Starting phenix.real_space_refine (version: dev) on Fri Apr 8 10:04:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ase_11893/04_2022/7ase_11893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ase_11893/04_2022/7ase_11893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ase_11893/04_2022/7ase_11893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ase_11893/04_2022/7ase_11893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ase_11893/04_2022/7ase_11893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ase_11893/04_2022/7ase_11893_updated.pdb" } resolution = 3.33 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= 0.000 sd= 0.005 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 "f PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 136847 Number of models: 1 Model: "" Number of chains: 54 Chain: "f" Number of atoms: 12257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 12257 Classifications: {'peptide': 1523} Link IDs: {'CIS': 45, 'PTRANS': 49, 'TRANS': 1424, 'PCIS': 4} Chain breaks: 1 Chain: "1" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1606 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna3p_pur': 35, 'rna2p_pyr': 4, 'rna3p_pyr': 28} Link IDs: {'rna3p': 63, 'rna2p': 11} Chain: "0" Number of atoms: 45795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2150, 45795 Inner-chain residues flagged as termini: ['pdbres=" A 0 974 "', 'pdbres=" U 0 975 "', 'pdbres=" C 01066 "', 'pdbres=" C 01179 "', 'pdbres=" C 01850 "'] Classifications: {'RNA': 2150} Modifications used: {'5*END': 6, 'rna2p_pur': 201, 'rna3p_pur': 921, 'rna2p_pyr': 194, 'rna3p_pyr': 834} Link IDs: {'rna3p': 1755, 'rna2p': 394} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 3 Chain: "y" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "s" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2365 Classifications: {'peptide': 295} Link IDs: {'CIS': 7, 'PTRANS': 11, 'TRANS': 275, 'PCIS': 1} Chain: "j" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "n" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1796 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 219} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "p" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2405 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain: "r" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1113 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain: "u" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1108 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'CIS': 4, 'TRANS': 127} Chain: "m" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1116 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "Z" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1404 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "o" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1493 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "q" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1670 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "R" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1143 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "S" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "t" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "U" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "v" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1011 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "X" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1212 Classifications: {'peptide': 148} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 138} Chain: "B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1483 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain: "F" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1658 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain: "d" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1726 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "g" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 635 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "a" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 553 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "J" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1358 Classifications: {'peptide': 173} Link IDs: {'CIS': 9, 'PTRANS': 6, 'TRANS': 157} Chain: "h" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "5" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3245 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 21, 'CIS': 1, 'TRANS': 397, 'PCIS': 1} Chain: "P" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1983 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 992 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'CIS': 7, 'TRANS': 110} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 784 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1587 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 2, 'TRANS': 197} Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 780 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "O" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1116 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "b" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1019 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "c" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "V" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 789 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "w" 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': 4, 'CIS': 1, 'TRANS': 141} Chain: "E" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3119 Classifications: {'peptide': 391} Link IDs: {'CIS': 20, 'PTRANS': 7, 'TRANS': 363} Chain: "Y" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1387 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'CIS': 1, 'TRANS': 164} Chain: "Q" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 462 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'TRANS': 56} Chain: "D" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 294 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "G" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2414 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'CIS': 6, 'TRANS': 288} Chain: "K" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1566 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'CIS': 2, 'TRANS': 188} Chain: "T" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 123} Chain: "C" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5630 Classifications: {'peptide': 696} Link IDs: {'CIS': 39, 'PTRANS': 14, 'TRANS': 641, 'PCIS': 1} Chain: "8" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4596 Classifications: {'peptide': 576} Link IDs: {'CIS': 19, 'PTRANS': 18, 'TRANS': 535, 'PCIS': 3} Chain: "W" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1781 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'CIS': 2, 'TRANS': 209} Chain: "I" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2770 Classifications: {'peptide': 344} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 333} Chain: "H" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2388 Classifications: {'peptide': 297} Link IDs: {'CIS': 8, 'PTRANS': 12, 'TRANS': 276} Chain: "A" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3891 Classifications: {'peptide': 483} Link IDs: {'CIS': 5, 'PTRANS': 22, 'TRANS': 455} Chain: "l" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2038 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 13, 'TRANS': 244} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GNP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 65044 SG CYS n 288 64.278 202.612 119.295 1.00 0.00 S ATOM 65064 SG CYS n 291 60.735 202.413 116.856 1.00 0.00 S ATOM 65214 SG CYS n 309 63.516 205.186 120.137 1.00 0.00 S Time building chain proxies: 54.86, per 1000 atoms: 0.40 Number of scatterers: 136847 At special positions: 0 Unit cell: (309.1, 289.3, 266.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 469 16.00 P 2220 15.00 Mg 1 11.99 O 31800 8.00 N 24887 7.00 C 77469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS t 78 " - pdb=" SG CYS t 81 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 42.01 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN n 401 " pdb="ZN ZN n 401 " - pdb=" SG CYS n 291 " pdb="ZN ZN n 401 " - pdb=" SG CYS n 309 " pdb="ZN ZN n 401 " - pdb=" SG CYS n 288 " 22178 Ramachandran restraints generated. 11089 Oldfield, 0 Emsley, 11089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB TYR f 296 " pdb=" CB TYR f 305 " pdb=" CB TYR f 772 " pdb=" CB TYR E 281 " pdb=" CB SER C 429 " pdb=" CB PRO I 337 " pdb=" CB TYR I 350 " Number of C-beta restraints generated: 21064 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: 389 helices and 83 sheets defined 47.9% alpha, 11.3% beta 559 base pairs and 1017 stacking pairs defined. Time for finding SS restraints: 63.63 Creating SS restraints... Processing helix chain 'f' and resid 1 through 16 removed outlier: 4.696A pdb=" N TYR f 5 " --> pdb=" O MET f 1 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 39 removed outlier: 4.073A pdb=" N VAL f 33 " --> pdb=" O ARG f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 79 removed outlier: 6.333A pdb=" N ALA f 60 " --> pdb=" O THR f 56 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG f 61 " --> pdb=" O ILE f 57 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER f 79 " --> pdb=" O ARG f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 109 removed outlier: 3.845A pdb=" N GLU f 94 " --> pdb=" O ALA f 90 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG f 95 " --> pdb=" O ASP f 91 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU f 96 " --> pdb=" O GLU f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 112 through 131 removed outlier: 4.186A pdb=" N VAL f 116 " --> pdb=" O ILE f 112 " (cutoff:3.500A) Processing helix chain 'f' and resid 139 through 144 removed outlier: 4.757A pdb=" N LEU f 143 " --> pdb=" O MET f 139 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER f 144 " --> pdb=" O PHE f 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 139 through 144' Processing helix chain 'f' and resid 152 through 162 removed outlier: 3.559A pdb=" N LEU f 156 " --> pdb=" O ASP f 152 " (cutoff:3.500A) Processing helix chain 'f' and resid 177 through 191 removed outlier: 3.568A pdb=" N GLN f 181 " --> pdb=" O ILE f 177 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N CYS f 189 " --> pdb=" O TYR f 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG f 190 " --> pdb=" O ASP f 186 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY f 191 " --> pdb=" O MET f 187 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 227 removed outlier: 5.102A pdb=" N MET f 215 " --> pdb=" O ALA f 211 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU f 217 " --> pdb=" O LEU f 213 " (cutoff:3.500A) Processing helix chain 'f' and resid 246 through 257 removed outlier: 7.412A pdb=" N THR f 250 " --> pdb=" O GLU f 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR f 251 " --> pdb=" O ALA f 247 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL f 252 " --> pdb=" O PHE f 248 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP f 255 " --> pdb=" O TYR f 251 " (cutoff:3.500A) Proline residue: f 257 - end of helix Processing helix chain 'f' and resid 274 through 289 Proline residue: f 281 - end of helix removed outlier: 3.562A pdb=" N THR f 287 " --> pdb=" O ALA f 283 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS f 288 " --> pdb=" O ALA f 284 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP f 289 " --> pdb=" O ASN f 285 " (cutoff:3.500A) Processing helix chain 'f' and resid 668 through 681 removed outlier: 3.856A pdb=" N ALA f 672 " --> pdb=" O SER f 668 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN f 678 " --> pdb=" O GLY f 674 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN f 679 " --> pdb=" O ASN f 675 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS f 680 " --> pdb=" O SER f 676 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR f 681 " --> pdb=" O ALA f 677 " (cutoff:3.500A) Processing helix chain 'f' and resid 684 through 696 removed outlier: 5.824A pdb=" N ASN f 688 " --> pdb=" O ALA f 684 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS f 689 " --> pdb=" O LYS f 685 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU f 690 " --> pdb=" O LYS f 686 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG f 695 " --> pdb=" O HIS f 691 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN f 696 " --> pdb=" O ALA f 692 " (cutoff:3.500A) Processing helix chain 'f' and resid 725 through 730 removed outlier: 4.661A pdb=" N LEU f 729 " --> pdb=" O GLN f 725 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU f 730 " --> pdb=" O MET f 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 725 through 730' Processing helix chain 'f' and resid 737 through 763 removed outlier: 5.866A pdb=" N THR f 741 " --> pdb=" O HIS f 737 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG f 758 " --> pdb=" O ALA f 754 " (cutoff:3.500A) Processing helix chain 'f' and resid 776 through 794 removed outlier: 5.054A pdb=" N THR f 780 " --> pdb=" O GLY f 776 " (cutoff:3.500A) Proline residue: f 783 - end of helix removed outlier: 3.608A pdb=" N LEU f 791 " --> pdb=" O GLU f 787 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL f 793 " --> pdb=" O TRP f 789 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA f 794 " --> pdb=" O ARG f 790 " (cutoff:3.500A) Processing helix chain 'f' and resid 808 through 824 removed outlier: 4.728A pdb=" N LEU f 812 " --> pdb=" O GLU f 808 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS f 813 " --> pdb=" O ASP f 809 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP f 823 " --> pdb=" O SER f 819 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER f 824 " --> pdb=" O LYS f 820 " (cutoff:3.500A) Processing helix chain 'f' and resid 834 through 845 removed outlier: 5.244A pdb=" N ASN f 838 " --> pdb=" O PHE f 834 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN f 839 " --> pdb=" O HIS f 835 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE f 840 " --> pdb=" O VAL f 836 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL f 841 " --> pdb=" O ILE f 837 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU f 842 " --> pdb=" O ASN f 838 " (cutoff:3.500A) Processing helix chain 'f' and resid 853 through 860 removed outlier: 3.522A pdb=" N ALA f 860 " --> pdb=" O PRO f 856 " (cutoff:3.500A) Processing helix chain 'f' and resid 866 through 909 removed outlier: 4.261A pdb=" N ARG f 870 " --> pdb=" O ILE f 866 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET f 883 " --> pdb=" O SER f 879 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU f 889 " --> pdb=" O ILE f 885 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN f 900 " --> pdb=" O LEU f 896 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP f 901 " --> pdb=" O GLN f 897 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA f 908 " --> pdb=" O GLU f 904 " (cutoff:3.500A) Processing helix chain 'f' and resid 918 through 934 Proline residue: f 922 - end of helix removed outlier: 4.405A pdb=" N VAL f 934 " --> pdb=" O HIS f 930 " (cutoff:3.500A) Processing helix chain 'f' and resid 944 through 955 removed outlier: 3.996A pdb=" N SER f 952 " --> pdb=" O ASP f 948 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA f 953 " --> pdb=" O THR f 949 " (cutoff:3.500A) Processing helix chain 'f' and resid 960 through 976 removed outlier: 3.858A pdb=" N TYR f 964 " --> pdb=" O PRO f 960 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN f 965 " --> pdb=" O ASP f 961 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS f 966 " --> pdb=" O SER f 962 " (cutoff:3.500A) Processing helix chain 'f' and resid 999 through 1006 removed outlier: 5.377A pdb=" N ILE f1003 " --> pdb=" O MET f 999 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N HIS f1004 " --> pdb=" O LEU f1000 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY f1006 " --> pdb=" O LEU f1002 " (cutoff:3.500A) Processing helix chain 'f' and resid 1026 through 1039 removed outlier: 3.981A pdb=" N ARG f1030 " --> pdb=" O ASP f1026 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU f1031 " --> pdb=" O ASN f1027 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP f1034 " --> pdb=" O ARG f1030 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE f1035 " --> pdb=" O GLU f1031 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL f1036 " --> pdb=" O LEU f1032 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY f1038 " --> pdb=" O ASP f1034 " (cutoff:3.500A) Processing helix chain 'f' and resid 1052 through 1065 removed outlier: 3.931A pdb=" N SER f1056 " --> pdb=" O LYS f1052 " (cutoff:3.500A) Processing helix chain 'f' and resid 1080 through 1095 removed outlier: 4.061A pdb=" N GLN f1084 " --> pdb=" O ALA f1080 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR f1093 " --> pdb=" O VAL f1089 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY f1094 " --> pdb=" O CYS f1090 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER f1095 " --> pdb=" O ALA f1091 " (cutoff:3.500A) Processing helix chain 'f' and resid 1127 through 1137 removed outlier: 3.645A pdb=" N GLU f1132 " --> pdb=" O PRO f1128 " (cutoff:3.500A) Processing helix chain 'f' and resid 1138 through 1147 removed outlier: 5.876A pdb=" N ASP f1142 " --> pdb=" O PRO f1138 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TRP f1143 " --> pdb=" O LYS f1139 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL f1144 " --> pdb=" O TYR f1140 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU f1145 " --> pdb=" O THR f1141 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU f1146 " --> pdb=" O ASP f1142 " (cutoff:3.500A) Processing helix chain 'f' and resid 1154 through 1162 removed outlier: 4.715A pdb=" N MET f1158 " --> pdb=" O