GLY N 76 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU N 84 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL N 89 " --> pdb=" O LYS N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 removed outlier: 4.507A pdb=" N LYS N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 140 through 145' Processing helix chain 'N' and resid 158 through 170 removed outlier: 4.250A pdb=" N GLN N 168 " --> pdb=" O ARG N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 17 Processing helix chain 'O' and resid 49 through 59 removed outlier: 4.545A pdb=" N ALA O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 21 removed outlier: 3.825A pdb=" N PHE P 12 " --> pdb=" O ARG P 8 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG P 21 " --> pdb=" O GLN P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 30 removed outlier: 4.351A pdb=" N ARG P 28 " --> pdb=" O PRO P 24 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET P 29 " --> pdb=" O GLN P 25 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS P 30 " --> pdb=" O TRP P 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 30' Processing helix chain 'Q' and resid 17 through 22 removed outlier: 4.533A pdb=" N ARG Q 21 " --> pdb=" O ASP Q 17 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL Q 22 " --> pdb=" O TRP Q 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 17 through 22' Processing helix chain 'Q' and resid 27 through 47 removed outlier: 3.514A pdb=" N ILE Q 33 " --> pdb=" O PRO Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 85 removed outlier: 3.667A pdb=" N VAL Q 83 " --> pdb=" O GLU Q 79 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 95 removed outlier: 4.765A pdb=" N ARG Q 92 " --> pdb=" O LYS Q 88 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR Q 93 " --> pdb=" O LYS Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.527A pdb=" N ALA Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN Q 113 " --> pdb=" O SER Q 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 144 removed outlier: 3.890A pdb=" N GLU Q 143 " --> pdb=" O SER Q 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU Q 144 " --> pdb=" O SER Q 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 139 through 144' Processing helix chain 'Q' and resid 170 through 176 removed outlier: 4.480A pdb=" N PHE Q 176 " --> pdb=" O GLU Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 192 removed outlier: 3.749A pdb=" N LEU Q 182 " --> pdb=" O ALA Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 204 removed outlier: 4.558A pdb=" N GLU Q 204 " --> pdb=" O LYS Q 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 91 removed outlier: 3.876A pdb=" N TYR R 89 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 56 removed outlier: 4.099A pdb=" N MET S 55 " --> pdb=" O PRO S 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN S 56 " --> pdb=" O PHE S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 51 through 56' Processing helix chain 'S' and resid 69 through 81 removed outlier: 5.145A pdb=" N ALA S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP S 81 " --> pdb=" O TRP S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 removed outlier: 4.770A pdb=" N ALA S 87 " --> pdb=" O ASN S 83 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA S 88 " --> pdb=" O THR S 84 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ARG S 90 " --> pdb=" O TRP S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 104 removed outlier: 5.130A pdb=" N MET S 104 " --> pdb=" O ARG S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 135 removed outlier: 3.510A pdb=" N MET S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA S 133 " --> pdb=" O LYS S 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA S 134 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU S 135 " --> pdb=" O GLN S 131 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 34 removed outlier: 3.879A pdb=" N ARG T 32 " --> pdb=" O ASN T 28 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS T 34 " --> pdb=" O HIS T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 57 removed outlier: 3.609A pdb=" N LYS T 47 " --> pdb=" O PRO T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 74 removed outlier: 3.560A pdb=" N ASN T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS T 70 " --> pdb=" O THR T 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 14 removed outlier: 4.227A pdb=" N LYS U 13 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS U 14 " --> pdb=" O LEU U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 34 removed outlier: 3.597A pdb=" N PHE U 21 " --> pdb=" O ASP U 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN U 32 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU U 33 " --> pdb=" O GLN U 29 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N SER U 34 " --> pdb=" O TYR U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 52 Processing helix chain 'U' and resid 83 through 88 removed outlier: 4.430A pdb=" N HIS U 87 " --> pdb=" O LYS U 83 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 83 through 88' Processing helix chain 'U' and resid 97 through 111 removed outlier: 4.083A pdb=" N GLY U 111 " --> pdb=" O GLY U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 145 removed outlier: 4.321A pdb=" N ASN U 145 " --> pdb=" O ALA U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 153 removed outlier: 4.696A pdb=" N THR U 152 " --> pdb=" O THR U 148 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 148 through 153' Processing helix chain 'U' and resid 158 through 163 Processing helix chain 'U' and resid 165 through 173 removed outlier: 4.979A pdb=" N SER U 171 " --> pdb=" O ALA U 167 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG U 172 " --> pdb=" O GLY U 168 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 197 Processing helix chain 'V' and resid 15 through 30 removed outlier: 3.945A pdb=" N GLY V 30 " --> pdb=" O GLN V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 60 removed outlier: 3.925A pdb=" N LYS V 60 " --> pdb=" O ALA V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 70 removed outlier: 3.963A pdb=" N GLY V 69 " --> pdb=" O ASN V 65 " (cutoff:3.500A) Proline residue: V 70 - end of helix No H-bonds generated for 'chain 'V' and resid 65 through 70' Processing helix chain 'V' and resid 75 through 89 removed outlier: 3.849A pdb=" N MET V 87 " --> pdb=" O THR V 83 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU V 88 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Proline residue: V 89 - end of helix Processing helix chain 'V' and resid 92 through 102 removed outlier: 3.927A pdb=" N ARG V 101 " --> pdb=" O ALA V 97 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU V 102 " --> pdb=" O ALA V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 110 through 116 removed outlier: 4.687A pdb=" N LYS V 114 " --> pdb=" O PRO V 110 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS V 115 " --> pdb=" O PRO V 111 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LYS V 116 " --> pdb=" O TYR V 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 110 through 116' Processing helix chain 'V' and resid 124 through 129 Processing helix chain 'V' and resid 137 through 146 removed outlier: 3.505A pdb=" N VAL V 145 " --> pdb=" O LEU V 141 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 190 removed outlier: 3.571A pdb=" N HIS V 167 " --> pdb=" O LYS V 163 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS V 170 " --> pdb=" O ILE V 166 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN V 173 " --> pdb=" O ARG V 169 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS V 183 " --> pdb=" O LYS V 179 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS V 187 " --> pdb=" O LYS V 183 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS V 188 " --> pdb=" O ASN V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 200 removed outlier: 4.254A pdb=" N VAL V 195 " --> pdb=" O LYS V 191 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU V 196 " --> pdb=" O TYR V 192 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS V 199 " --> pdb=" O VAL V 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 46 removed outlier: 4.055A pdb=" N SER W 46 " --> pdb=" O ASP W 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 35 removed outlier: 3.666A pdb=" N VAL X 26 " --> pdb=" O