GLU f1154 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER f1160 " --> pdb=" O HIS f1156 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASN f1161 " --> pdb=" O SER f1157 " (cutoff:3.500A) Processing helix chain 'f' and resid 1163 through 1174 removed outlier: 5.274A pdb=" N TRP f1167 " --> pdb=" O ASN f1163 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU f1168 " --> pdb=" O GLY f1164 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG f1169 " --> pdb=" O ASP f1165 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE f1170 " --> pdb=" O VAL f1166 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU f1173 " --> pdb=" O ARG f1169 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU f1174 " --> pdb=" O ILE f1170 " (cutoff:3.500A) Processing helix chain 'f' and resid 1189 through 1207 removed outlier: 3.653A pdb=" N TRP f1194 " --> pdb=" O GLN f1190 " (cutoff:3.500A) Processing helix chain 'f' and resid 1226 through 1231 removed outlier: 5.078A pdb=" N ARG f1230 " --> pdb=" O LYS f1226 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TRP f1231 " --> pdb=" O SER f1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1226 through 1231' Processing helix chain 'f' and resid 1270 through 1277 Processing helix chain 'f' and resid 1288 through 1304 removed outlier: 3.649A pdb=" N LEU f1293 " --> pdb=" O GLU f1289 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL f1304 " --> pdb=" O LYS f1300 " (cutoff:3.500A) Processing helix chain 'f' and resid 1312 through 1331 removed outlier: 7.088A pdb=" N LYS f1316 " --> pdb=" O LEU f1312 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU f1326 " --> pdb=" O LEU f1322 " (cutoff:3.500A) Proline residue: f1327 - end of helix Processing helix chain 'f' and resid 1340 through 1362 removed outlier: 4.239A pdb=" N GLN f1344 " --> pdb=" O GLU f1340 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR f1345 " --> pdb=" O ARG f1341 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS f1361 " --> pdb=" O ALA f1357 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU f1362 " --> pdb=" O TYR f1358 " (cutoff:3.500A) Processing helix chain 'f' and resid 1381 through 1402 removed outlier: 4.448A pdb=" N ALA f1385 " --> pdb=" O SER f1381 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS f1396 " --> pdb=" O THR f1392 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU f1401 " --> pdb=" O LEU f1397 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA f1402 " --> pdb=" O ASN f1398 " (cutoff:3.500A) Processing helix chain 'f' and resid 1403 through 1436 removed outlier: 3.866A pdb=" N HIS f1407 " --> pdb=" O LEU f1403 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU f1436 " --> pdb=" O GLU f1432 " (cutoff:3.500A) Processing helix chain 'f' and resid 1472 through 1490 removed outlier: 5.410A pdb=" N ARG f1476 " --> pdb=" O ARG f1472 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU f1477 " --> pdb=" O GLN f1473 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS f1478 " --> pdb=" O PHE f1474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU f1480 " --> pdb=" O ARG f1476 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN f1481 " --> pdb=" O GLU f1477 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU f1486 " --> pdb=" O VAL f1482 " (cutoff:3.500A) Processing helix chain 'f' and resid 1500 through 1526 removed outlier: 7.108A pdb=" N CYS f1504 " --> pdb=" O GLU f1500 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY f1505 " --> pdb=" O SER f1501 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS f1524 " --> pdb=" O SER f1520 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR f1525 " --> pdb=" O ARG f1521 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN f1526 " --> pdb=" O TYR f1522 " (cutoff:3.500A) Processing helix chain 'f' and resid 1527 through 1555 removed outlier: 4.110A pdb=" N LYS f1554 " --> pdb=" O GLU f1550 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN f1555 " --> pdb=" O SER f1551 " (cutoff:3.500A) Processing helix chain 'f' and resid 1588 through 1596 removed outlier: 4.296A pdb=" N PHE f1592 " --> pdb=" O VAL f1588 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR f1593 " --> pdb=" O LEU f1589 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE f1594 " --> pdb=" O PRO f1590 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY f1596 " --> pdb=" O PHE f1592 " (cutoff:3.500A) Processing helix chain 'f' and resid 1602 through 1617 removed outlier: 3.848A pdb=" N VAL f1606 " --> pdb=" O GLU f1602 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU f1614 " --> pdb=" O MET f1610 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS f1615 " --> pdb=" O GLU f1611 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU f1616 " --> pdb=" O ASP f1612 " (cutoff:3.500A) Processing helix chain 'f' and resid 1620 through 1628 removed outlier: 4.668A pdb=" N GLY f1628 " --> pdb=" O ALA f1624 " (cutoff:3.500A) Processing helix chain 'f' and resid 1637 through 1651 Processing helix chain 'f' and resid 1660 through 1665 Processing helix chain 'f' and resid 1683 through 1694 removed outlier: 3.880A pdb=" N GLY f1692 " --> pdb=" O ARG f1688 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG f1693 " --> pdb=" O GLN f1689 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA f1694 " --> pdb=" O MET f1690 " (cutoff:3.500A) Processing helix chain 'f' and resid 1711 through 1720 removed outlier: 4.981A pdb=" N ILE f1715 " --> pdb=" O THR f1711 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS f1716 " --> pdb=" O MET f1712 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG f1717 " --> pdb=" O ARG f1713 " (cutoff:3.500A) Processing helix chain 'f' and resid 1733 through 1749 removed outlier: 3.744A pdb=" N ASN f1737 " --> pdb=" O ASP f1733 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN f1747 " --> pdb=" O LEU f1743 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR f1748 " --> pdb=" O TYR f1744 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU f1749 " --> pdb=" O ASP f1745 " (cutoff:3.500A) Processing helix chain 'f' and resid 1752 through 1771 removed outlier: 3.646A pdb=" N ALA f1756 " --> pdb=" O LEU f1752 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE f1770 " --> pdb=" O ALA f1766 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL f1771 " --> pdb=" O GLU f1767 " (cutoff:3.500A) Processing helix chain 'f' and resid 1775 through 1782 removed outlier: 3.955A pdb=" N ARG f1779 " --> pdb=" O PHE f1775 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN f1780 " --> pdb=" O PHE f1776 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER f1781 " --> pdb=" O GLN f1777 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL f1782 " --> pdb=" O GLY f1778 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1775 through 1782' Processing helix chain 'f' and resid 1790 through 1805 removed outlier: 4.490A pdb=" N TRP f1794 " --> pdb=" O PHE f1790 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG f1804 " --> pdb=" O GLY f1800 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU f1805 " --> pdb=" O TYR f1801 " (cutoff:3.500A) Processing helix chain 'f' and resid 1821 through 1834 removed outlier: 3.592A pdb=" N VAL f1826 " --> pdb=" O ASP f1822 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE f1827 " --> pdb=" O ALA f1823 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL f1832 " --> pdb=" O ARG f1828 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY f1833 " --> pdb=" O GLU f1829 " (cutoff:3.500A) Processing helix chain 'f' and resid 1839 through 1850 removed outlier: 4.496A pdb=" N LEU f1843 " --> pdb=" O PHE f1839 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS f1850 " --> pdb=" O GLY f1846 " (cutoff:3.500A) Processing helix chain 'f' and resid 1856 through 1867 removed outlier: 3.584A pdb=" N LEU f1861 " --> pdb=" O TYR f1857 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL f1865 " --> pdb=" O LEU f1861 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP f1867 " --> pdb=" O SER f1863 " (cutoff:3.500A) Processing helix chain 'y' and resid 42 through 55 removed outlier: 4.172A pdb=" N ILE y 46 " --> pdb=" O PRO y 42 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 4.622A pdb=" N ILE y 62 " --> pdb=" O ASP y 58 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N SER y 63 " --> pdb=" O GLU y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 58 through 63' Processing helix chain 'y' and resid 85 through 92 removed outlier: 3.974A pdb=" N LEU y 89 " --> pdb=" O ASP y 85 " (cutoff:3.500A) Processing helix chain 'y' and resid 94 through 102 removed outlier: 3.641A pdb=" N LYS y 98 " --> pdb=" O PRO y 94 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU y 101 " --> pdb=" O ARG y 97 " (cutoff:3.500A) Processing helix chain 'y' and resid 110 through 125 removed outlier: 4.117A pdb=" N VAL y 114 " --> pdb=" O ALA y 110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG y 120 " --> pdb=" O GLU y 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN y 121 " --> pdb=" O ARG y 117 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS y 122 " --> pdb=" O ARG y 118 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS y 123 " --> pdb=" O ASN y 119 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE y 124 " --> pdb=" O ARG y 120 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG y 125 " --> pdb=" O ASN y 121 " (cutoff:3.500A) Processing helix chain 's' and resid 102 through 114 removed outlier: 3.502A pdb=" N ARG s 108 " --> pdb=" O LYS s 104 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS s 113 " --> pdb=" O PHE s 109 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU s 114 " --> pdb=" O LEU s 110 " (cutoff:3.500A) Processing helix chain 's' and resid 204 through 209 removed outlier: 5.175A pdb=" N VAL s 208 " --> pdb=" O SER s 204 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR s 209 " --> pdb=" O LYS s 205 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 204 through 209' Processing helix chain 's' and resid 211 through 238 removed outlier: 7.079A pdb=" N GLU s 215 " --> pdb=" O LYS s 211 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS s 216 " --> pdb=" O GLU s 212 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS s 232 " --> pdb=" O SER s 228 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU s 236 " --> pdb=" O HIS s 232 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS s 237 " --> pdb=" O VAL s 233 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY s 238 " --> pdb=" O ALA s 234 " (cutoff:3.500A) Processing helix chain 's' and resid 240 through 257 removed outlier: 3.959A pdb=" N ALA s 244 " --> pdb=" O PRO s 240 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR s 250 " --> pdb=" O GLU s 246 " (cutoff:3.500A) Proline residue: s 251 - end of helix removed outlier: 4.423A pdb=" N GLN s 256 " --> pdb=" O LEU s 252 " (cutoff:3.500A) Proline residue: s 257 - end of helix Processing helix chain 's' and resid 267 through 274 removed outlier: 4.198A pdb=" N ASN s 271 " --> pdb=" O GLU s 267 " (cutoff:3.500A) Processing helix chain 's' and resid 284 through 298 removed outlier: 4.833A pdb=" N GLN s 288 " --> pdb=" O PRO s 284 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS s 289 " --> pdb=" O GLU s 285 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR s 298 " --> pdb=" O THR s 294 " (cutoff:3.500A) Processing helix chain 's' and resid 318 through 331 removed outlier: 4.593A pdb=" N ALA s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU s 329 " --> pdb=" O ASP s 325 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG s 331 " --> pdb=" O LEU s 327 " (cutoff:3.500A) Processing helix chain 's' and resid 363 through 378 removed outlier: 4.030A pdb=" N ARG s 367 " --> pdb=" O GLU s 363 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG s 368 " --> pdb=" O GLU s 364 " (cutoff:3.500A) Processing helix chain 's' and resid 275 through 280 removed outlier: 6.802A pdb=" N LEU s 278 " --> pdb=" O GLU s 275 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY s 279 " --> pdb=" O GLY s 276 " (cutoff:3.500A) Proline residue: s 280 - end of helix No H-bonds generated for 'chain 's' and resid 275 through 280' Processing helix chain 's' and resid 379 through 384 removed outlier: 4.973A pdb=" N LYS s 382 " --> pdb=" O GLU s 379 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG s 383 " --> pdb=" O ILE s 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY s 384 " --> pdb=" O ALA s 381 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 379 through 384' Processing helix chain 'j' and resid 95 through 102 removed outlier: 3.649A pdb=" N LYS j 99 " --> pdb=" O MET j 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 123 through 128 removed outlier: 4.993A pdb=" N ALA j 127 " --> pdb=" O VAL j 124 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY j 128 " --> pdb=" O CYS j 125 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 139 removed outlier: 3.725A pdb=" N GLU n 138 " --> pdb=" O ARG n 134 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS n 139 " --> pdb=" O ARG n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 140 through 160 Proline residue: n 150 - end of helix Processing helix chain 'n' and resid 164 through 178 removed outlier: 3.677A pdb=" N GLU n 178 " --> pdb=" O LYS n 174 " (cutoff:3.500A) Processing helix chain 'n' and resid 179 through 193 removed outlier: 3.590A pdb=" N MET n 187 " --> pdb=" O ASN n 183 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE n 193 " --> pdb=" O ARG n 189 " (cutoff:3.500A) Processing helix chain 'n' and resid 199 through 204 Processing helix chain 'n' and resid 227 through 236 removed outlier: 3.851A pdb=" N PHE n 235 " --> pdb=" O ILE n 231 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN n 236 " --> pdb=" O CYS n 232 " (cutoff:3.500A) Processing helix chain 'n' and resid 238 through 251 removed outlier: 4.313A pdb=" N VAL n 242 " --> pdb=" O PRO n 238 " (cutoff:3.500A) Processing helix chain 'n' and resid 274 through 285 removed outlier: 3.849A pdb=" N LEU n 278 " --> pdb=" O PHE n 274 " (cutoff:3.500A) Processing helix chain 'n' and resid 332 through 340 removed outlier: 6.204A pdb=" N ALA n 336 " --> pdb=" O LYS n 332 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG n 337 " --> pdb=" O ARG n 333 " (cutoff:3.500A) Processing helix chain 'p' and resid 279 through 284 removed outlier: 3.756A pdb=" N LYS p 283 " --> pdb=" O GLN p 279 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS p 284 " --> pdb=" O GLN p 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 279 through 284' Processing helix chain 'r' and resid 47 through 59 removed outlier: 4.350A pdb=" N ALA r 57 " --> pdb=" O LYS r 53 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL r 58 " --> pdb=" O ILE r 54 " (cutoff:3.500A) Processing helix chain 'r' and resid 63 through 68 removed outlier: 4.305A pdb=" N ALA r 67 " --> pdb=" O SER r 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG r 68 " --> pdb=" O ARG r 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 63 through 68' Processing helix chain 'r' and resid 80 through 102 Processing helix chain 'r' and resid 104 through 119 removed outlier: 3.989A pdb=" N LYS r 108 " --> pdb=" O ASN r 104 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP r 119 " --> pdb=" O TYR r 115 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 35 removed outlier: 3.946A pdb=" N ALA u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N MET u 33 " --> pdb=" O PHE u 29 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL u 34 " --> pdb=" O ALA u 30 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS u 35 " --> pdb=" O LEU u 31 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 48 removed outlier: 3.639A pdb=" N PHE u 41 " --> pdb=" O VAL u 37 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA u 42 " --> pdb=" O GLY u 38 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR u 43 " --> pdb=" O ILE u 39 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N MET u 44 " --> pdb=" O ARG u 40 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL u 45 " --> pdb=" O PHE u 41 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS u 46 " --> pdb=" O ALA u 42 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS u 48 " --> pdb=" O MET u 44 " (cutoff:3.500A) Processing helix chain 'u' and resid 64 through 75 removed outlier: 4.343A pdb=" N ILE u 68 " --> pdb=" O GLU u 64 " (cutoff:3.500A) Proline residue: u 75 - end of helix Processing helix chain 'u' and resid 100 through 119 removed outlier: 5.840A pdb=" N VAL u 104 " --> pdb=" O THR u 100 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASP u 105 " --> pdb=" O SER u 101 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR u 106 " --> pdb=" O ALA u 102 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU u 108 " --> pdb=" O VAL u 104 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG u 109 " --> pdb=" O ASP u 105 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN u 118 " --> pdb=" O ARG u 114 " (cutoff:3.500A) Processing helix chain 'u' and resid 120 through 129 removed outlier: 3.618A pdb=" N HIS u 126 " --> pdb=" O ARG u 122 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA u 127 " --> pdb=" O GLY u 123 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR u 128 " --> pdb=" O VAL u 124 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY u 129 " --> pdb=" O ARG u 125 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 25 removed outlier: 4.142A pdb=" N LEU m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP m 22 " --> pdb=" O ARG m 18 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA m 23 " --> pdb=" O LYS m 19 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP m 24 " --> pdb=" O ASN m 20 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS m 25 " --> pdb=" O ARG m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 32 removed outlier: 3.591A pdb=" N SER m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 40 removed outlier: 4.270A pdb=" N LYS m 37 " --> pdb=" O PHE m 33 " (cutoff:3.500A) Proline residue: m 40 - end of helix Processing helix chain 'm' and resid 90 through 95 removed outlier: 4.248A pdb=" N ILE m 94 " --> pdb=" O CYS m 90 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU m 95 " --> pdb=" O LEU m 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 90 through 95' Processing helix chain 'm' and resid 129 through 136 removed outlier: 4.403A pdb=" N LEU m 133 " --> pdb=" O GLY m 129 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG m 135 " --> pdb=" O TYR m 131 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN m 136 " --> pdb=" O ALA m 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 removed outlier: 4.505A pdb=" N VAL Z 91 " --> pdb=" O SER Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 116 removed outlier: 3.709A pdb=" N ALA Z 114 " --> pdb=" O LYS Z 110 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS Z 116 " --> pdb=" O TRP Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 157 through 171 removed outlier: 4.935A pdb=" N ARG Z 161 " --> pdb=" O ASP Z 157 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS Z 162 " --> pdb=" O GLU Z 158 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET Z 164 " --> pdb=" O LYS Z 160 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG Z 167 " --> pdb=" O TRP Z 163 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN Z 169 " --> pdb=" O LEU Z 165 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N HIS Z 170 " --> pdb=" O ARG Z 166 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS Z 171 " --> pdb=" O ARG Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 183 removed outlier: 4.249A pdb=" N GLN Z 179 " --> pdb=" O ALA Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 192 through 197 removed outlier: 3.897A pdb=" N THR Z 196 " --> pdb=" O ARG Z 192 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA Z 197 " --> pdb=" O PRO Z 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 192 through 197' Processing helix chain 'Z' and resid 206 through 216 removed outlier: 3.509A pdb=" N PHE Z 211 " --> pdb=" O ALA Z 207 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS Z 215 " --> pdb=" O PHE Z 211 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Z 216 " --> pdb=" O TYR Z 212 " (cutoff:3.500A) Processing helix chain 'o' and resid 1 through 6 removed outlier: 7.710A pdb=" N ALA o 5 " --> pdb=" O MET o 1 " (cutoff:3.500A) Proline residue: o 6 - end of helix No H-bonds generated for 'chain 'o' and resid 1 through 6' Processing helix chain 'o' and resid 21 through 29 removed outlier: 3.513A pdb=" N SER o 25 " --> pdb=" O GLU o 21 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP o 26 " --> pdb=" O ILE o 22 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N HIS o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER o 29 " --> pdb=" O SER o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 64 removed outlier: 4.227A pdb=" N GLY o 61 " --> pdb=" O ARG o 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET o 63 " --> pdb=" O THR o 59 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE o 64 " --> pdb=" O ASN o 60 " (cutoff:3.500A) Processing helix chain 'o' and resid 71 through 90 removed outlier: 3.804A pdb=" N HIS o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 93 through 106 removed outlier: 3.965A pdb=" N VAL o 97 " --> pdb=" O ASN o 93 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP o 100 " --> pdb=" O GLN o 96 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER o 103 " --> pdb=" O ILE o 99 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA o 106 " --> pdb=" O VAL o 102 " (cutoff:3.500A) Processing helix chain 'o' and resid 128 through 151 removed outlier: 3.564A pdb=" N ARG o 132 " --> pdb=" O SER o 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE o 149 " --> pdb=" O ARG o 145 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG o 150 " --> pdb=" O GLU o 146 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN o 151 " --> pdb=" O ALA o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 156 through 169 removed outlier: 4.503A pdb=" N ALA o 160 " --> pdb=" O PRO o 156 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY o 169 " --> pdb=" O ASN o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 173 through 190 removed outlier: 4.221A pdb=" N LYS o 177 " --> pdb=" O SER o 173 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA o 188 " --> pdb=" O ARG o 184 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG o 190 " --> pdb=" O ALA o 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 11 removed outlier: 5.300A pdb=" N LEU q 10 " --> pdb=" O HIS q 6 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG q 11 " --> pdb=" O LEU q 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 6 through 11' Processing helix chain 'q' and resid 19 through 34 removed outlier: 3.997A pdb=" N ASP q 23 " --> pdb=" O SER q 19 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER q 24 " --> pdb=" O GLU q 20 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL q 25 " --> pdb=" O ASP q 21 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA q 34 " --> pdb=" O PHE q 30 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 48 removed outlier: 6.568A pdb=" N GLN q 42 " --> pdb=" O THR q 38 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Proline residue: q 44 - end of helix removed outlier: 3.761A pdb=" N HIS q 47 " --> pdb=" O LEU q 43 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE q 48 " --> pdb=" O PRO q 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 38 through 48' Processing helix chain 'q' and resid 69 through 80 removed outlier: 4.463A pdb=" N LEU q 73 " --> pdb=" O PRO q 69 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N MET q 74 " --> pdb=" O LEU q 70 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU q 75 " --> pdb=" O ARG q 71 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS q 78 " --> pdb=" O MET q 74 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE q 79 " --> pdb=" O LEU q 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 92 removed outlier: 3.794A pdb=" N ARG q 90 " --> pdb=" O GLU q 86 " (cutoff:3.500A) Proline residue: q 92 - end of helix Processing helix chain 'q' and resid 110 through 117 removed outlier: 3.729A pdb=" N GLN q 115 " --> pdb=" O VAL q 111 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS q 116 " --> pdb=" O TYR q 112 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 122 through 136 Processing helix chain 'q' and resid 160 through 168 removed outlier: 3.702A pdb=" N ARG q 164 " --> pdb=" O ASP q 160 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG q 166 " --> pdb=" O ARG q 162 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL q 167 " --> pdb=" O ASP q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 170 through 182 Processing helix chain 'R' and resid 29 through 44 removed outlier: 3.513A pdb=" N VAL R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 58 Processing helix chain 'R' and resid 62 through 67 removed outlier: 4.141A pdb=" N VAL R 66 " --> pdb=" O GLN R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 79 Processing helix chain 'R' and resid 85 through 106 removed outlier: 3.792A pdb=" N LEU R 91 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG R 104 " --> pdb=" O LYS R 100 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 133 removed outlier: 5.227A pdb=" N LYS R 112 " --> pdb=" O ASP R 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU R 117 " --> pdb=" O PHE R 113 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS R 133 " --> pdb=" O TYR R 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 19 removed outlier: 4.647A pdb=" N GLU S 16 " --> pdb=" O THR S 12 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET S 18 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 't' and resid 33 through 38 removed outlier: 5.364A pdb=" N VAL t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 48 through 59 removed outlier: 3.714A pdb=" N ASP t 54 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ALA t 58 " --> pdb=" O ASP t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 78 through 86 Processing helix chain 't' and resid 92 through 97 removed outlier: 6.462A pdb=" N LYS t 97 " --> pdb=" O THR t 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 81 removed outlier: 7.137A pdb=" N ALA U 81 " --> pdb=" O GLU U 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 76 through 81' Processing helix chain 'v' and resid 50 through 56 removed outlier: 4.102A pdb=" N LYS v 54 " --> pdb=" O THR v 50 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL v 55 " --> pdb=" O GLY v 51 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS v 56 " --> pdb=" O GLY v 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 50 through 56' Processing helix chain 'v' and resid 63 through 82 removed outlier: 3.780A pdb=" N ALA v 67 " --> pdb=" O SER v 63 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP v 73 " --> pdb=" O MET v 69 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG v 77 " --> pdb=" O ASP v 73 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU v 80 " --> pdb=" O ALA v 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS v 81 " --> pdb=" O ARG v 77 " (cutoff:3.500A) Processing helix chain 'v' and resid 103 through 116 removed outlier: 4.639A pdb=" N ALA v 107 " --> pdb=" O PRO v 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA v 108 " --> pdb=" O GLY v 104 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU v 109 " --> pdb=" O ALA v 105 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG v 110 " --> pdb=" O GLN v 106 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG v 114 " --> pdb=" O ARG v 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY v 116 " --> pdb=" O LEU v 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 19 removed outlier: 4.594A pdb=" N GLN X 18 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N HIS X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 14 through 19' Processing helix chain 'X' and resid 60 through 66 removed outlier: 4.231A pdb=" N ILE X 64 " --> pdb=" O PRO X 60 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN X 65 " --> pdb=" O LYS X 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 removed outlier: 3.532A pdb=" N GLN B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 34 " --> pdb=" O CYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 62 removed outlier: 4.214A pdb=" N ILE B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.624A pdb=" N ALA B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 removed outlier: 5.292A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 98 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 removed outlier: 4.180A pdb=" N ILE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 4.247A pdb=" N PHE B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.621A pdb=" N ALA B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 4.938A pdb=" N ARG B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 25 removed outlier: 3.638A pdb=" N VAL F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 removed outlier: 3.801A pdb=" N LYS F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS F 39 " --> pdb=" O ASN F 35 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS F 42 " --> pdb=" O LYS F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 71 removed outlier: 4.033A pdb=" N THR F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 98 removed outlier: 4.214A pdb=" N ARG F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA F 89 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE F 91 " --> pdb=" O GLN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.502A pdb=" N ASP F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS F 134 " --> pdb=" O PRO F 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 129 through 134' Processing helix chain 'F' and resid 135 through 144 removed outlier: 4.161A pdb=" N LEU F 142 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 190 removed outlier: 3.556A pdb=" N ILE F 174 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 207 removed outlier: 4.063A pdb=" N PHE F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 207' Processing helix chain 'd' and resid 44 through 53 removed outlier: 4.687A pdb=" N GLN d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 65 removed outlier: 4.520A pdb=" N ILE d 61 " --> pdb=" O SER d 57 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE d 64 " --> pdb=" O GLU d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 78 removed outlier: 4.522A pdb=" N VAL d 74 " --> pdb=" O GLU d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 143 removed outlier: 3.830A pdb=" N ALA d 131 " --> pdb=" O GLU d 127 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU d 141 " --> pdb=" O ILE d 137 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 142 " --> pdb=" O ALA d 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL d 143 " --> pdb=" O ALA d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 199 removed outlier: 3.704A pdb=" N LYS d 193 " --> pdb=" O PRO d 189 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE d 194 " --> pdb=" O VAL d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 213 through 231 removed outlier: 3.960A pdb=" N LYS d 227 " --> pdb=" O TYR d 223 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR d 229 " --> pdb=" O LEU d 225 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY d 230 " --> pdb=" O ARG d 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE d 231 " --> pdb=" O LYS d 227 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 251 Processing helix chain 'd' and resid 252 through 259 removed outlier: 3.734A pdb=" N LYS d 259 " --> pdb=" O THR d 255 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 67 removed outlier: 3.846A pdb=" N ARG g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG g 65 " --> pdb=" O GLY g 61 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 81 removed outlier: 4.670A pdb=" N SER g 79 " --> pdb=" O HIS g 75 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS g 80 " --> pdb=" O LEU g 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 63 removed outlier: 3.542A pdb=" N MET a 53 " --> pdb=" O ASP a 49 " (cutoff:3.500A) Proline residue: a 61 - end of helix Processing helix chain 'a' and resid 67 through 75 removed outlier: 4.339A pdb=" N ILE a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP a 73 " --> pdb=" O SER a 69 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG a 74 " --> pdb=" O ILE a 70 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU a 75 " --> pdb=" O ILE a 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 67 through 75' Processing helix chain 'a' and resid 78 through 93 removed outlier: 4.067A pdb=" N ALA a 82 " --> pdb=" O SER a 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA a 83 " --> pdb=" O VAL a 79 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS a 84 " --> pdb=" O ALA a 80 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS a 88 " --> pdb=" O LYS a 84 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN a 92 " --> pdb=" O HIS a 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 89 removed outlier: 3.595A pdb=" N ASP J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR J 89 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 121 removed outlier: 4.016A pdb=" N LYS J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Proline residue: J 144 - end of helix No H-bonds generated for 'chain 'J' and resid 140 through 146' Processing helix chain 'J' and resid 163 through 171 removed outlier: 5.260A pdb=" N LEU J 167 " --> pdb=" O LYS J 163 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE J 170 " --> pdb=" O ILE J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 203 removed outlier: 4.213A pdb=" N GLN J 197 " --> pdb=" O PRO J 193 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA J 199 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.599A pdb=" N LEU J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 41 removed outlier: 4.094A pdb=" N VAL h 40 " --> pdb=" O LYS h 36 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN h 41 " --> pdb=" O SER h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 57 removed outlier: 4.379A pdb=" N VAL h 50 " --> pdb=" O GLY h 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG h 56 " --> pdb=" O ARG h 52 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 85 removed outlier: 3.571A pdb=" N LEU h 76 " --> pdb=" O GLU h 72 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE h 77 " --> pdb=" O TYR h 73 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU h 85 " --> pdb=" O ALA h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 102 removed outlier: 3.752A pdb=" N LEU h 97 " --> pdb=" O GLU h 93 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA h 98 " --> pdb=" O ARG h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 138 Processing helix chain '5' and resid 64 through 73 removed outlier: 6.287A pdb=" N VAL 5 68 " --> pdb=" O GLY 5 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL 5 69 " --> pdb=" O LYS 5 65 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 5 72 " --> pdb=" O VAL 5 68 " (cutoff:3.500A) Processing helix chain '5' and resid 79 through 86 removed outlier: 6.787A pdb=" N GLU 5 83 " --> pdb=" O LYS 5 79 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA 5 84 " --> pdb=" O TYR 5 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 5 85 " --> pdb=" O HIS 5 81 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 157 removed outlier: 4.186A pdb=" N ALA 5 157 " --> pdb=" O LEU 5 153 " (cutoff:3.500A) Processing helix chain '5' and resid 