LEU X 22 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS X 28 " --> pdb=" O LYS X 24 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE X 29 " --> pdb=" O MET X 25 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS X 34 " --> pdb=" O GLU X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 92 removed outlier: 4.192A pdb=" N THR X 78 " --> pdb=" O THR X 74 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP X 91 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN X 92 " --> pdb=" O GLU X 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 15 removed outlier: 4.289A pdb=" N SER Y 14 " --> pdb=" O ASN Y 10 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS Y 15 " --> pdb=" O PRO Y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 10 through 15' Processing helix chain 'Y' and resid 25 through 37 removed outlier: 3.702A pdb=" N ALA Y 35 " --> pdb=" O GLU Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 54 Processing helix chain 'Y' and resid 84 through 106 removed outlier: 3.581A pdb=" N MET Y 94 " --> pdb=" O PHE Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 76 removed outlier: 3.808A pdb=" N ALA Y 73 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS Y 74 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN Y 75 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP Y 76 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 76' Processing helix chain 'Z' and resid 22 through 39 removed outlier: 3.987A pdb=" N LEU Z 27 " --> pdb=" O ILE Z 23 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS Z 30 " --> pdb=" O ARG Z 26 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU Z 31 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE Z 34 " --> pdb=" O LYS Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 54 removed outlier: 3.953A pdb=" N GLN Z 45 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE Z 52 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET Z 53 " --> pdb=" O LYS Z 49 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER Z 54 " --> pdb=" O ARG Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.884A pdb=" N LEU Z 72 " --> pdb=" O ARG Z 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 117 removed outlier: 3.609A pdb=" N ARG Z 115 " --> pdb=" O SER Z 111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA Z 116 " --> pdb=" O ARG Z 112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 130 removed outlier: 3.759A pdb=" N ALA Z 127 " --> pdb=" O PHE Z 123 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP Z 129 " --> pdb=" O GLN Z 125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 146 through 153 removed outlier: 4.371A pdb=" N ARG Z 150 " --> pdb=" O ARG Z 146 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS Z 151 " --> pdb=" O GLU Z 147 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE Z 152 " --> pdb=" O VAL Z 148 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY Z 153 " --> pdb=" O TYR Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 146 through 153' Processing helix chain 'Z' and resid 171 through 176 removed outlier: 5.294A pdb=" N GLU Z 175 " --> pdb=" O GLY Z 171 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG Z 176 " --> pdb=" O ARG Z 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 171 through 176' Processing helix chain 'Z' and resid 7 through 12 removed outlier: 3.649A pdb=" N ASP Z 10 " --> pdb=" O HIS Z 7 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG Z 11 " --> pdb=" O ASN Z 8 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS Z 12 " --> pdb=" O LYS Z 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 7 through 12' Processing helix chain 'a' and resid 4 through 16 removed outlier: 3.547A pdb=" N SER a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 23 removed outlier: 3.710A pdb=" N VAL a 22 " --> pdb=" O GLY a 18 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP a 23 " --> pdb=" O LYS a 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 18 through 23' Processing helix chain 'a' and resid 28 through 36 removed outlier: 3.638A pdb=" N ILE a 32 " --> pdb=" O GLU a 28 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN a 36 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 48 removed outlier: 6.241A pdb=" N ARG a 42 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS a 43 " --> pdb=" O GLN a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 73 removed outlier: 3.520A pdb=" N LYS a 72 " --> pdb=" O LEU a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 82 removed outlier: 4.792A pdb=" N ARG a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS a 82 " --> pdb=" O ILE a 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 77 through 82' Processing helix chain 'a' and resid 84 through 113 Proline residue: a 90 - end of helix removed outlier: 6.536A pdb=" N VAL a 93 " --> pdb=" O MET a 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG a 110 " --> pdb=" O LEU a 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU a 111 " --> pdb=" O ARG a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 116 through 130 removed outlier: 3.829A pdb=" N SER a 122 " --> pdb=" O HIS a 118 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU a 125 " --> pdb=" O HIS a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 154 removed outlier: 3.638A pdb=" N LEU a 138 " --> pdb=" O ASN a 134 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS a 144 " --> pdb=" O GLU a 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 52 removed outlier: 3.691A pdb=" N TRP b 45 " --> pdb=" O LYS b 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR b 46 " --> pdb=" O SER b 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE b 47 " --> pdb=" O ARG b 43 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN b 50 " --> pdb=" O TYR b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 117 removed outlier: 3.619A pdb=" N VAL b 106 " --> pdb=" O THR b 102 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 125 removed outlier: 3.971A pdb=" N ILE b 124 " --> pdb=" O ARG b 120 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN b 125 " --> pdb=" O ALA b 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 120 through 125' Processing helix chain 'b' and resid 139 through 146 removed outlier: 4.734A pdb=" N PHE b 145 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS b 146 " --> pdb=" O VAL b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 166 Proline residue: b 165 - end of helix No H-bonds generated for 'chain 'b' and resid 161 through 166' Processing helix chain 'c' and resid 11 through 16 removed outlier: 4.329A pdb=" N SER c 16 " --> pdb=" O ARG c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 32 removed outlier: 4.787A pdb=" N TYR c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET c 31 " --> pdb=" O LEU c 27 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG c 32 " --> pdb=" O ALA c 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 26 through 32' Processing helix chain 'c' and resid 92 through 97 removed outlier: 4.181A pdb=" N ILE c 96 " --> pdb=" O ARG c 92 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS c 97 " --> pdb=" O ILE c 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 92 through 97' Processing helix chain 'c' and resid 99 through 123 removed outlier: 3.680A pdb=" N ASP c 103 " --> pdb=" O SER c 99 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS c 120 " --> pdb=" O LYS c 116 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU c 121 " --> pdb=" O LYS c 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 32 removed outlier: 3.704A pdb=" N ASP d 31 " --> pdb=" O HIS d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 47 removed outlier: 3.508A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 60 removed outlier: 4.190A pdb=" N GLY d 59 " --> pdb=" O ASN d 55 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL d 60 " --> pdb=" O LEU d 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 55 through 60' Processing helix chain 'd' and resid 79 through 95 removed outlier: 4.256A pdb=" N LEU d 83 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 74 removed outlier: 3.853A pdb=" N ARG e 73 " --> pdb=" O LYS e 69 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS e 74 " --> pdb=" O PRO e 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 69 through 74' Processing helix chain 