174 through 188 removed outlier: 4.154A pdb=" N LEU 5 178 " --> pdb=" O GLN 5 174 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 5 186 " --> pdb=" O LYS 5 182 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET 5 187 " --> pdb=" O ALA 5 183 " (cutoff:3.500A) Processing helix chain '5' and resid 198 through 203 removed outlier: 6.033A pdb=" N VAL 5 202 " --> pdb=" O LYS 5 198 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLY 5 203 " --> pdb=" O ILE 5 199 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 198 through 203' Processing helix chain '5' and resid 204 through 222 removed outlier: 5.219A pdb=" N GLN 5 208 " --> pdb=" O GLU 5 204 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP 5 219 " --> pdb=" O ARG 5 215 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER 5 220 " --> pdb=" O ASN 5 216 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR 5 221 " --> pdb=" O TYR 5 217 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE 5 222 " --> pdb=" O ILE 5 218 " (cutoff:3.500A) Processing helix chain '5' and resid 238 through 250 removed outlier: 3.632A pdb=" N LEU 5 242 " --> pdb=" O ASN 5 238 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 5 245 " --> pdb=" O TYR 5 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE 5 249 " --> pdb=" O TYR 5 245 " (cutoff:3.500A) Proline residue: 5 250 - end of helix Processing helix chain 'P' and resid 19 through 27 removed outlier: 4.554A pdb=" N LEU P 23 " --> pdb=" O THR P 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG P 25 " --> pdb=" O GLU P 21 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL P 26 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 43 removed outlier: 4.193A pdb=" N PHE P 42 " --> pdb=" O ASP P 38 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY P 43 " --> pdb=" O GLY P 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 38 through 43' Processing helix chain 'P' and resid 125 through 130 removed outlier: 6.379A pdb=" N ASP P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL P 130 " --> pdb=" O GLY P 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 125 through 130' Processing helix chain 'P' and resid 140 through 149 removed outlier: 3.622A pdb=" N PHE P 148 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 160 removed outlier: 4.452A pdb=" N TYR P 159 " --> pdb=" O ASP P 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL P 160 " --> pdb=" O VAL P 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 155 through 160' Processing helix chain 'P' and resid 186 through 249 removed outlier: 4.069A pdb=" N ALA P 195 " --> pdb=" O ARG P 191 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS P 196 " --> pdb=" O ALA P 192 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG P 231 " --> pdb=" O ASN P 227 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU P 245 " --> pdb=" O GLN P 241 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE P 246 " --> pdb=" O ALA P 242 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 20 removed outlier: 3.535A pdb=" N LYS i 10 " --> pdb=" O THR i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 39 removed outlier: 3.510A pdb=" N VAL i 34 " --> pdb=" O GLN i 30 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP i 37 " --> pdb=" O ARG i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 64 removed outlier: 3.878A pdb=" N LYS i 47 " --> pdb=" O SER i 43 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG i 60 " --> pdb=" O HIS i 56 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG i 63 " --> pdb=" O LYS i 59 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY i 64 " --> pdb=" O ARG i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 80 removed outlier: 3.694A pdb=" N GLU i 75 " --> pdb=" O LEU i 71 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG i 80 " --> pdb=" O GLU i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 98 removed outlier: 6.612A pdb=" N GLN i 93 " --> pdb=" O SER i 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE i 95 " --> pdb=" O VAL i 91 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY i 98 " --> pdb=" O ALA i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 113 removed outlier: 3.724A pdb=" N PHE i 106 " --> pdb=" O ASP i 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG i 111 " --> pdb=" O SER i 107 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET i 112 " --> pdb=" O MET i 108 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU i 113 " --> pdb=" O LEU i 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 33 removed outlier: 4.249A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.814A pdb=" N ARG L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 93 through 103 removed outlier: 5.219A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE L 101 " --> pdb=" O LYS L 97 " (cutoff:3.500A) Proline residue: L 102 - end of helix Processing helix chain 'M' and resid 6 through 27 removed outlier: 4.948A pdb=" N ILE M 10 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE M 11 " --> pdb=" O LYS M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.934A pdb=" N VAL M 57 " --> pdb=" O LYS M 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY M 59 " --> pdb=" O ARG M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 Processing helix chain 'M' and resid 79 through 84 removed outlier: 3.911A pdb=" N LEU M 83 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N GLN M 84 " --> pdb=" O GLU M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 84' Processing helix chain 'M' and resid 96 through 111 removed outlier: 3.721A pdb=" N GLN M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER M 110 " --> pdb=" O PHE M 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN M 111 " --> pdb=" O LYS M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 129 removed outlier: 4.956A pdb=" N ALA M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY M 129 " --> pdb=" O VAL M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 167 removed outlier: 6.030A pdb=" N LYS M 164 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN M 165 " --> pdb=" O THR M 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL M 167 " --> pdb=" O HIS M 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 160 through 167' Processing helix chain 'N' and resid 9 through 21 removed outlier: 5.122A pdb=" N THR N 19 " --> pdb=" O ARG N 15 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU N 20 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 60 removed outlier: 4.623A pdb=" N VAL N 49 " --> pdb=" O PRO N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 88 removed outlier: 3.593A pdb=" N VAL N 80 " --> pdb=" O ASN N 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU N 81 " --> pdb=" O ASP N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 99 removed outlier: 3.772A pdb=" N THR N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS N 98 " --> pdb=" O VAL N 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS N 99 " --> pdb=" O PRO N 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 93 through 99' Processing helix chain 'O' and resid 21 through 36 removed outlier: 3.883A pdb=" N ASP O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS O 27 " --> pdb=" O MET O 23 " (cutoff:3.500A) Proline residue: O 28 - end of helix removed outlier: 4.123A pdb=" N LEU O 34 " --> pdb=" O ARG O 30 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N CYS O 35 " --> pdb=" O TRP O 31 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 77 Proline residue: O 64 - end of helix Proline residue: O 67 - end of helix removed outlier: 4.168A pdb=" N TYR O 70 " --> pdb=" O ASN O 66 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG O 73 " --> pdb=" O TRP O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 89 removed outlier: 4.607A pdb=" N ARG O 84 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Proline residue: O 85 - end of helix removed outlier: 3.874A pdb=" N GLY O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR O 89 " --> pdb=" O PRO O 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 80 through 89' Processing helix chain 'O' and resid 106 through 118 removed outlier: 4.554A pdb=" N VAL O 110 " --> pdb=" O PRO O 106 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU O 117 " --> pdb=" O SER O 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS O 118 " --> pdb=" O LYS O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 143 removed outlier: 3.806A pdb=" N SER O 135 " --> pdb=" O GLU O 131 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS O 138 " --> pdb=" O GLU O 134 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE O 140 " --> pdb=" O SER O 136 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR O 141 " --> pdb=" O GLY O 137 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS O 142 " --> pdb=" O HIS O 138 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN O 143 " --> pdb=" O ARG O 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 21 removed outlier: 3.817A pdb=" N ASN b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N CYS b 13 " --> pdb=" O ASN b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 45 removed outlier: 4.111A pdb=" N VAL b 35 " --> pdb=" O SER b 31 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS b 36 " --> pdb=" O LYS b 32 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET b 41 " --> pdb=" O PHE b 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS b 43 " --> pdb=" O GLN b 39 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 93 removed outlier: 4.166A pdb=" N TRP b 89 " --> pdb=" O ASP b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 112 through 120 Processing helix chain 'c' and resid 12 through 18 removed outlier: 3.837A pdb=" N ASN c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN c 17 " --> pdb=" O LYS c 13 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR c 18 " --> pdb=" O VAL c 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 12 through 18' Processing helix chain 'c' and resid 32 through 44 removed outlier: 3.758A pdb=" N LYS c 36 " --> pdb=" O GLY c 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG c 43 " --> pdb=" O LYS c 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 22 removed outlier: 4.257A pdb=" N GLU V 22 " --> pdb=" O GLN V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 62 removed outlier: 3.746A pdb=" N ILE V 54 " --> pdb=" O ASN V 50 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU V 57 " --> pdb=" O ARG V 53 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG V 60 " --> pdb=" O ARG V 56 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP V 62 " --> pdb=" O PHE V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 96 removed outlier: 5.412A pdb=" N ILE V 88 " --> pdb=" O TRP V 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE V 91 " --> pdb=" O GLU V 87 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU V 92 " --> pdb=" O ILE V 88 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP V 94 " --> pdb=" O LYS V 90 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU V 95 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN V 96 " --> pdb=" O LEU V 92 " (cutoff:3.500A) Processing helix chain 'w' and resid 101 through 112 removed outlier: 3.564A pdb=" N VAL w 105 " --> pdb=" O ASN w 101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG w 106 " --> pdb=" O PRO w 102 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA w 107 " --> pdb=" O ALA w 103 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU w 112 " --> pdb=" O LEU w 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 28 removed outlier: 3.518A pdb=" N ASP E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 62 Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.615A pdb=" N LEU E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 86 Processing helix chain 'E' and resid 98 through 109 removed outlier: 4.500A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS E 109 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 125 removed outlier: 3.517A pdb=" N GLU E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 4.097A pdb=" N ALA E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 165 removed outlier: 3.592A pdb=" N LEU E 155 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 189 removed outlier: 4.770A pdb=" N ASN E 184 " --> pdb=" O ARG E 180 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 Processing helix chain 'E' and resid 222 through 232 removed outlier: 4.566A pdb=" N LEU E 226 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 227 " --> pdb=" O SER E 223 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASP E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 244 removed outlier: 6.287A pdb=" N VAL E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'E' and resid 266 through 277 removed outlier: 4.248A pdb=" N ASN E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 296 removed outlier: 4.005A pdb=" N VAL E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 312 Proline residue: E 306 - end of helix Processing helix chain 'E' and resid 318 through 341 removed outlier: 5.329A pdb=" N ALA E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 323 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS E 341 " --> pdb=" O TYR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.721A pdb=" N LYS E 352 " --> pdb=" O TYR E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 371 removed outlier: 3.636A pdb=" N ALA E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU E 370 " --> pdb=" O ASN E 366 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 402 removed outlier: 4.127A pdb=" N THR E 396 " --> pdb=" O SER E 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 224 removed outlier: 4.594A pdb=" N LYS Y 211 " --> pdb=" O GLU Y 207 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE Y 212 " --> pdb=" O PRO Y 208 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA Y 214 " --> pdb=" O GLN Y 210 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR Y 220 " --> pdb=" O CYS Y 216 " (cutoff:3.500A) Proline residue: Y 221 - end of helix removed outlier: 3.701A pdb=" N SER Y 224 " --> pdb=" O TYR Y 220 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 239 removed outlier: 4.750A pdb=" N GLU Y 233 " --> pdb=" O ARG Y 229 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET Y 235 " --> pdb=" O CYS Y 231 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR Y 236 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR Y 237 " --> pdb=" O GLU Y 233 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN Y 239 " --> pdb=" O MET Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 244 through 252 removed outlier: 4.128A pdb=" N LEU Y 248 " --> pdb=" O MET Y 244 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP Y 251 " --> pdb=" O LEU Y 247 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY Y 252 " --> pdb=" O LEU Y 248 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 258 removed outlier: 4.034A pdb=" N GLU Y 257 " --> pdb=" O ILE Y 253 " (cutoff:3.500A) Processing helix chain 'Y' and resid 260 through 268 removed outlier: 4.361A pdb=" N ARG Y 265 " --> pdb=" O MET Y 261 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER Y 268 " --> pdb=" O LEU Y 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 269 through 275 Processing helix chain 'Y' and resid 288 through 318 removed outlier: 4.087A pdb=" N LYS Y 292 " --> pdb=" O ASP Y 288 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER Y 293 " --> pdb=" O GLU Y 289 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG Y 298 " --> pdb=" O ASP Y 294 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Y 302 " --> pdb=" O ARG Y 298 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER Y 304 " --> pdb=" O LYS Y 300 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE Y 307 " --> pdb=" O GLN Y 303 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU Y 308 " --> pdb=" O SER Y 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA Y 315 " --> pdb=" O ALA Y 311 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG Y 316 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG Y 317 " --> pdb=" O ILE Y 313 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Y 318 " --> pdb=" O CYS Y 314 " (cutoff:3.500A) Processing helix chain 'Y' and resid 319 through 334 removed outlier: 3.611A pdb=" N MET Y 323 " --> pdb=" O GLU Y 319 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL Y 324 " --> pdb=" O PRO Y 320 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Y 326 " --> pdb=" O GLN Y 322 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU Y 333 " --> pdb=" O VAL Y 329 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY Y 334 " --> pdb=" O LEU Y 330 " (cutoff:3.500A) Processing helix chain 'Y' and resid 339 through 350 removed outlier: 3.750A pdb=" N GLU Y 343 " --> pdb=" O ALA Y 339 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASP Y 347 " --> pdb=" O GLU Y 343 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU Y 348 " --> pdb=" O TRP Y 344 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS Y 349 " --> pdb=" O CYS Y 345 " (cutoff:3.500A) Proline residue: Y 350 - end of helix Processing helix chain 'Y' and resid 358 through 375 removed outlier: 4.924A pdb=" N LYS Y 363 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA Y 366 " --> pdb=" O MET Y 362 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA Y 367 " --> pdb=" O LYS Y 363 " (cutoff:3.500A) Proline residue: Y 368 - end of helix removed outlier: 4.277A pdb=" N GLY Y 375 " --> pdb=" O GLU Y 371 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 14 removed outlier: 3.599A pdb=" N GLN Q 6 " --> pdb=" O GLY Q 2 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER Q 9 " --> pdb=" O GLU Q 5 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ARG Q 10 " --> pdb=" O GLN Q 6 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLN Q 11 " --> pdb=" O TRP Q 7 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE Q 13 " --> pdb=" O SER Q 9 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 49 removed outlier: 4.170A pdb=" N ALA Q 49 " --> pdb=" O ARG Q 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 34 removed outlier: 3.791A pdb=" N LYS D 16 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE D 19 " --> pdb=" O HIS D 15 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.870A pdb=" N ALA G 15 " --> pdb=" O PRO G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 76 removed outlier: 6.087A pdb=" N GLU G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 106 Proline residue: G 106 - end of helix Processing helix chain 'G' and resid 165 through 178 removed outlier: 3.975A pdb=" N MET G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 209 removed outlier: 4.370A pdb=" N VAL G 199 " --> pdb=" O ASN G 195 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU G 209 " --> pdb=" O SER G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 246 removed outlier: 6.161A pdb=" N ARG G 223 " --> pdb=" O ASP G 219 " (cutoff:3.500A) Proline residue: G 224 - end of helix removed outlier: 4.118A pdb=" N ILE G 246 " --> pdb=" O HIS G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 276 removed outlier: 7.327A pdb=" N GLU G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG G 257 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN G 258 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU G 260 " --> pdb=" O GLU G 256 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER G 276 " --> pdb=" O LEU G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 314 removed outlier: 3.878A pdb=" N PHE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.794A pdb=" N LYS K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 34 removed outlier: 3.816A pdb=" N PHE K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY K 34 " --> pdb=" O TYR K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 53 Proline residue: K 51 - end of helix Processing helix chain 'K' and resid 56 through 65 Processing helix chain 'K' and resid 66 through 72 removed outlier: 5.162A pdb=" N ALA K 72 " --> pdb=" O HIS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 105 through 112 removed outlier: 3.590A pdb=" N ALA K 109 " --> pdb=" O LYS K 105 " (cutoff:3.500A) Proline residue: K 112 - end of helix Processing helix chain 'K' and resid 113 through 130 Processing helix chain 'K' and resid 134 through 143 removed outlier: 3.636A pdb=" N LEU K 142 " --> pdb=" O MET K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 154 removed outlier: 3.537A pdb=" N SER K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 203 removed outlier: 4.527A pdb=" N ASP K 197 " --> pdb=" O LEU K 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 35 removed outlier: 3.760A pdb=" N LEU T 32 " --> pdb=" O GLU T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 45 removed outlier: 3.791A pdb=" N LEU T 43 " --> pdb=" O GLU T 39 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 56 Processing helix chain 'T' and resid 60 through 74 removed outlier: 3.693A pdb=" N LEU T 64 " --> pdb=" O ALA T 60 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS T 65 " --> pdb=" O PRO T 61 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA T 70 " --> pdb=" O ARG T 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL T 74 " --> pdb=" O ALA T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 128 removed outlier: 5.146A pdb=" N PHE T 126 " --> pdb=" O TYR T 122 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER T 127 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET T 128 " --> pdb=" O GLY T 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 122 through 128' Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.721A pdb=" N PHE C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 4.235A pdb=" N LYS C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 95 removed outlier: 3.654A pdb=" N ALA C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.893A pdb=" N LEU C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR C 112 " --> pdb=" O CYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 159 removed outlier: 4.108A pdb=" N HIS C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 4.439A pdb=" N GLN C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 4.594A pdb=" N GLN C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 230 removed outlier: 4.285A pdb=" N THR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 257 removed outlier: 4.240A pdb=" N SER C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 245 " --> pdb=" O TRP C 241 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 4.941A pdb=" N ILE C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 301 removed outlier: 3.576A pdb=" N LYS C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 328 removed outlier: 4.951A pdb=" N PHE C 308 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 353 through 359 removed outlier: 4.513A pdb=" N HIS C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 383 removed outlier: 4.527A pdb=" N GLU C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 408 removed outlier: 5.437A pdb=" N LEU C 398 " --> pdb=" O CYS C 394 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.809A pdb=" N GLY C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 430 removed outlier: 4.205A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N SER C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 430' Processing helix chain 'C' and resid 431 through 451 Processing helix chain 'C' and resid 452 through 465 removed outlier: 4.572A pdb=" N ALA C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 4.601A pdb=" N PHE C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 523 removed outlier: 3.685A pdb=" N THR C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Proline residue: C 521 - end of helix Processing helix chain 'C' and resid 533 through 540 removed outlier: 3.668A pdb=" N PHE C 537 " --> pdb=" O HIS C 533 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 538 " --> pdb=" O GLN C 534 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 570 removed outlier: 4.844A pdb=" N LEU C 560 " --> pdb=" O PHE C 556 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 569 " --> pdb=" O ILE C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 580 removed outlier: 6.741A pdb=" N ALA C 575 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 614 removed outlier: 3.520A pdb=" N LEU C 595 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR C 612 " --> pdb=" O ARG C 608 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN C 614 " --> pdb=" O PHE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 removed outlier: 4.757A pdb=" N MET C 627 " --> pdb=" O VAL C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 removed outlier: 6.173A pdb=" N ILE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 696 removed outlier: 3.572A pdb=" N GLN C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 21 removed outlier: 6.380A pdb=" N CYS 8 10 " --> pdb=" O LYS 8 6 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS 8 13 " --> pdb=" O GLY 8 9 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER 8 20 " --> pdb=" O THR 8 16 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY 8 21 " --> pdb=" O LEU 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 34 Processing helix chain '8' and resid 41 through 55 removed outlier: 7.210A pdb=" N ILE 8 45 " --> pdb=" O GLY 8 41 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA 8 47 " --> pdb=" O MET 8 43 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS 8 55 " --> pdb=" O LEU 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 67 through 75 removed outlier: 4.389A pdb=" N PHE 8 71 " --> pdb=" O PHE 8 67 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG 8 75 " --> pdb=" O PHE 8 71 " (cutoff:3.500A) Processing helix chain '8' and resid 83 through 117 removed outlier: 3.628A pdb=" N THR 8 113 " --> pdb=" O ASN 8 109 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY 8 114 " --> pdb=" O ALA 8 110 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU 8 115 " --> pdb=" O LYS 8 111 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR 8 116 " --> pdb=" O ALA 8 112 " (cutoff:3.500A) Proline residue: 8 117 - end of helix Processing helix chain '8' and resid 118 through 127 removed outlier: 5.788A pdb=" N LEU 8 122 " --> pdb=" O SER 8 118 " (cutoff:3.500A) Processing helix chain '8' and resid 132 through 158 removed outlier: 4.796A pdb=" N ALA 8 136 " --> pdb=" O PRO 8 132 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU 8 138 " --> pdb=" O GLN 8 134 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG 8 139 " --> pdb=" O ARG 8 135 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR 8 140 " --> pdb=" O ALA 8 136 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU 8 141 " --> pdb=" O LYS 8 137 " (cutoff:3.500A) Proline residue: 8 143 - end of helix removed outlier: 5.042A pdb=" N SER 8 157 " --> pdb=" O SER 8 153 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE 8 158 " --> pdb=" O GLU 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 167 through 186 removed outlier: 4.489A pdb=" N TYR 8 171 " --> pdb=" O LEU 8 167 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU 8 172 " --> pdb=" O LEU 8 168 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP 8 173 " --> pdb=" O PRO 8 169 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR 8 174 " --> pdb=" O ILE 8 170 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS 8 185 " --> pdb=" O TYR 8 181 " (cutoff:3.500A) Processing helix chain '8' and resid 190 through 203 removed outlier: 6.929A pdb=" N ILE 8 194 " --> pdb=" O ALA 8 190 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL 8 199 " --> pdb=" O ALA 8 195 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 8 203 " --> pdb=" O VAL 8 199 " (cutoff:3.500A) Processing helix chain '8' and resid 220 through 238 removed outlier: 3.668A pdb=" N MET 8 224 " --> pdb=" O HIS 8 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR 8 236 " --> pdb=" O ARG 8 232 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS 8 237 " --> pdb=" O GLU 8 233 " (cutoff:3.500A) Processing helix chain '8' and resid 241 through 259 removed outlier: 4.240A pdb=" N ALA 8 245 " --> pdb=" O ASN 8 241 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR 8 257 " --> pdb=" O LEU 8 253 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU 8 258 " --> pdb=" O GLN 8 254 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N MET 8 259 " --> pdb=" O THR 8 255 " (cutoff:3.500A) Processing helix chain '8' and resid 264 through 277 Processing helix chain '8' and resid 284 through 305 removed outlier: 3.860A pdb=" N ALA 8 296 " --> pdb=" O ILE 8 292 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET 8 297 " --> pdb=" O ALA 8 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL 8 300 " --> pdb=" O ALA 8 296 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 8 301 " --> pdb=" O MET 8 297 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP 8 302 " --> pdb=" O ALA 8 298 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS 8 303 " --> pdb=" O ALA 8 299 " (cutoff:3.500A) Processing helix chain '8' and resid 306 through 321 removed outlier: 5.650A pdb=" N HIS 8 310 " --> pdb=" O HIS 8 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 8 320 " --> pdb=" O VAL 8 316 " (cutoff:3.500A) Processing helix chain '8' and resid 324 through 340 removed outlier: 4.486A pdb=" N VAL 8 335 " --> pdb=" O ALA 8 331 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU 8 336 " --> pdb=" O SER 8 332 " (cutoff:3.500A) Processing helix chain '8' and resid 351 through 370 removed outlier: 4.108A pdb=" N SER 8 355 " --> pdb=" O PHE 8 351 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU 8 368 " --> pdb=" O ARG 8 364 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE 8 369 " --> pdb=" O ILE 8 365 " (cutoff:3.500A) Processing helix chain '8' and resid 377 through 388 removed outlier: 3.545A pdb=" N TRP 8 381 " --> pdb=" O GLY 8 377 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN 8 388 " --> pdb=" O LEU 8 384 " (cutoff:3.500A) Processing helix chain '8' and resid 394 through 406 Processing helix chain '8' and resid 410 through 424 removed outlier: 3.645A pdb=" N ALA 8 414 " --> pdb=" O ASP 8 410 " (cutoff:3.500A) Processing helix chain '8' and resid 428 through 454 removed outlier: 4.123A pdb=" N GLU 8 432 " --> pdb=" O ASP 8 428 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS 8 436 " --> pdb=" O GLU 8 432 " (cutoff:3.500A) Proline residue: 8 437 - end of helix removed outlier: 4.428A pdb=" N ILE 8 443 " --> pdb=" O ARG 8 439 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN 8 444 " --> pdb=" O LYS 8 440 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR 8 454 " --> pdb=" O MET 8 450 " (cutoff:3.500A) Processing helix chain '8' and resid 459 through 468 removed outlier: 3.668A pdb=" N GLN 8 463 " --> pdb=" O ALA 8 459 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU 8 468 " --> pdb=" O ILE 8 464 " (cutoff:3.500A) Processing helix chain '8' and resid 474 through 486 removed outlier: 3.779A pdb=" N GLU 8 479 " --> pdb=" O ILE 8 475 " (cutoff:3.500A) Proline residue: 8 480 - end of helix removed outlier: 5.023A pdb=" N SER 8 486 " --> pdb=" O ILE 8 482 " (cutoff:3.500A) Processing helix chain '8' and resid 505 through 519 removed outlier: 3.736A pdb=" N VAL 8 509 " --> pdb=" O THR 8 505 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU 8 518 " --> pdb=" O ASP 8 514 " (cutoff:3.500A) Processing helix chain '8' and resid 522 through 547 Proline residue: 8 535 - end of helix removed outlier: 3.648A pdb=" N ILE 8 547 " --> pdb=" O ASP 8 543 " (cutoff:3.500A) Processing helix chain '8' and resid 550 through 581 removed outlier: 6.580A pdb=" N THR 8 554 " --> pdb=" O ARG 8 550 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 64 removed outlier: 4.397A pdb=" N TYR W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG W 62 " --> pdb=" O ALA W 58 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLY W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG W 64 " --> pdb=" O TYR W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 75 removed outlier: 6.094A pdb=" N ASN W 74 " --> pdb=" O LEU W 70 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS W 75 " --> pdb=" O ALA W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 117 removed outlier: 4.411A pdb=" N VAL W 112 " --> pdb=" O THR W 108 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR W 113 " --> pdb=" O SER W 109 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE W 114 " --> pdb=" O ASP W 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG W 117 " --> pdb=" O TYR W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 182 removed outlier: 4.451A pdb=" N VAL W 163 " --> pdb=" O LYS W 159 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL W 166 " --> pdb=" O LEU W 162 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU W 178 " --> pdb=" O ILE W 174 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER W 179 " --> pdb=" O ARG W 175 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS W 180 " --> pdb=" O GLN W 176 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL W 181 " --> pdb=" O ARG W 177 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN W 182 " --> pdb=" O LEU W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 183 through 193 removed outlier: 3.843A pdb=" N THR W 188 " --> pdb=" O ASN W 184 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU W 190 " --> pdb=" O ALA W 186 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG W 192 " --> pdb=" O THR W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 194 through 204 removed outlier: 3.784A pdb=" N ARG W 198 " --> pdb=" O ILE W 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG W 202 " --> pdb=" O ARG W 198 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 235 removed outlier: 4.472A pdb=" N LEU W 230 " --> pdb=" O ASP W 226 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA W 233 " --> pdb=" O ALA W 229 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS W 234 " --> pdb=" O LEU W 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 147 removed outlier: 3.575A pdb=" N ILE I 129 " --> pdb=" O LEU I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 173 removed outlier: 3.897A pdb=" N GLN I 158 " --> pdb=" O ASN I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 193 removed outlier: 4.120A pdb=" N ASP I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) Proline residue: I 184 - end of helix removed outlier: 5.154A pdb=" N CYS I 193 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 215 Processing helix chain 'I' and resid 218 through 226 removed outlier: 4.755A pdb=" N ASP I 222 " --> pdb=" O LEU I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 233 removed outlier: 4.691A pdb=" N LEU I 231 " --> pdb=" O GLY I 227 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU I 232 " --> pdb=" O ARG I 228 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL I 233 " --> pdb=" O GLN I 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 227 through 233' Processing helix chain 'I' and resid 235 through 253 Processing helix chain 'I' and resid 254 through 265 removed outlier: 4.042A pdb=" N ARG I 260 " --> pdb=" O ALA I 256 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU I 264 " --> pdb=" O ARG I 260 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER I 265 " --> pdb=" O VAL I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 295 removed outlier: 4.600A pdb=" N PHE I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 323 Proline residue: I 307 - end of helix Processing helix chain 'I' and resid 324 through 341 Proline residue: I 337 - end