'e' and resid 122 through 130 removed outlier: 3.613A pdb=" N LEU e 128 " --> pdb=" O GLU e 124 " (cutoff:3.500A) Proline residue: e 130 - end of helix Processing helix chain 'e' and resid 131 through 137 removed outlier: 4.123A pdb=" N ASN e 135 " --> pdb=" O ARG e 131 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA e 136 " --> pdb=" O ILE e 132 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY e 137 " --> pdb=" O ALA e 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 131 through 137' Processing helix chain 'f' and resid 33 through 43 removed outlier: 4.036A pdb=" N LYS f 43 " --> pdb=" O ALA f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 50 removed outlier: 4.104A pdb=" N ILE f 49 " --> pdb=" O ASN f 45 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASN f 50 " --> pdb=" O PRO f 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 45 through 50' Processing helix chain 'f' and resid 52 through 60 removed outlier: 3.990A pdb=" N LYS f 60 " --> pdb=" O ARG f 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 78 removed outlier: 3.920A pdb=" N ILE g 77 " --> pdb=" O HIS g 73 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS g 78 " --> pdb=" O TYR g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 93 removed outlier: 3.679A pdb=" N LYS g 88 " --> pdb=" O GLU g 84 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS g 89 " --> pdb=" O SER g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 117 removed outlier: 3.573A pdb=" N GLN g 111 " --> pdb=" O HIS g 107 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR g 117 " --> pdb=" O VAL g 113 " (cutoff:3.500A) Processing helix chain 'g' and resid 145 through 154 removed outlier: 3.649A pdb=" N ASN g 151 " --> pdb=" O LEU g 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 21 removed outlier: 3.742A pdb=" N ALA h 21 " --> pdb=" O ARG h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 31 removed outlier: 4.559A pdb=" N LYS h 28 " --> pdb=" O HIS h 24 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER h 31 " --> pdb=" O ARG h 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 43 removed outlier: 4.266A pdb=" N ASN h 43 " --> pdb=" O ARG h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 105 removed outlier: 4.091A pdb=" N VAL h 104 " --> pdb=" O HIS h 100 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL h 105 " --> pdb=" O PRO h 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 100 through 105' Processing helix chain 'h' and resid 112 through 131 removed outlier: 3.651A pdb=" N LYS h 116 " --> pdb=" O ASP h 112 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE h 118 " --> pdb=" O ASP h 114 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG h 126 " --> pdb=" O LYS h 122 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY h 129 " --> pdb=" O SER h 125 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU h 131 " --> pdb=" O GLN h 127 " (cutoff:3.500A) Processing helix chain 'i' and resid 58 through 67 removed outlier: 3.809A pdb=" N LYS i 64 " --> pdb=" O LYS i 60 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS i 67 " --> pdb=" O ALA i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 81 removed outlier: 3.903A pdb=" N LEU i 80 " --> pdb=" O ASN i 76 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N MET i 81 " --> pdb=" O TYR i 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 76 through 81' Processing helix chain 'i' and resid 92 through 97 removed outlier: 5.306A pdb=" N ASN i 97 " --> pdb=" O LYS i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 99 through 104 removed outlier: 5.305A pdb=" N ASP i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) Proline residue: i 104 - end of helix No H-bonds generated for 'chain 'i' and resid 99 through 104' Processing helix chain 'i' and resid 105 through 125 removed outlier: 3.604A pdb=" N VAL i 116 " --> pdb=" O ARG i 112 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS i 123 " --> pdb=" O GLU i 119 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR i 124 " --> pdb=" O GLU i 120 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY i 125 " --> pdb=" O ARG i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 127 through 133 removed outlier: 3.822A pdb=" N PHE i 131 " --> pdb=" O ASN i 127 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN i 132 " --> pdb=" O LYS i 128 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS i 133 " --> pdb=" O TRP i 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 127 through 133' Processing helix chain 'l' and resid 2 through 13 removed outlier: 3.506A pdb=" N VAL l 9 " --> pdb=" O LEU l 5 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN l 12 " --> pdb=" O MET l 8 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS l 13 " --> pdb=" O VAL l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 98 removed outlier: 3.729A pdb=" N LEU l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 103 through 123 removed outlier: 4.503A pdb=" N ARG l 107 " --> pdb=" O ARG l 103 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N MET l 108 " --> pdb=" O PRO l 104 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA l 109 " --> pdb=" O ASP l 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN l 121 " --> pdb=" O ILE l 117 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) Proline residue: l 123 - end of helix Processing helix chain 'm' and resid 5 through 13 removed outlier: 6.044A pdb=" N LYS m 10 " --> pdb=" O ARG m 6 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY m 11 " --> pdb=" O GLY m 7 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA m 12 " --> pdb=" O GLN m 8 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY m 13 " --> pdb=" O ARG m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 38 Processing helix chain 'm' and resid 181 through 193 removed outlier: 3.632A pdb=" N ALA m 185 " --> pdb=" O LYS m 181 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA m 191 " --> pdb=" O HIS m 187 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS m 192 " --> pdb=" O LYS m 188 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 3.798A pdb=" N MET m 204 " --> pdb=" O ARG m 200 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN m 205 " --> pdb=" O GLY m 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 200 through 205' Processing helix chain 'm' and resid 173 through 178 removed outlier: 3.535A pdb=" N ASP m 176 " --> pdb=" O GLY m 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS m 177 " --> pdb=" O ARG m 174 " (cutoff:3.500A) Proline residue: m 178 - end of helix No H-bonds generated for 'chain 'm' and resid 173 through 178' Processing helix chain 'r' and resid 9 through 16 removed outlier: 3.672A pdb=" N PHE r 13 " --> pdb=" O ASN r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 3.546A pdb=" N GLY r 26 " --> pdb=" O ARG r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 37 removed outlier: 3.835A pdb=" N ARG r 35 " --> pdb=" O TYR r 31 " (cutoff:3.500A) Processing helix chain 'r' and resid 79 through 87 removed outlier: 4.296A pdb=" N LEU r 83 " --> pdb=" O TYR r 79 " (cutoff:3.500A) Proline residue: r 84 - end of helix removed outlier: 4.384A pdb=" N GLY r 87 " --> pdb=" O LEU r 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 79 through 87' Processing helix chain 'r' and resid 94 through 114 Processing helix chain 'r' and resid 157 through 170 removed outlier: 3.856A pdb=" N GLY r 161 " --> pdb=" O ASN r 157 " (cutoff:3.500A) Processing helix chain 'r' and resid 191 through 201 removed outlier: 6.437A pdb=" N HIS r 195 " --> pdb=" O ASN r 191 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG r 196 " --> pdb=" O ALA r 192 " (cutoff:3.500A) Processing helix chain 'r' and resid 202 through 215 removed outlier: 3.638A pdb=" N GLU r 213 " --> pdb=" O ARG r 209 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU r 214 " --> pdb=" O TYR r 210 " (cutoff:3.500A) Processing helix chain 'r' and resid 216 through 224 removed outlier: 3.869A pdb=" N SER r 224 " --> pdb=" O LYS r 220 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 230 removed outlier: 5.113A pdb=" N ASN r 229 " --> pdb=" O GLN r 225 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER r 230 " --> pdb=" O TYR r 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 225 through 230' Processing helix chain 'r' and resid 235 through 