of helix removed outlier: 3.530A pdb=" N LEU I 340 " --> pdb=" O SER I 336 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA I 341 " --> pdb=" O PRO I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 379 removed outlier: 5.909A pdb=" N ASP I 354 " --> pdb=" O TYR I 350 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 362 " --> pdb=" O LEU I 358 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA I 366 " --> pdb=" O LEU I 362 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE I 379 " --> pdb=" O LYS I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 399 Processing helix chain 'I' and resid 402 through 414 removed outlier: 4.609A pdb=" N MET I 407 " --> pdb=" O PRO I 403 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG I 412 " --> pdb=" O ARG I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 423 removed outlier: 3.856A pdb=" N ASP I 422 " --> pdb=" O GLY I 418 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU I 423 " --> pdb=" O SER I 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 418 through 423' Processing helix chain 'I' and resid 438 through 466 removed outlier: 5.325A pdb=" N ASN I 442 " --> pdb=" O VAL I 438 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE I 443 " --> pdb=" O LYS I 439 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU I 465 " --> pdb=" O ARG I 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 58 removed outlier: 4.589A pdb=" N SER H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 124 removed outlier: 3.573A pdb=" N ARG H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 148 removed outlier: 3.865A pdb=" N SER H 147 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 160 removed outlier: 5.949A pdb=" N LEU H 157 " --> pdb=" O GLN H 153 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP H 160 " --> pdb=" O GLN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 removed outlier: 5.143A pdb=" N TYR H 195 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 196' Processing helix chain 'H' and resid 206 through 220 removed outlier: 3.852A pdb=" N MET H 211 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS H 218 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY H 219 " --> pdb=" O ASN H 215 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY H 220 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 242 removed outlier: 4.474A pdb=" N PHE H 242 " --> pdb=" O CYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 262 removed outlier: 4.242A pdb=" N TYR H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 289 removed outlier: 4.557A pdb=" N ILE H 267 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU H 268 " --> pdb=" O ALA H 264 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N HIS H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA H 274 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER H 283 " --> pdb=" O ARG H 279 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 286 " --> pdb=" O HIS H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 332 Processing helix chain 'H' and resid 177 through 182 removed outlier: 5.117A pdb=" N LEU H 180 " --> pdb=" O MET H 177 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR H 181 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H 182 " --> pdb=" O LYS H 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 177 through 182' Processing helix chain 'A' and resid 41 through 57 removed outlier: 3.785A pdb=" N LEU A 45 " --> pdb=" O PRO A 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.525A pdb=" N ALA A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.675A pdb=" N ALA A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.063A pdb=" N GLU A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.810A pdb=" N PHE A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 removed outlier: 4.733A pdb=" N ASP A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.660A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 291 removed outlier: 3.739A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 6.306A pdb=" N LEU A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.010A pdb=" N ILE A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.935A pdb=" N CYS A 391 " --> pdb=" O TRP A 387 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 removed outlier: 4.087A pdb=" N LEU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.591A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing helix chain 'l' and resid 40 through 46 Processing helix chain 'l' and resid 54 through 65 removed outlier: 3.539A pdb=" N ALA l 58 " --> pdb=" O ASN l 54 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN l 64 " --> pdb=" O MET l 60 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY l 65 " --> pdb=" O ILE l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 112 through 119 removed outlier: 3.992A pdb=" N ASN l 117 " --> pdb=" O GLU l 113 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE l 118 " --> pdb=" O ALA l 114 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS l 119 " --> pdb=" O GLU l 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 218 through 223 removed outlier: 4.649A pdb=" N ILE l 222 " --> pdb=" O ARG l 218 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE l 223 " --> pdb=" O ALA l 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 218 through 223' Processing helix chain 'l' and resid 245 through 258 removed outlier: 4.313A pdb=" N GLU l 258 " --> pdb=" O LEU l 254 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'f' and resid 134 through 137 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'f' and resid 235 through 238 removed outlier: 3.618A pdb=" N PHE f 198 " --> pdb=" O ILE f 151 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'f' and resid 1105 through 1108 removed outlier: 3.506A pdb=" N TYR f1074 " --> pdb=" O LEU f1124 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR f1126 " --> pdb=" O TYR f1074 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL f1179 " --> pdb=" O VAL f1150 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU f1152 " --> pdb=" O VAL f1179 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU f1181 " --> pdb=" O LEU f1152 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'f' and resid 1232 through 1238 removed outlier: 3.799A pdb=" N ASP f1233 " --> pdb=" O TYR f1701 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG f1671 " --> pdb=" O LEU f1702 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE f1495 " --> pdb=" O SER f1672 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR f1494 " --> pdb=" O GLY f1654 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY f1630 " --> pdb=" O VAL f1655 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR f1659 " --> pdb=" O HIS f1632 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'f' and resid 1557 through 1560 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'y' and resid 10 through 15 removed outlier: 6.667A pdb=" N THR y 11 " --> pdb=" O ASN y 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG y 13 " --> pdb=" O GLU y 31 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE y 29 " --> pdb=" O SER y 15 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN y 27 " --> pdb=" O LYS y 18 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'y' and resid 64 through 68 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'y' and resid 25 through 33 removed outlier: 3.691A pdb=" N PHE y 28 " --> pdb=" O GLY y 80 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY y 78 " --> pdb=" O VAL y 30 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR y 76 " --> pdb=" O VAL y 32 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 's' and resid 137 through 140 Processing sheet with id= 10, first strand: chain 's' and resid 148 through 155 removed outlier: 7.986A pdb=" N THR s 148 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR s 166 " --> pdb=" O THR s 148 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS s 160 " --> pdb=" O LEU s 154 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 's' and resid 351 through 360 removed outlier: 3.546A pdb=" N ALA s 357 " --> pdb=" O ILE s 306 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE s 306 " --> pdb=" O ALA s 357 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA s 304 " --> pdb=" O THR s 359 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR s 313 " --> pdb=" O ILE s 386 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'j' and resid 137 through 140 Processing sheet with id= 13, first strand: chain 'n' and resid 215 through 218 Processing sheet with id= 14, first strand: chain 'n' and resid 296 through 299 removed outlier: 5.555A pdb=" N THR n 299 " --> pdb=" O GLU n 306 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU n 306 " --> pdb=" O THR n 299 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'p' and resid 6 through 10 removed outlier: 4.816A pdb=" N GLY p 7 " --> pdb=" O VAL p 311 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASN p 298 " --> pdb=" O VAL p 314 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR p 299 " --> pdb=" O SER p 294 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER p 290 " --> pdb=" O GLY p 303 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'p' and resid 17 through 21 removed outlier: 3.838A pdb=" N ALA p 18 " --> pdb=" O THR p 34 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA p 31 " --> pdb=" O TRP p 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE p 41 " --> pdb=" O SER p 33 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER p 35 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR p 39 " --> pdb=" O SER p 35 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'p' and resid 71 through 76 removed outlier: 4.892A pdb=" N ASP p 72 " --> pdb=" O ALA p 85 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N PHE p 81 " --> pdb=" O SER p 76 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 113 through 118 removed outlier: 6.136A pdb=" N GLN p 123 " --> pdb=" O SER p 118 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU p 133 " --> pdb=" O LEU p 146 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 157 through 161 removed outlier: 4.053A pdb=" N CYS p 157 " --> pdb=" O GLY p 172 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER p 161 " --> pdb=" O LEU p 168 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU p 168 " --> pdb=" O SER p 161 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE p 183 " --> pdb=" O PRO p 167 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU p 177 " --> pdb=" O GLY p 173 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL p 180 " --> pdb=" O LEU p 189 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'p' and resid 201 through 205 removed outlier: 4.603A pdb=" N SER p 201 " --> pdb=" O SER p 214 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER p 214 " --> pdb=" O SER p 201 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU p 210 " --> pdb=" O SER p 205 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N SER p 209 " --> pdb=" O LEU p 225 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU p 225 " --> pdb=" O SER p 209 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET p 234 " --> pdb=" O ALA p 220 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER p 232 " --> pdb=" O LEU p 222 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'p' and resid 241 through 246 removed outlier: 3.612A pdb=" N GLN p 242 " --> pdb=" O ALA p 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS p 253 " --> pdb=" O CYS p 244 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP p 251 " --> pdb=" O SER p 246 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET p 252 " --> pdb=" O PHE p 263 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE p 263 " --> pdb=" O MET p 252 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE p 262 " --> pdb=" O ILE p 271 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'p' and resid 259 through 262 removed outlier: 3.723A pdb=" N VAL p 272 " --> pdb=" O ILE p 262 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'r' and resid 11 through 17 removed outlier: 3.655A pdb=" N ASP r 72 " --> pdb=" O THR r 26 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'm' and resid 46 through 50 removed outlier: 6.141A pdb=" N LEU m 101 " --> pdb=" O VAL m 123 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS m 121 " --> pdb=" O SER m 103 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'm' and resid 53 through 58 removed outlier: 4.072A pdb=" N GLU m 53 " --> pdb=" O ARG m 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Z' and resid 42 through 48 removed outlier: 3.876A pdb=" N ARG Z 56 " --> pdb=" O SER Z 44 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN Z 52 " --> pdb=" O ALA Z 48 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Z' and resid 71 through 77 removed outlier: 3.964A pdb=" N ILE Z 72 " --> pdb=" O TRP Z 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP Z 67 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA Z 76 " --> pdb=" O GLY Z 63 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA Z 199 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN Z 64 " --> pdb=" O ALA Z 199 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA Z 66 " --> pdb=" O GLY Z 201 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N SER Z 68 " --> pdb=" O LEU Z 203 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 99 through 105 removed outlier: 3.998A pdb=" N CYS Z 100 " --> pdb=" O ILE Z 189 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Z 185 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'q' and resid 50 through 56 removed outlier: 3.878A pdb=" N VAL q 51 " --> pdb=" O PHE q 67 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL q 99 " --> pdb=" O VAL q 66 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR q 68 " --> pdb=" O VAL q 99 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'q' and resid 141 through 148 removed outlier: 3.890A pdb=" N GLY q 142 " --> pdb=" O PHE q 158 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR q 152 " --> pdb=" O ARG q 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER q 187 " --> pdb=" O MET q 155 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU q 159 " --> pdb=" O GLY q 189 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 44 through 48 removed outlier: 5.532A pdb=" N PHE S 33 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS S 83 " --> pdb=" O PHE S 33 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 64 through 67 removed outlier: 6.684A pdb=" N LEU S 64 " --> pdb=" O THR S 75 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 47 through 52 removed outlier: 5.071A pdb=" N ASP U 97 " --> pdb=" O ILE U 52 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 65 through 71 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'v' and resid 32 through 39 removed outlier: 4.073A pdb=" N ASP v 32 " --> pdb=" O SER v 29 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL v 88 " --> pdb=" O GLY v 120 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'X' and resid 84 through 87 removed outlier: 6.263A pdb=" N ARG X 84 " --> pdb=" O GLN X 142 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE X 139 " --> pdb=" O LEU X 155 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'X' and resid 99 through 108 Processing sheet with id= 38, first strand: chain 'F' and resid 77 through 81 removed outlier: 4.314A pdb=" N THR F 78 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR F 128 " --> pdb=" O CYS F 80 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE F 150 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'd' and resid 83 through 88 removed outlier: 6.899A pdb=" N PHE d 108 " --> pdb=" O MET d 88 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'd' and resid 164 through 168 removed outlier: 4.834A pdb=" N ALA d 179 " --> pdb=" O ASP d 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP d 202 " --> pdb=" O ALA d 179 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'd' and resid 104 through 113 Processing sheet with id= 42, first strand: chain 'g' and resid 37 through 41 removed outlier: 3.817A pdb=" N THR g 55 " --> pdb=" O ILE g 41 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'J' and resid 94 through 99 removed outlier: 3.531A pdb=" N GLY J 95 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG J 99 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'J' and resid 175 through 179 removed outlier: 3.899A pdb=" N VAL J 175 " --> pdb=" O TYR J 189 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR J 185 " --> pdb=" O ARG J 179 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG J 214 " --> pdb=" O SER J 154 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'h' and resid 42 through 45 removed outlier: 5.618A pdb=" N GLY h 42 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP h 87 " --> pdb=" O HIS h 60 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '5' and resid 92 through 99 removed outlier: 3.678A pdb=" N ASP 5 141 " --> pdb=" O GLY 5 93 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA 5 95 " --> pdb=" O PHE 5 139 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA 5 97 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE 5 137 " --> pdb=" O ALA 5 97 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG 5 135 " --> pdb=" O VAL 5 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL 5 53 " --> pdb=" O HIS 5 136 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLY 5 59 " --> pdb=" O CYS 5 142 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY 5 144 " --> pdb=" O GLY 5 59 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS 5 60 " --> pdb=" O LEU 5 165 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA 5 167 " --> pdb=" O HIS 5 60 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASN 5 191 " --> pdb=" O ASP 5 160 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA 5 162 " --> pdb=" O ASN 5 191 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL 5 193 " --> pdb=" O ALA 5 162 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '5' and resid 122 through 125 removed outlier: 7.336A pdb=" N THR 5 122 " --> pdb=" O LEU 5 131 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU 5 131 " --> pdb=" O THR 5 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER 5 129 " --> pdb=" O CYS 5 124 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '5' and resid 320 through 325 removed outlier: 4.556A pdb=" N GLN 5 299 " --> pdb=" O ALA 5 325 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET 5 364 " --> pdb=" O ARG 5 304 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 372 through 376 Processing sheet with id= 50, first strand: chain '5' and resid 418 through 423 removed outlier: 3.822A pdb=" N VAL 5 415 " --> pdb=" O LEU 5 418 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR 5 410 " --> pdb=" O LEU 5 455 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU 5 455 " --> pdb=" O THR 5 410 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER 5 453 " --> pdb=" O GLN 5 412 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG 5 454 " --> pdb=" O ARG 5 461 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN 5 459 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '5' and resid 433 through 437 removed outlier: 7.646A pdb=" N GLU 5 379 " --> pdb=" O ARG 5 469 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE 5 463 " --> pdb=" O PHE 5 385 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '5' and resid 449 through 453 removed outlier: 3.563A pdb=" N GLY 5 464 " --> pdb=" O ILE 5 452 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'P' and resid 13 through 18 removed outlier: 3.967A pdb=" N ILE P 18 " --> pdb=" O MET P 1 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS P 2 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU P 112 " --> pdb=" O LYS P 2 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN P 113 " --> pdb=" O GLN P 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL P 115 " --> pdb=" O LYS P 52 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR P 50 " --> pdb=" O VAL P 117 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'P' and resid 74 through 77 Processing sheet with id= 55, first strand: chain 'P' and resid 162 through 168 removed outlier: 5.994A pdb=" N ARG P 163 " --> pdb=" O PHE P 174 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE P 174 " --> pdb=" O ARG P 163 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL P 165 " --> pdb=" O ASP P 172 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP P 172 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS P 167 " --> pdb=" O LYS P 170 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 51 through 64 removed outlier: 3.935A pdb=" N VAL L 17 " --> pdb=" O LEU L 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU L 18 " --> pdb=" O ILE L 113 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 47 through 52 removed outlier: 3.500A pdb=" N VAL M 90 " --> pdb=" O ALA M 51 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 147 through 153 removed outlier: 3.603A pdb=" N LYS M 147 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY M 132 " --> pdb=" O MET M 188 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU M 134 " --> pdb=" O LYS M 186 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY M 138 " --> pdb=" O GLY M 182 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY M 179 " --> pdb=" O LEU M 176 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU M 176 " --> pdb=" O GLY M 179 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 22 through 26 Processing sheet with id= 60, first strand: chain 'b' and resid 23 through 28 removed outlier: 6.725A pdb=" N ARG b 23 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU b 51 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN b 64 " --> pdb=" O GLU b 49 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU b 49 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'b' and resid 78 through 82 removed outlier: 4.893A pdb=" N PHE b 79 " --> pdb=" O VAL b 125 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'V' and resid 66 through 70 removed outlier: 3.694A pdb=" N THR V 67 " --> pdb=" O GLN V 79 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN V 79 " --> pdb=" O THR V 67 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR V 40 " --> pdb=" O LEU V 80 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL V 39 " --> pdb=" O GLN V 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN V 31 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG V 29 " --> pdb=" O SER V 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL V 26 " --> pdb=" O ASN V 102 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS V 106 " --> pdb=" O ILE V 28 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL V 30 " --> pdb=" O HIS V 106 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'w' and resid 36 through 40 removed outlier: 5.012A pdb=" N GLY w 36 " --> pdb=" O LYS w 85 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS w 85 " --> pdb=" O GLY w 36 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU w 38 " --> pdb=" O VAL w 83 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'w' and resid 50 through 54 removed outlier: 3.828A pdb=" N LEU w 51 " --> pdb=" O GLY w 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU w 53 " --> pdb=" O ALA w 61 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'E' and resid 374 through 378 removed outlier: 6.857A pdb=" N ARG E 374 " --> pdb=" O GLY E 387 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.691A pdb=" N ILE G 41 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER G 28 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA G 29 " --> pdb=" O CYS G 49 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'K' and resid 162 through 166 Processing sheet with id= 68, first strand: chain 'T' and resid 82 through 86 removed outlier: 3.683A pdb=" N THR T 85 " --> pdb=" O GLY T 102 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR T 104 " --> pdb=" O THR T 85 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER T 99 " --> pdb=" O ILE T 114 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE T 103 " --> pdb=" O ASN T 110 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'C' and resid 655 through 658 Processing sheet with id= 70, first strand: chain 'W' and resid 44 through 50 removed outlier: 4.702A pdb=" N GLY W 44 " --> pdb=" O VAL W 32 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL W 32 " --> pdb=" O GLY W 44 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR W 30 " --> pdb=" O THR W 46 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS W 48 " --> pdb=" O GLU W 28 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ARG W 26 " --> pdb=" O LYS W 50 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR W 100 " --> pdb=" O VAL W 33 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'W' and resid 65 through 68 removed outlier: 3.900A pdb=" N TYR W 66 " --> pdb=" O PHE W 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE W 88 " --> pdb=" O TYR W 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS W 85 " --> pdb=" O GLU W 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER W 104 " --> pdb=" O LYS W 87 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'W' and resid 121 through 131 removed outlier: 5.602A pdb=" N THR W 121 " --> pdb=" O THR W 145 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR W 145 " --> pdb=" O THR W 121 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA W 125 " --> pdb=" O VAL W 141 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU W 139 " --> pdb=" O VAL W 127 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR W 135 " --> pdb=" O THR W 131 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE W 140 " --> pdb=" O ARG W 215 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE W 142 " --> pdb=" O ARG W 213 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'W' and resid 136 through 140 removed outlier: 6.565A pdb=" N THR W 136 " --> pdb=" O VAL W 220 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS W 216 " --> pdb=" O PHE W 140 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'H' and resid 81 through 84 removed outlier: 3.619A pdb=" N GLY H 133 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'H' and resid 165 through 168 Processing sheet with id= 76, first strand: chain 'A' and resid 139 through 145 removed outlier: 3.838A pdb=" N ILE A 144 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR A 314 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 335 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR A 327 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP A 328 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 204 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR A 206 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 203 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 234 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS A 222 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER A 468 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP A 224 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'A' and resid 165 through 168 removed outlier: 4.054A pdb=" N ILE A 166 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N HIS A 418 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'A' and resid 422 through 425 removed outlier: 3.550A pdb=" N PHE A 402 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU A 351 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'A' and resid 336 through 339 No H-bonds generated for sheet with id= 79 Processing sheet with id= 80, first strand: chain 'l' and resid 95 through 100 removed outlier: 4.926A pdb=" N ARG l 95 " --> pdb=" O VAL l 111 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL l 111 " --> pdb=" O ARG l 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG l 97 " --> pdb=" O VAL l 109 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'l' and resid 120 through 123 removed outlier: 3.970A pdb=" N LEU l 121 " --> pdb=" O LEU l 157 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP l 155 " --> pdb=" O VAL l 123 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'l' and resid 125 through 130 removed outlier: 3.646A pdb=" N ASN l 125 " --> pdb=" O MET l 137 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'l' and resid 193 through 197 removed outlier: 3.603A pdb=" N SER l 194 " --> pdb=" O ARG l 206 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE l 215 " --> pdb=" O LEU l 207 " (cutoff:3.500A) 3345 hydrogen bonds defined for protein. 9960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1398 hydrogen bonds 2292 hydrogen bond angles 0 basepair planarities 559 basepair parallelities 1017 stacking parallelities Total time for adding SS restraints: 118.10 Time building geometry restraints manager: 47.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.34: 19755 1.34 - 1.82: 123888 1.82 - 2.30: 401 2.30 - 2.78: 0 2.78 - 3.26: 1 Bond restraints: 144045 Sorted by residual: bond pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " ideal model delta sigma weight residual 1.458 3.260 -1.802 1.40e-02 5.10e+03 1.66e+04 bond pdb=" C ARG 5 282 " pdb=" N GLY 5 283 " ideal model delta sigma weight residual 1.331 2.085 -0.755 1.46e-02 4.69e+03 2.67e+03 bond pdb=" CA GLU f 301 " pdb=" C GLU f 301 " ideal model delta sigma weight residual 1.523 1.023 0.500 1.34e-02 5.57e+03 1.39e+03 bond pdb=" C TYR f1149 " pdb=" N VAL f1150 " ideal model delta sigma weight residual 1.331 1.724 -0.393 1.29e-02 6.01e+03 9.30e+02 bond pdb=" C GLU f 301 " pdb=" O GLU f 301 " ideal model delta sigma weight residual 1.235 0.857 0.379 1.26e-02 6.30e+03 9.03e+02 ... (remaining 144040 not shown) Histogram of bond angle deviations from ideal: 33.95 - 59.59: 1 59.59 - 85.24: 9 85.24 - 110.89: 62911 110.89 - 136.54: 142239 136.54 - 162.18: 64 Bond angle restraints: 205224 Sorted by residual: angle pdb=" O GLN 5 412 " pdb=" C GLN 5 412 " pdb=" N ILE 5 413 " ideal model delta sigma weight residual 121.65 66.11 55.54 8.30e-01 1.45e+00 4.48e+03 angle pdb=" O ARG 5 282 " pdb=" C ARG 5 282 " pdb=" N GLY 5 283 " ideal model delta sigma weight residual 122.59 33.95 88.64 1.33e+00 5.65e-01 4.44e+03 angle pdb=" O GLY f 234 " pdb=" C GLY f 234 " pdb=" N LEU f 235 " ideal model delta sigma weight residual 122.68 66.87 55.81 1.41e+00 5.03e-01 1.57e+03 angle pdb=" C LEU 5 411 " pdb=" N GLN 5 412 " pdb=" CA GLN 5 412 " ideal model delta sigma weight residual 123.13 82.45 40.68 1.07e+00 8.73e-01 1.45e+03 angle pdb=" O ILE f1147 " pdb=" C ILE f1147 " pdb=" N ASP f1148 " ideal model delta sigma weight residual 122.62 160.84 -38.22 1.17e+00 7.31e-01 1.07e+03 ... (remaining 205219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 79567 35.99 - 71.98: 2632 71.98 - 107.98: 304 107.98 - 143.97: 81 143.97 - 179.96: 34 Dihedral angle restraints: 82618 sinusoidal: 50092 harmonic: 32526 Sorted by residual: dihedral pdb=" CA LYS 8 392 " pdb=" C LYS 8 392 " pdb=" N ALA 8 393 " pdb=" CA ALA 8 393 " ideal model delta harmonic sigma weight residual -180.00 -45.02 -134.98 0 5.00e+00 4.00e-02 7.29e+02 dihedral pdb=" CA ARG J 182 " pdb=" C ARG J 182 " pdb=" N ASN J 183 " pdb=" CA ASN J 183 " ideal model delta harmonic sigma weight residual 180.00 45.51 134.49 0 5.00e+00 4.00e-02 7.23e+02 dihedral pdb=" CA GLY A 17 " pdb=" C GLY A 17 " pdb=" N PRO A 18 " pdb=" CA PRO A 18 " ideal model delta harmonic sigma weight residual -180.00 -45.52 -134.48 0 5.00e+00 4.00e-02 7.23e+02 ... (remaining 82615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 24701 0.989 - 1.979: 11 1.979 - 2.968: 2 2.968 - 3.958: 1 3.958 - 4.947: 6 Chirality restraints: 24721 Sorted by residual: chirality pdb=" CA TYR I 350 " pdb=" N TYR I 350 " pdb=" C TYR I 350 " pdb=" CB TYR I 350 " both_signs ideal model delta sigma weight residual False 2.51 -2.44 4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" CA PRO I 337 " pdb=" N PRO I 337 " pdb=" C PRO I 337 " pdb=" CB PRO I 337 " both_signs ideal model delta sigma weight residual False 2.72 -2.22 4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" C1' A 0 974 " pdb=" O4' A 0 974 " pdb=" C2' A 0 974 " pdb=" N9 A 0 974 " both_signs ideal model delta sigma weight residual False 2.46 -2.40 4.85 2.00e-01 2.50e+01 5.89e+02 ... (remaining 24718 not shown) Planarity restraints: 18046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 02102 " 0.285 2.00e-02 2.50e+03 1.85e-01 7.68e+02 pdb=" N1 U 02102 " -0.132 2.00e-02 2.50e+03 pdb=" C2 U 02102 " -0.105 2.00e-02 2.50e+03 pdb=" O2 U 02102 " 0.094 2.00e-02 2.50e+03 pdb=" N3 U 02102 " -0.277 2.00e-02 2.50e+03 pdb=" C4 U 02102 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U 02102 " 0.308 2.00e-02 2.50e+03 pdb=" C5 U 02102 " -0.064 2.00e-02 2.50e+03 pdb=" C6 U 02102 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 5 412 " -0.168 2.00e-02 2.50e+03 2.36e-01 5.57e+02 pdb=" C GLN 5 412 " 0.407 2.00e-02 2.50e+03 pdb=" O GLN 5 412 " -0.137 2.00e-02 2.50e+03 pdb=" N ILE 5 413 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY f 234 " -0.136 2.00e-02 2.50e+03 2.18e-01 4.77e+02 pdb=" C GLY f 234 " 0.377 2.00e-02 2.50e+03 pdb=" O GLY f 234 " -0.096 2.00e-02 2.50e+03 pdb=" N LEU f 235 " -0.144 2.00e-02 2.50e+03 ... (remaining 18043 not shown) Histogram of nonbonded interaction distances: 0.50 - 1.38: 11 1.38 - 2.26: 191 2.26 - 3.14: 98584 3.14 - 4.02: 374707 4.02 - 4.90: 637355 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1110848 Sorted by model distance: nonbonded pdb=" CD2 TYR f 243 " pdb=" CE LYS f 323 " model vdw 0.502 3.740 nonbonded pdb=" CZ TYR f 243 " pdb=" CD LYS f 323 " model vdw 1.068 3.660 nonbonded pdb=" CD2 TYR f 243 " pdb=" NZ LYS f 323 " model vdw 1.168 3.420 nonbonded pdb=" CE2 TYR f 243 " pdb=" CE LYS f 323 " model vdw 1.194 3.740 nonbonded pdb=" CE2 TYR f 243 " pdb=" CD LYS f 323 " model vdw 1.215 3.740 ... (remaining 1110843 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2220 5.49 5 Mg 1 5.21 5 S 469 5.16 5 C 77469 2.51 5 N 24887 2.21 5 O 31800 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 23.760 Check model and map are aligned: 1.490 Convert atoms to be neutral: 0.900 Process input model: 402.820 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 438.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 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 : 0.019 1.802 144045 Z= 1.235 Angle : 2.201 88.643 205224 Z= 1.381 Chirality : 0.141 4.947 24721 Planarity : 0.019 0.236 18046 Dihedral : 16.871 179.959 61551 Min Nonbonded Distance : 0.502 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 6.75 % Allowed : 14.18 % Favored : 79.07 % Rotamer Outliers : 3.37 % Cbeta Deviations : 1.41 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 1.33 % Twisted Proline : 8.96 % Twisted General : 5.61 % 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: -4.38 (0.07), residues: 11089 helix: -2.23 (0.07), residues: 4105 sheet: -2.81 (0.12), residues: 1233 loop : -3.53 (0.07), residues: 5751 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22178 Ramachandran restraints generated. 11089 Oldfield, 0 Emsley, 11089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22178 Ramachandran restraints generated. 11089 Oldfield, 0 Emsley, 11089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3250 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 2925 time to evaluate : 10.