250 Processing helix chain 'r' and resid 272 through 292 removed outlier: 3.635A pdb=" N VAL r 280 " --> pdb=" O LYS r 276 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA r 281 " --> pdb=" O LYS r 277 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU r 292 " --> pdb=" O LEU r 288 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 29 removed outlier: 3.843A pdb=" N TYR t 28 " --> pdb=" O GLN t 24 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL t 29 " --> pdb=" O SER t 25 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 24 through 29' Processing helix chain 't' and resid 43 through 48 Processing helix chain 't' and resid 81 through 90 removed outlier: 4.530A pdb=" N VAL t 87 " --> pdb=" O LYS t 83 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU t 88 " --> pdb=" O GLU t 84 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU t 89 " --> pdb=" O LEU t 85 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N MET t 90 " --> pdb=" O GLU t 86 " (cutoff:3.500A) Processing helix chain 't' and resid 104 through 119 removed outlier: 3.525A pdb=" N LYS t 109 " --> pdb=" O SER t 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA t 110 " --> pdb=" O LYS t 106 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN t 117 " --> pdb=" O GLU t 113 " (cutoff:3.500A) Processing helix chain 'u' and resid 35 through 40 removed outlier: 3.827A pdb=" N THR u 39 " --> pdb=" O ALA u 35 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU u 40 " --> pdb=" O ARG u 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 35 through 40' Processing helix chain 'v' and resid 58 through 67 Processing helix chain 'v' and resid 132 through 137 removed outlier: 3.696A pdb=" N HIS v 136 " --> pdb=" O PRO v 132 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL v 137 " --> pdb=" O PHE v 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 132 through 137' Processing helix chain 'v' and resid 190 through 195 removed outlier: 4.131A pdb=" N VAL v 194 " --> pdb=" O HIS v 190 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE v 195 " --> pdb=" O GLN v 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 190 through 195' Processing helix chain 'v' and resid 213 through 218 removed outlier: 3.811A pdb=" N PHE v 217 " --> pdb=" O THR v 213 " (cutoff:3.500A) Processing helix chain 'v' and resid 235 through 240 removed outlier: 4.135A pdb=" N LYS v 239 " --> pdb=" O THR v 235 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR v 240 " --> pdb=" O GLU v 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 235 through 240' Processing helix chain 'v' and resid 243 through 262 removed outlier: 3.554A pdb=" N LYS v 247 " --> pdb=" O THR v 243 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN v 250 " --> pdb=" O ARG v 246 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN v 256 " --> pdb=" O ALA v 252 " (cutoff:3.500A) Proline residue: v 259 - end of helix Processing helix chain 'v' and resid 266 through 274 removed outlier: 5.299A pdb=" N VAL v 274 " --> pdb=" O TYR v 270 " (cutoff:3.500A) Processing helix chain 'v' and resid 282 through 287 removed outlier: 6.039A pdb=" N VAL v 287 " --> pdb=" O PRO v 283 " (cutoff:3.500A) Processing helix chain 'w' and resid 24 through 79 removed outlier: 6.543A pdb=" N LEU w 28 " --> pdb=" O ASN w 24 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS w 29 " --> pdb=" O PHE w 25 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE w 30 " --> pdb=" O ALA w 26 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE w 37 " --> pdb=" O LEU w 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS w 40 " --> pdb=" O LYS w 36 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG w 43 " --> pdb=" O GLN w 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG w 62 " --> pdb=" O HIS w 58 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE w 69 " --> pdb=" O TYR w 65 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA w 72 " --> pdb=" O GLU w 68 " (cutoff:3.500A) Processing helix chain 'w' and resid 102 through 113 removed outlier: 3.655A pdb=" N GLN w 110 " --> pdb=" O ARG w 106 " (cutoff:3.500A) Processing helix chain 'w' and resid 126 through 137 removed outlier: 4.134A pdb=" N MET w 132 " --> pdb=" O ALA w 128 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE w 135 " --> pdb=" O ASN w 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL w 136 " --> pdb=" O MET w 132 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU w 137 " --> pdb=" O LEU w 133 " (cutoff:3.500A) Processing helix chain 'w' and resid 146 through 156 Processing helix chain 'w' and resid 171 through 179 removed outlier: 4.140A pdb=" N ILE w 175 " --> pdb=" O ASP w 171 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER w 178 " --> pdb=" O LEU w 174 " (cutoff:3.500A) Processing helix chain 'w' and resid 186 through 197 removed outlier: 4.211A pdb=" N VAL w 197 " --> pdb=" O GLU w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 200 through 209 removed outlier: 5.410A pdb=" N TRP w 209 " --> pdb=" O ASN w 205 " (cutoff:3.500A) Processing helix chain 'w' and resid 239 through 248 removed outlier: 3.869A pdb=" N LEU w 243 " --> pdb=" O GLN w 239 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '3' and resid 186 through 190 removed outlier: 3.928A pdb=" N ARG 3 187 " --> pdb=" O TYR 3 198 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS 3 154 " --> pdb=" O TYR 3 238 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS 3 221 " --> pdb=" O SER 3 243 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '3' and resid 253 through 256 removed outlier: 4.347A pdb=" N ASN 3 253 " --> pdb=" O CYS 3 274 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS 3 282 " --> pdb=" O ILE 3 275 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN 3 290 " --> pdb=" O ASP 3 285 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 320 through 323 removed outlier: 4.242A pdb=" N GLU 3 344 " --> pdb=" O SER 3 322 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY 3 343 " --> pdb=" O THR 3 363 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 375 through 378 removed outlier: 6.523A pdb=" N LEU 3 376 " --> pdb=" O ILE 3 404 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '6' and resid 23 through 28 Processing sheet with id= 6, first strand: chain '6' and resid 114 through 117 Processing sheet with id= 7, first strand: chain 'A' and resid 31 through 35 removed outlier: 5.469A pdb=" N VAL A 32 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 34 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 53 through 58 removed outlier: 3.532A pdb=" N GLU B 74 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.672A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 179 through 184 removed outlier: 5.084A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 286 through 290 removed outlier: 4.588A pdb=" N PHE B 330 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 76 through 80 Processing sheet with id= 13, first strand: chain 'B' and resid 88 through 93 removed outlier: 3.594A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 214 through 218 removed outlier: 4.376A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 7 through 10 removed outlier: 4.929A pdb=" N LYS D 20 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.201A pdb=" N TYR D 211 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE D 249 " --> pdb=" O GLY D 206 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 26 through 29 removed outlier: 6.352A pdb=" N LYS E 26 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 45 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY E 70 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN E 50 " --> pdb=" O TYR E 74 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 20 through 24 Processing sheet with id= 19, first strand: chain 'G' and resid 179 through 185 removed outlier: 3.766A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 5 through 12 removed outlier: 6.162A pdb=" N SER I 6 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS I 53 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG I 54 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU I 44 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 17 through 20 Processing sheet with id= 22, first strand: chain 'I' and resid 102 through 106 removed outlier: 6.210A pdb=" N ASN I 102 " --> pdb=" O ARG I 115 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU I 111 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER I 110 " --> pdb=" O MET I 128 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG I 124 " --> pdb=" O ILE I 114 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 132 through 137 removed outlier: 6.580A pdb=" N GLU I 143 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP I 142 " --> pdb=" O SER I 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS I 91 " --> pdb=" O SER I 182 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 87 through 91 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'J' and resid 34 through 37 removed outlier: 6.702A pdb=" N PHE J 34 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET J 136 " --> pdb=" O MET J 52 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE J 138 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR J 140 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY J 49 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS J 166 " --> pdb=" O HIS J 51 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 189 through 192 removed outlier: 5.499A pdb=" N CYS J 189 " --> pdb=" O VAL J 200 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 98 through 101 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'N' and resid 48 through 51 removed outlier: 5.768A pdb=" N ILE N 68 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL N 74 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS N 19 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS N 21 " --> pdb=" O TYR N 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR N 131 " --> pdb=" O CYS N 21 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN N 23 " --> pdb=" O ASP N 129 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N CYS N 25 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY N 127 " --> pdb=" O CYS N 25 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 2 through 5 removed outlier: 4.406A pdb=" N VAL O 46 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER O 22 " --> pdb=" O ARG O 37 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE O 25 " --> pdb=" O LYS O 67 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 93 through 97 removed outlier: 4.290A pdb=" N ALA R 101 " --> pdb=" O CYS R 96 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 11 through 16 removed outlier: 4.228A pdb=" N ARG S 11 " --> pdb=" O ILE S 27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS S 23 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU S 37 " --> pdb=" O VAL S 28 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY S 40 " --> pdb=" O ARG S 46 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG S 46 " --> pdb=" O GLY S 40 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'T' and resid 61 through 64 removed outlier: 5.652A pdb=" N ASP T 61 " --> pdb=" O LEU T 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR T 104 " --> pdb=" O ASP T 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL T 21 " --> pdb=" O ARG T 90 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR T 22 " --> pdb=" O VAL T 122 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 35 through 39 removed outlier: 6.097A pdb=" N ALA U 35 " --> pdb=" O ARG U 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG U 65 " --> pdb=" O ALA U 35 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE U 61 " --> pdb=" O ALA U 39 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE U 133 " --> pdb=" O LEU U 116 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 117 through 121 removed outlier: 3.745A pdb=" N ASN U 117 " --> pdb=" O ILE U 133 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE U 129 " --> pdb=" O VAL U 121 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'V' and resid 6 through 10 Processing sheet with id= 36, first strand: chain 'W' and resid 7 through 10 removed outlier: 3.696A pdb=" N ARG W 8 " --> pdb=" O HIS W 21 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS W 64 " --> pdb=" O ARG W 87 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG W 87 " --> pdb=" O LYS W 64 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE W 66 " --> pdb=" O ILE W 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'X' and resid 47 through 50 removed outlier: 6.803A pdb=" N ILE X 54 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY X 53 " --> pdb=" O GLY X 66 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS X 62 " --> pdb=" O CYS X 57 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Y' and resid 16 through 20 removed outlier: 6.657A pdb=" N ILE Y 149 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Y' and resid 116 through 122 Processing sheet with id= 40, first strand: chain 'Y' and resid 124 through 131 No H-bonds generated for sheet with id= 40 Processing sheet with id= 41, first strand: chain 'Z' and resid 78 through 82 Processing sheet with id= 42, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id= 43, first strand: chain 'b' and resid 27 through 33 removed outlier: 6.585A pdb=" N VAL b 13 " --> pdb=" O VAL b 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 90 through 98 removed outlier: 4.278A pdb=" N ASN b 77 " --> pdb=" O ILE b 132 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 9 through 13 removed outlier: 4.735A pdb=" N GLU b 9 " --> pdb=" O VAL b 67 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 39 through 43 removed outlier: 3.891A pdb=" N LYS c 60 " --> pdb=" O ILE c 42 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 72 through 79 Processing sheet with id= 48, first strand: chain 'd' and resid 61 through 65 removed outlier: 4.170A pdb=" N VAL d 72 " --> pdb=" O PHE d 21 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE d 21 " --> pdb=" O VAL d 72 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR d 110 " --> pdb=" O THR d 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU d 112 " --> pdb=" O ASP d 24 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 24 through 27 removed outlier: 4.494A pdb=" N ALA e 24 " --> pdb=" O ILE e 39 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET e 62 " --> pdb=" O ILE e 40 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP e 59 " --> pdb=" O VAL e 81 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP e 100 " --> pdb=" O ARG e 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG e 85 " --> pdb=" O ASP e 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 87 through 90 removed outlier: 5.663A pdb=" N VAL e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 3 through 6 removed outlier: 6.226A pdb=" N GLU f 4 " --> pdb=" O LYS f 12 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS f 12 " --> pdb=" O GLU f 4 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS f 6 " --> pdb=" O GLY f 10 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 18 through 22 Processing sheet with id= 53, first strand: chain 'g' and resid 95 through 100 removed outlier: 4.010A pdb=" N LYS g 134 " --> pdb=" O VAL g 100 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU g 133 " --> pdb=" O ARG g 129 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS g 123 " --> pdb=" O ARG g 139 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 53 through 56 removed outlier: 4.873A pdb=" N ASP h 53 " --> pdb=" O VAL h 70 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 72 through 75 removed outlier: 3.616A pdb=" N GLN h 72 " --> pdb=" O TYR h 81 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 86 through 89 removed outlier: 4.600A pdb=" N THR h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 9 through 13 removed outlier: 4.399A pdb=" N LYS i 9 " --> pdb=" O ILE i 25 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG i 21 " --> pdb=" O VAL i 13 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 26 through 30 removed outlier: 6.527A pdb=" N HIS i 40 " --> pdb=" O ILE i 29 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'l' and resid 48 through 53 removed outlier: 4.995A pdb=" N THR l 48 " --> pdb=" O LYS l 65 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER l 76 " --> pdb=" O ARG l 66 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 47 through 50 removed outlier: 3.840A pdb=" N ASP m 47 " --> pdb=" O LYS m 60 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS m 60 " --> pdb=" O LYS m 46 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN m 86 " --> pdb=" O VAL m 45 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'm' and resid 111 through 114 removed outlier: 4.032A pdb=" N THR m 111 " --> pdb=" O VAL m 136 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG m 147 " --> pdb=" O ILE m 137 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 58 through 65 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'm' and resid 146 through 150 removed outlier: 4.263A pdb=" N SER m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'r' and resid 60 through 66 Processing sheet with id= 65, first strand: chain 't' and resid 74 through 80 Processing sheet with id= 66, first strand: chain 'u' and resid 56 through 60 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'u' and resid 9 through 13 removed outlier: 6.705A pdb=" N LEU u 27 " --> pdb=" O ALA u 12 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG u 85 " --> pdb=" O THR u 75 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS u 45 " --> pdb=" O VAL u 74 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG u 46 " --> pdb=" O MET u 104 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'u' and resid 6 through 12 removed outlier: 4.305A pdb=" N HIS u 99 " --> pdb=" O PHE u 11 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 149 through 153 removed outlier: 4.027A pdb=" N LYS v 160 " --> pdb=" O ILE v 152 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 173 through 176 Processing sheet with id= 71, first strand: chain 'w' and resid 139 through 144 removed outlier: 7.626A pdb=" N TYR w 139 " --> pdb=" O ILE w 95 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS w 88 " --> pdb=" O LEU w 125 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG w 94 " --> pdb=" O ASN w 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN w 119 " --> pdb=" O ARG w 94 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE w 118 " --> pdb=" O LEU w 213 " (cutoff:3.500A) 1908 hydrogen bonds defined for protein. 5645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2936 hydrogen bonds 5032 hydrogen bond angles 0 basepair planarities 1120 basepair parallelities 2095 stacking parallelities Total time for adding SS restraints: 328.48 Time building geometry restraints manager: 53.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.36: 45316 1.36 - 1.65: 104175 1.65 - 1.94: 437 1.94 - 2.22: 3 2.22 - 2.51: 4 Bond restraints: 149935 Sorted by residual: bond pdb=" CD ARG r 23 " pdb=" NE ARG r 23 " ideal model delta sigma weight residual 1.458 2.510 -1.052 1.40e-02 5.10e+03 5.64e+03 bond pdb=" C6 A 24280 " pdb=" N1 A 24280 " ideal model delta sigma weight residual 1.351 2.260 -0.909 2.00e-02 2.50e+03 2.07e+03 bond pdb=" N3 A 24280 " pdb=" C4 A 24280 " ideal model delta sigma weight residual 1.344 2.236 -0.892 2.00e-02 2.50e+03 1.99e+03 bond pdb=" N1 A 24280 " pdb=" C2 A 24280 " ideal model delta sigma weight residual 1.339 2.227 -0.888 2.00e-02 2.50e+03 1.97e+03 bond pdb=" C2 A 24280 " pdb=" N3 A 24280 " ideal model delta sigma weight residual 1.331 2.187 -0.856 2.00e-02 2.50e+03 1.83e+03 ... (remaining 149930 not shown) Histogram of bond angle deviations from ideal: 93.09 - 106.77: 27133 106.77 - 120.44: 141915 120.44 - 134.12: 51735 134.12 - 147.80: 72 147.80 - 161.47: 1 Bond angle restraints: 220856 Sorted by residual: angle pdb=" CD ARG r 23 " pdb=" NE ARG r 23 " pdb=" CZ ARG r 23 " ideal model delta sigma weight residual 124.40 161.47 -37.07 1.40e+00 5.10e-01 7.01e+02 angle pdb=" C1' 1MA 21322 " pdb=" N9 1MA 21322 " pdb=" C4 1MA 21322 " ideal model delta sigma weight residual 158.43 118.82 39.61 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C1' 1MA 21322 " pdb=" N9 1MA 21322 " pdb=" C8 1MA 21322 " ideal model delta sigma weight residual 93.44 132.83 -39.39 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C1' 1MA 24415 " pdb=" N9 1MA 24415 " pdb=" C8 1MA 24415 " ideal model delta sigma weight residual 93.44 132.69 -39.25 3.00e+00 1.11e-01 1.71e+02 angle pdb=" C1' 1MA 24415 " pdb=" N9 1MA 24415 " pdb=" C4 1MA 24415 " ideal model delta sigma weight residual 158.43 119.26 39.17 3.00e+00 1.11e-01 1.71e+02 ... (remaining 220851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 77852 35.87 - 71.75: 3620 71.75 - 107.62: 263 107.62 - 143.49: 17 143.49 - 179.37: 48 Dihedral angle restraints: 81800 sinusoidal: 61211 harmonic: 20589 Sorted by residual: dihedral pdb=" CA TYR u 106 " pdb=" C TYR u 106 " pdb=" N PRO u 107 " pdb=" CA PRO u 107 " ideal model delta harmonic sigma weight residual -180.00 -109.40 -70.60 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA THR 3 341 " pdb=" C THR 3 341 " pdb=" N LEU 3 342 " pdb=" CA LEU 3 342 " ideal model delta harmonic sigma weight residual 180.00 131.88 48.12 0 5.00e+00 4.00e-02 9.26e+01 dihedral pdb=" C5' C 24547 " pdb=" C4' C 24547 " pdb=" C3' C 24547 " pdb=" O3' C 24547 " ideal model delta sinusoidal sigma weight residual 147.00 81.07 65.93 1 8.00e+00 1.56e-02 8.88e+01 ... (remaining 81797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 24719 0.110 - 0.219: 2332 0.219 - 0.329: 158 0.329 - 0.439: 27 0.439 - 0.549: 6 Chirality restraints: 27242 Sorted by residual: chirality pdb=" C3' B9H 22786 " pdb=" C4' B9H 22786 " pdb=" O3' B9H 22786 " pdb=" C2' B9H 22786 " both_signs ideal model delta sigma weight residual False -2.48 -1.93 -0.55 2.00e-01 2.50e+01 7.52e+00 chirality pdb=" C1* PSU 24403 " pdb=" O4* PSU 24403 " pdb=" C2* PSU 24403 " pdb=" C5 PSU 24403 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" C3' G 21353 " pdb=" C4' G 21353 " pdb=" O3' G 21353 " pdb=" C2' G 21353 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 27239 not shown) Planarity restraints: 13784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 24550 " -0.091 2.00e-02 2.50e+03 6.42e-01 9.29e+03 pdb=" C4' 7MG 24550 " -0.452 2.00e-02 2.50e+03 pdb=" O4' 7MG 24550 " -0.663 2.00e-02 2.50e+03 pdb=" C3' 7MG 24550 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 7MG 24550 " 0.717 2.00e-02 2.50e+03 pdb=" C2' 7MG 24550 " 0.139 2.00e-02 2.50e+03 pdb=" O2' 7MG 24550 " -1.055 2.00e-02 2.50e+03 pdb=" C1' 7MG 24550 " -0.199 2.00e-02 2.50e+03 pdb=" N9 7MG 24550 " 1.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 22522 " 0.094 2.00e-02 2.50e+03 6.37e-01 9.14e+03 pdb=" C4' 7MG 22522 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 7MG 22522 " 0.622 2.00e-02 2.50e+03 pdb=" C3' 7MG 22522 " -0.597 2.00e-02 2.50e+03 pdb=" O3' 7MG 22522 " -0.722 2.00e-02 2.50e+03 pdb=" C2' 7MG 22522 " -0.132 2.00e-02 2.50e+03 pdb=" O2' 7MG 22522 " 1.076 2.00e-02 2.50e+03 pdb=" C1' 7MG 22522 " 0.201 2.00e-02 2.50e+03 pdb=" N9 7MG 22522 " -0.986 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 24536 " 0.103 2.00e-02 2.50e+03 6.15e-01 8.51e+03 pdb=" C4' OMC 24536 " 0.417 2.00e-02 2.50e+03 pdb=" O4' OMC 24536 " 0.544 2.00e-02 2.50e+03 pdb=" C3' OMC 24536 " -0.616 2.00e-02 2.50e+03 pdb=" O3' OMC 24536 " -0.714 2.00e-02 2.50e+03 pdb=" C2' OMC 24536 " -0.135 2.00e-02 2.50e+03 pdb=" O2' OMC 24536 " 1.080 2.00e-02 2.50e+03 pdb=" C1' OMC 24536 " 0.217 2.00e-02 2.50e+03 pdb=" N1 OMC 24536 " -0.896 2.00e-02 2.50e+03 ... (remaining 13781 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 17 2.02 - 2.74: 20546 2.74 - 3.46: 164880 3.46 - 4.18: 440685 4.18 - 4.90: 628844 Nonbonded interactions: 1254972 Sorted by model distance: nonbonded pdb="MG MG 25259 " pdb="MG MG 25260 " model vdw 1.296 1.300 nonbonded pdb=" CG2 VAL v 96 " pdb=" O GLY v 103 " model vdw 1.828 3.460 nonbonded pdb=" N1 A 24280 " pdb=" NE ARG r 23 " model vdw 1.861 2.600 nonbonded pdb=" N3 A 24280 " pdb=" NE ARG r 23 " model vdw 1.931 2.600 nonbonded pdb=" O6 G 24320 " pdb="MG MG 25331 " model vdw 1.991 2.170 ... (remaining 1254967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3805 5.49 5 Mg 251 5.21 5 S 272 5.16 5 C 72817 2.51 5 N 26099 2.21 5 O 36220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 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: 0.120 Extract box with map and model: 30.740 Check model and map are aligned: 1.450 Convert atoms to be neutral: 0.830 Process input model: 595.150 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 640.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.016 1.052 149935 Z= 0.975 Angle : 1.301 39.608 220856 Z= 0.635 Chirality : 0.067 0.549 27242 Planarity : 0.031 0.642 13784 Dihedral : 17.193 179.366 68513 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.42 % Favored : 92.35 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 1.04 % Twisted General : 0.31 % 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: -3.93 (0.08), residues: 7011 helix: -2.95 (0.08), residues: 2256 sheet: -1.63 (0.15), residues: 980 loop : -2.68 (0.08), residues: 3775 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 815 time to evaluate : 7.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 74 residues processed: 902 average time/residue: 1.3251 time to fit residues: 2056.3593 Evaluate side-chains 727 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 653 time to evaluate : 7.020 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 1.0212 time to fit residues: 154.7050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 2.9990 chunk 812 optimal weight: 0.9990 chunk 450 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 548 optimal weight: 0.8980 chunk 434 optimal weight: 0.0170 chunk 840 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 510 optimal weight: 0.9980 chunk 625 optimal weight: 3.9990 chunk 973 optimal weight: 0.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 183 GLN 3 232 HIS ** 3 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 340 HIS 3 358 GLN 3 370 ASN 3 391 ASN 6 10 ASN 6 66 ASN 6 75 ASN ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN A 40 ASN A 84 HIS ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN B 3 HIS B 42 HIS B 204 GLN B 302 ASN C 50 ASN D 50 GLN G 85 GLN G 141 ASN G 195 HIS G 227 ASN H 20 GLN I 7 ASN I 78 GLN I 116 ASN J 51 HIS J 213 HIS L 67 GLN L 120 GLN M 66 HIS N 3 GLN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN N 112 HIS O 28 ASN Q 87 HIS Q 159 ASN S 131 GLN U 37 HIS U 196 ASN W 19 GLN W 102 GLN X 56 HIS Y 25 HIS Y 28 ASN Y 80 GLN Y 116 HIS Z 44 ASN Z 160 HIS a 7 GLN a 39 GLN a 40 GLN a 75 HIS d 44 GLN d 94 ASN d 95 ASN d 116 GLN e 77 HIS e 135 ASN f 59 HIS g 151 ASN l 6 GLN m 132 ASN r 225 GLN t 107 ASN t 117 GLN v 191 GLN v 250 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.469 149935 Z= 0.231 Angle : 0.783 31.293 220856 Z= 0.430 Chirality : 0.037 0.407 27242 Planarity : 0.008 0.196 13784 Dihedral : 16.494 179.139 53396 Min Nonbonded Distance : 1.239 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.32 % Favored : 94.66 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.69 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.09), residues: 7011 helix: -1.32 (0.10), residues: 2299 sheet: -1.18 (0.16), residues: 958 loop : -2.20 (0.09), residues: 3754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 785 time to evaluate : 7.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 51 residues processed: 855 average time/residue: 1.2725 time to fit residues: 1916.4411 Evaluate side-chains 727 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 676 time to evaluate : 7.082 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 1.0450 time to fit residues: 110.2541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 810 optimal weight: 0.1980 chunk 662 optimal weight: 0.6980 chunk 268 optimal weight: 8.9990 chunk 975 optimal weight: 0.9980 chunk 1053 optimal weight: 5.9990 chunk 868 optimal weight: 2.9990 chunk 967 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 782 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN C 50 ASN C 58 GLN F 100 GLN H 20 GLN H 108 GLN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN N 104 ASN S 131 GLN W 102 GLN d 95 ASN m 132 ASN m 162 ASN t 107 ASN v 101 ASN ** v 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 131 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.466 149935 Z= 0.238 Angle : 0.733 28.774 220856 Z= 0.404 Chirality : 0.035 0.392 27242 Planarity : 0.008 0.218 13784 Dihedral : 16.091 179.221 53396 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.96 % Favored : 94.02 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.09), residues: 7011 helix: -0.43 (0.11), residues: 2294 sheet: -0.93 (0.16), residues: 933 loop : -1.89 (0.09), residues: 3784 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 757 time to evaluate : 6.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 69 residues processed: 838 average time/residue: 1.2482 time to fit residues: 1854.4805 Evaluate side-chains 750 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 681 time to evaluate : 7.055 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 1.0734 time to fit residues: 151.2974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 5.9990 chunk 733 optimal weight: 0.9990 chunk 506 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 465 optimal weight: 7.9990 chunk 654 optimal weight: 6.9990 chunk 978 optimal weight: 0.9990 chunk 1036 optimal weight: 0.7980 chunk 511 optimal weight: 9.9990 chunk 927 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 204 HIS ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN H 20 GLN H 108 GLN I 78 GLN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 HIS J 166 HIS K 92 ASN M 57 ASN ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN S 48 GLN S 131 GLN U 99 GLN Y 34 GLN a 39 GLN d 95 ASN e 135 ASN l 4 HIS m 86 GLN m 132 ASN ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 131 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.471 149935 Z= 0.330 Angle : 0.779 28.768 220856 Z= 0.423 Chirality : 0.038 0.374 27242 Planarity : 0.009 0.171 13784 Dihedral : 16.159 179.311 53396 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.44 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.09), residues: 7011 helix: -0.18 (0.11), residues: 2285 sheet: -0.92 (0.16), residues: 981 loop : -1.78 (0.09), residues: 3745 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 683 time to evaluate : 7.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 74 residues processed: 779 average time/residue: 1.2735 time to fit residues: 1764.0486 Evaluate side-chains 724 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 650 time to evaluate : 7.176 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 1.1052 time to fit residues: 165.4001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 1.9990 chunk 588 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 771 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 chunk 884 optimal weight: 8.9990 chunk 716 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 529 optimal weight: 5.9990 chunk 930 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 50 ASN H 20 GLN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 HIS K 92 ASN ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 46 GLN d 95 ASN l 4 HIS ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.468 149935 Z= 0.331 Angle : 0.779 28.697 220856 Z= 0.423 Chirality : 0.038 0.380 27242 Planarity : 0.008 0.157 13784 Dihedral : 16.160 178.913 53396 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % 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: -1.53 (0.10), residues: 7011 helix: -0.03 (0.11), residues: 2285 sheet: -0.86 (0.16), residues: 955 loop : -1.72 (0.09), residues: 3771 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 680 time to evaluate : 7.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 79 residues processed: 781 average time/residue: 1.2412 time to fit residues: 1723.2978 Evaluate side-chains 726 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 647 time to evaluate : 7.103 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 1.0668 time to fit residues: 168.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 20.0000 chunk 933 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 chunk 608 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 1037 optimal weight: 9.9990 chunk 861 optimal weight: 0.0980 chunk 480 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 83 HIS ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN D 50 GLN J 51 HIS J 95 HIS ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN N 98 ASN Q 19 GLN Q 40 GLN Y 118 GLN l 4 HIS ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.468 149935 Z= 0.426 Angle : 0.840 28.762 220856 Z= 0.449 Chirality : 0.042 0.385 27242 Planarity : 0.009 0.152 13784 Dihedral : 16.335 179.790 53396 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.12 % Favored : 92.79 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 7011 helix: -0.09 (0.11), residues: 2261 sheet: -0.93 (0.16), residues: 986 loop : -1.74 (0.09), residues: 3764 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 660 time to evaluate : 6.915 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 80 residues processed: 761 average time/residue: 1.2639 time to fit residues: 1714.1690 Evaluate side-chains 721 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 641 time to evaluate : 7.221 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 1.0605 time to fit residues: 170.1429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 590 optimal weight: 1.9990 chunk 757 optimal weight: 0.9980 chunk 586 optimal weight: 0.6980 chunk 873 optimal weight: 7.9990 chunk 579 optimal weight: 4.9990 chunk 1033 optimal weight: 9.9990 chunk 646 optimal weight: 0.9990 chunk 629 optimal weight: 0.5980 chunk 477 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN E 33 GLN H 20 GLN H 108 GLN I 163 GLN J 143 GLN ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN N 98 ASN N 104 ASN U 145 ASN Y 10 ASN m 86 GLN m 132 ASN w 131 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.465 149935 Z= 0.229 Angle : 0.726 28.398 220856 Z= 0.402 Chirality : 0.034 0.403 27242 Planarity : 0.008 0.141 13784 Dihedral : 15.926 178.946 53396 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 7011 helix: 0.40 (0.11), residues: 2266 sheet: -0.74 (0.17), residues: 929 loop : -1.55 (0.09), residues: 3816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 704 time to evaluate : 7.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 733 average time/residue: 1.2959 time to fit residues: 1687.9706 Evaluate side-chains 679 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 658 time to evaluate : 6.847 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 1.0430 time to fit residues: 49.9785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 7.9990 chunk 412 optimal weight: 10.0000 chunk 617 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 656 optimal weight: 5.9990 chunk 703 optimal weight: 1.9990 chunk 510 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 812 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN H 108 GLN J 95 HIS ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN N 104 ASN a 66 ASN a 141 HIS ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 80 HIS w 131 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.466 149935 Z= 0.421 Angle : 0.824 28.695 220856 Z= 0.441 Chirality : 0.041 0.371 27242 Planarity : 0.009 0.146 13784 Dihedral : 16.146 179.320 53396 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.84 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % 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: -1.37 (0.10), residues: 7011 helix: 0.16 (0.11), residues: 2269 sheet: -0.79 (0.16), residues: 966 loop : -1.63 (0.09), residues: 3776 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 654 time to evaluate : 7.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 57 residues processed: 700 average time/residue: 1.2339 time to fit residues: 1541.9127 Evaluate side-chains 690 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 633 time to evaluate : 7.030 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 1.0556 time to fit residues: 122.7849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 5.9990 chunk 989 optimal weight: 3.9990 chunk 903 optimal weight: 8.9990 chunk 962 optimal weight: 0.9990 chunk 579 optimal weight: 2.9990 chunk 419 optimal weight: 6.9990 chunk 756 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 870 optimal weight: 0.7980 chunk 910 optimal weight: 3.9990 chunk 959 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN J 95 HIS J 143 GLN ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN N 104 ASN ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 ASN ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.466 149935 Z= 0.301 Angle : 0.787 43.344 220856 Z= 0.426 Chirality : 0.038 0.373 27242 Planarity : 0.009 0.272 13784 Dihedral : 16.118 179.763 53396 Min Nonbonded Distance : 1.121 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.71 % Favored : 93.24 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % 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: -1.31 (0.10), residues: 7011 helix: 0.22 (0.11), residues: 2276 sheet: -0.77 (0.16), residues: 965 loop : -1.61 (0.09), residues: 3770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 656 time to evaluate : 7.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 677 average time/residue: 1.2880 time to fit residues: 1548.4745 Evaluate side-chains 666 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 640 time to evaluate : 6.736 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 1.0991 time to fit residues: 61.7802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 8.9990 chunk 1018 optimal weight: 7.9990 chunk 621 optimal weight: 5.9990 chunk 483 optimal weight: 0.0170 chunk 707 optimal weight: 0.9980 chunk 1067 optimal weight: 3.9990 chunk 982 optimal weight: 0.7980 chunk 850 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 656 optimal weight: 3.9990 chunk 521 optimal weight: 3.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN H 20 GLN J 51 HIS ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 98 ASN N 104 ASN N 155 HIS ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 ASN d 27 HIS l 95 HIS ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN w 131 ASN w 248 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.466 149935 Z= 0.272 Angle : 0.771 34.511 220856 Z= 0.421 Chirality : 0.036 0.377 27242 Planarity : 0.008 0.150 13784 Dihedral : 16.088 179.426 53396 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.58 % Favored : 93.39 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.10), residues: 7011 helix: 0.31 (0.11), residues: 2269 sheet: -0.71 (0.16), residues: 957 loop : -1.58 (0.09), residues: 3785 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14022 Ramachandran restraints generated. 7011 Oldfield, 0 Emsley, 7011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 661 time to evaluate : 7.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 676 average time/residue: 1.2562 time to fit residues: 1508.6367 Evaluate side-chains 661 residues out of total 6131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 646 time to evaluate : 6.948 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 1.0956 time to fit residues: 38.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 10.0000 chunk 905 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 784 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 851 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 874 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 174 GLN ** 6 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN J 177 ASN ** N 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN N 98 ASN N 104 ASN ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 66 ASN ** f 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN l 95 HIS m 140 ASN ** r 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 24 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074625 restraints weight = 285613.362| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.05 r_work: 0.3009 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2972 rms_B_bonded: 1.43 restraints_weight: 0.1250 r_work: 0.2947 rms_B_bonded: 1.84 restraints_weight: 0.0625 r_work: 0.2913 rms_B_bonded: 2.45 restraints_weight: 0.0312 r_work: 0.2866 rms_B_bonded: 3.36 restraints_weight: 0.0156 r_work: 0.2796 rms_B_bonded: 4.82 restraints_weight: 0.0078 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.467 149935 Z= 0.601 Angle : 0.963 31.938 220856 Z= 0.500 Chirality : 0.050 0.398 27242 Planarity : 0.010 0.149 13784 Dihedral : 16.607 179.864 53396 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.75 % Favored : 92.17 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.01 % Twisted Proline : 0.35 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.09), residues: 7011 helix: -0.20 (0.11), residues: 2269 sheet: -0.96 (0.16), residues: 975 loop : -1.78 (0.09), residues: 3767 =============================================================================== Job complete usr+sys time: 28396.14 seconds wall clock time: 495 minutes 18.11 seconds (29718.11 seconds total)