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 325 outliers final: 99 residues processed: 3168 average time/residue: 1.4429 time to fit residues: 7889.5225 Evaluate side-chains 1657 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1558 time to evaluate : 8.691 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 7 residues processed: 99 average time/residue: 1.3532 time to fit residues: 249.4800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 1115 optimal weight: 1.9990 chunk 1001 optimal weight: 7.9990 chunk 555 optimal weight: 9.9990 chunk 342 optimal weight: 0.9980 chunk 675 optimal weight: 3.9990 chunk 534 optimal weight: 3.9990 chunk 1035 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 629 optimal weight: 0.9980 chunk 770 optimal weight: 0.0970 chunk 1199 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 19 ASN f 128 HIS ** f 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 310 GLN f 725 GLN f 731 HIS f 737 HIS ** f 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 797 GLN f 835 HIS f 928 HIS f 956 HIS ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f1007 HIS f1068 ASN f1115 HIS f1542 GLN f1686 GLN f1808 HIS f1821 GLN y 24 ASN y 61 GLN s 146 ASN s 340 GLN j 133 GLN n 196 ASN n 208 ASN n 255 ASN n 339 GLN r 83 GLN r 100 GLN r 138 HIS m 63 ASN ** m 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 ASN m 97 ASN o 60 ASN o 69 ASN o 74 GLN q 36 HIS q 115 GLN ** q 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 9 HIS ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 HIS t 75 GLN X 116 GLN F 19 GLN F 116 GLN F 168 ASN d 94 GLN g 43 ASN ** a 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 HIS J 184 ASN 5 87 ASN 5 91 HIS 5 136 HIS ** 5 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 206 HIS 5 208 GLN ** 5 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 426 ASN P 4 ASN P 66 GLN P 113 ASN P 227 ASN i 56 HIS M 77 HIS M 195 ASN ** O 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 ASN b 42 GLN ** b 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 GLN V 101 GLN w 48 ASN w 98 HIS w 130 HIS E 184 ASN E 197 ASN E 209 HIS E 240 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 219 GLN Q 21 HIS G 191 ASN G 195 ASN G 231 ASN G 237 HIS G 238 GLN G 259 ASN K 70 GLN T 86 HIS T 108 GLN C 187 GLN C 298 GLN C 316 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 354 HIS C 359 HIS C 389 ASN C 403 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 GLN 8 185 HIS 8 385 GLN 8 426 GLN W 69 ASN W 97 ASN W 193 ASN I 136 GLN I 229 GLN I 359 GLN I 370 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN H 208 ASN H 282 HIS H 309 GLN A 57 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 HIS A 96 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 456 GLN l 230 GLN Total number of N/Q/H flips: 113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.207 144045 Z= 0.243 Angle : 0.948 26.518 205224 Z= 0.473 Chirality : 0.052 2.974 24721 Planarity : 0.007 0.123 18046 Dihedral : 14.307 179.530 39096 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 2.19 % Allowed : 10.20 % Favored : 87.61 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 1.60 % Twisted Proline : 5.97 % Twisted General : 2.64 % 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: -2.85 (0.07), residues: 11091 helix: -0.41 (0.08), residues: 4256 sheet: -1.67 (0.14), residues: 1247 loop : -3.27 (0.07), residues: 5588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2171 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 1817 time to evaluate : 8.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 354 outliers final: 156 residues processed: 2046 average time/residue: 1.2438 time to fit residues: 4465.9782 Evaluate side-chains 1519 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1363 time to evaluate : 8.671 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 156 outliers final: 1 residues processed: 156 average time/residue: 1.0472 time to fit residues: 320.0400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 666 optimal weight: 4.9990 chunk 372 optimal weight: 10.0000 chunk 998 optimal weight: 8.9990 chunk 816 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 1201 optimal weight: 8.9990 chunk 1298 optimal weight: 10.0000 chunk 1070 optimal weight: 20.0000 chunk 1191 optimal weight: 0.9990 chunk 409 optimal weight: 7.9990 chunk 964 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 142 HIS f 172 GLN ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 725 GLN f 853 GLN ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f1068 ASN f1302 ASN f1473 GLN f1514 GLN ** f1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 24 ASN ** s 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 292 HIS n 339 GLN ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 144 HIS ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 88 GLN u 135 GLN m 39 ASN m 73 GLN m 77 ASN Z 21 HIS o 81 HIS q 183 HIS q 197 GLN R 9 HIS R 62 GLN v 25 HIS X 32 ASN B 80 HIS F 19 GLN F 25 HIS F 35 ASN F 116 GLN F 144 ASN d 117 HIS g 23 HIS g 74 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 HIS J 165 GLN J 183 ASN J 184 ASN h 25 ASN h 139 HIS 5 145 HIS 5 234 GLN 5 381 GLN ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 48 ASN i 90 HIS L 31 ASN M 173 HIS O 27 HIS O 98 ASN ** O 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 42 GLN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 GLN V 27 HIS V 31 GLN w 101 ASN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN Y 219 GLN Q 3 HIS K 36 GLN ** T 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 HIS T 108 GLN C 86 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS C 469 HIS C 484 ASN C 601 HIS C 635 ASN 8 263 HIS 8 290 GLN 8 345 ASN 8 523 HIS I 229 GLN I 297 GLN I 359 GLN I 447 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN H 243 ASN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 418 HIS A 424 HIS l 5 HIS l 54 ASN Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.157 144045 Z= 0.370 Angle : 0.990 29.879 205224 Z= 0.492 Chirality : 0.049 1.127 24721 Planarity : 0.008 0.177 18046 Dihedral : 14.343 179.650 39096 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 1.69 % Allowed : 12.00 % Favored : 86.31 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 1.60 % Twisted Proline : 3.98 % Twisted General : 1.89 % 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: -2.45 (0.07), residues: 11091 helix: -0.02 (0.08), residues: 4312 sheet: -1.15 (0.14), residues: 1342 loop : -3.23 (0.07), residues: 5437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2069 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1650 time to evaluate : 8.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 419 outliers final: 193 residues processed: 1924 average time/residue: 1.2784 time to fit residues: 4324.7253 Evaluate side-chains 1520 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1327 time to evaluate : 8.818 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 193 outliers final: 1 residues processed: 193 average time/residue: 1.0728 time to fit residues: 403.1887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 1187 optimal weight: 20.0000 chunk 903 optimal weight: 1.9990 chunk 623 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 573 optimal weight: 0.8980 chunk 806 optimal weight: 0.6980 chunk 1206 optimal weight: 30.0000 chunk 1276 optimal weight: 9.9990 chunk 630 optimal weight: 10.0000 chunk 1143 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 275 GLN ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 886 GLN ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1118 HIS f1232 ASN y 24 ASN ** s 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 ASN j 144 HIS ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 339 GLN ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 GLN ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 ASN o 92 GLN o 189 ASN R 5 GLN R 9 HIS R 62 GLN U 88 ASN v 84 ASN X 19 HIS B 153 HIS F 116 GLN ** d 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 44 ASN 5 91 HIS ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 GLN 5 307 GLN ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS O 138 HIS O 143 ASN ** b 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 34 GLN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 GLN K 102 ASN C 54 ASN ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 HIS C 649 ASN 8 185 HIS 8 350 ASN W 176 GLN H 56 GLN H 72 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN A 418 HIS A 456 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.182 144045 Z= 0.249 Angle : 0.836 28.030 205224 Z= 0.412 Chirality : 0.042 0.819 24721 Planarity : 0.006 0.143 18046 Dihedral : 14.029 177.126 39096 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 1.49 % Allowed : 10.99 % Favored : 87.52 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 1.61 % Twisted Proline : 3.23 % Twisted General : 1.42 % 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: -2.06 (0.08), residues: 11091 helix: 0.40 (0.08), residues: 4324 sheet: -0.87 (0.14), residues: 1342 loop : -3.14 (0.07), residues: 5425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1702 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1449 time to evaluate : 8.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 123 residues processed: 1615 average time/residue: 1.2505 time to fit residues: 3586.6436 Evaluate side-chains 1422 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1299 time to evaluate : 8.874 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 123 outliers final: 1 residues processed: 123 average time/residue: 1.0537 time to fit residues: 257.4282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 1063 optimal weight: 10.0000 chunk 724 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 950 optimal weight: 8.9990 chunk 526 optimal weight: 10.0000 chunk 1089 optimal weight: 9.9990 chunk 882 optimal weight: 0.0670 chunk 1 optimal weight: 20.0000 chunk 652 optimal weight: 9.9990 chunk 1146 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 172 GLN f 275 GLN f 694 GLN f 886 GLN ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f1004 HIS ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1118 HIS f1481 ASN y 119 ASN s 135 ASN s 190 GLN ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 339 GLN ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 108 HIS ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 86 ASN u 121 HIS ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 9 HIS F 87 GLN ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN J 184 ASN 5 91 HIS ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 280 ASN 5 307 GLN ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 ASN N 65 GLN ** b 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 101 GLN w 54 GLN w 128 ASN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 HIS G 27 ASN G 143 ASN G 191 ASN K 148 GLN T 135 HIS ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 HIS C 600 GLN C 642 ASN ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 290 GLN H 131 HIS ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 139 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.196 144045 Z= 0.316 Angle : 0.883 28.484 205224 Z= 0.437 Chirality : 0.044 0.698 24721 Planarity : 0.007 0.171 18046 Dihedral : 14.109 175.206 39096 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 1.44 % Allowed : 12.42 % Favored : 86.13 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 1.61 % Twisted Proline : 3.48 % Twisted General : 1.18 % 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: -2.18 (0.08), residues: 11091 helix: 0.26 (0.08), residues: 4347 sheet: -0.88 (0.14), residues: 1371 loop : -3.21 (0.07), residues: 5373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1744 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1432 time to evaluate : 8.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 312 outliers final: 141 residues processed: 1639 average time/residue: 1.2439 time to fit residues: 3598.9760 Evaluate side-chains 1432 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1291 time to evaluate : 8.788 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 141 outliers final: 1 residues processed: 141 average time/residue: 1.0502 time to fit residues: 293.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 429 optimal weight: 7.9990 chunk 1149 optimal weight: 6.9990 chunk 252 optimal weight: 30.0000 chunk 749 optimal weight: 9.9990 chunk 315 optimal weight: 20.0000 chunk 1278 optimal weight: 3.9990 chunk 1061 optimal weight: 5.9990 chunk 591 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 422 optimal weight: 0.9990 chunk 670 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 886 GLN ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1481 ASN ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 104 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 136 HIS ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 ASN R 5 GLN ** R 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 91 HIS ** 5 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 GLN b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 101 GLN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 159 ASN ** 8 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 218 ASN ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.114 144045 Z= 0.391 Angle : 0.935 73.900 205224 Z= 0.458 Chirality : 0.043 0.640 24721 Planarity : 0.007 0.185 18046 Dihedral : 14.098 175.087 39096 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.39 % Allowed : 12.43 % Favored : 86.18 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 1.61 % Twisted Proline : 3.48 % Twisted General : 1.12 % 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: -2.18 (0.08), residues: 11091 helix: 0.27 (0.08), residues: 4345 sheet: -0.90 (0.14), residues: 1367 loop : -3.22 (0.07), residues: 5379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1305 time to evaluate : 8.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 98 residues processed: 1389 average time/residue: 1.3100 time to fit residues: 3217.2224 Evaluate side-chains 1352 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1254 time to evaluate : 8.757 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 98 outliers final: 1 residues processed: 98 average time/residue: 1.1238 time to fit residues: 216.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 1232 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 728 optimal weight: 0.4980 chunk 933 optimal weight: 0.5980 chunk 723 optimal weight: 3.9990 chunk 1075 optimal weight: 3.9990 chunk 713 optimal weight: 6.9990 chunk 1273 optimal weight: 8.9990 chunk 796 optimal weight: 9.9990 chunk 776 optimal weight: 0.5980 chunk 587 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 275 GLN ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 886 GLN ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1481 ASN f1514 GLN ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 ASN ** r 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 GLN ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 198 GLN R 62 GLN X 19 HIS ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 91 HIS ** 5 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 102 ASN w 54 GLN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 159 ASN ** 8 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.138 144045 Z= 0.335 Angle : 0.914 87.184 205224 Z= 0.443 Chirality : 0.041 0.626 24721 Planarity : 0.007 0.176 18046 Dihedral : 14.064 175.167 39096 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 1.35 % Allowed : 12.33 % Favored : 86.32 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 1.62 % Twisted Proline : 3.23 % Twisted General : 1.05 % 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: -2.11 (0.08), residues: 11091 helix: 0.36 (0.08), residues: 4349 sheet: -0.87 (0.14), residues: 1368 loop : -3.20 (0.07), residues: 5374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1329 time to evaluate : 8.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 58 residues processed: 1392 average time/residue: 1.2856 time to fit residues: 3158.7833 Evaluate side-chains 1331 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1273 time to evaluate : 8.589 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 58 outliers final: 1 residues processed: 58 average time/residue: 1.0746 time to fit residues: 128.8478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 787 optimal weight: 20.0000 chunk 508 optimal weight: 0.8980 chunk 760 optimal weight: 8.9990 chunk 383 optimal weight: 0.0370 chunk 250 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 809 optimal weight: 0.6980 chunk 867 optimal weight: 0.0070 chunk 629 optimal weight: 0.0010 chunk 118 optimal weight: 4.9990 chunk 1000 optimal weight: 30.0000 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 886 GLN ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 159 ASN ** 8 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.900 144045 Z= 0.350 Angle : 0.942 106.095 205224 Z= 0.455 Chirality : 0.041 0.608 24721 Planarity : 0.007 0.174 18046 Dihedral : 14.057 175.218 39096 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 1.35 % Allowed : 12.29 % Favored : 86.36 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 1.62 % Twisted Proline : 3.98 % Twisted General : 1.03 % 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: -2.10 (0.08), residues: 11091 helix: 0.37 (0.08), residues: 4348 sheet: -0.87 (0.14), residues: 1368 loop : -3.20 (0.07), residues: 5375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1290 time to evaluate : 8.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 36 residues processed: 1322 average time/residue: 1.2287 time to fit residues: 2855.4723 Evaluate side-chains 1302 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1266 time to evaluate : 8.226 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 1.0221 time to fit residues: 79.5052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 1158 optimal weight: 5.9990 chunk 1219 optimal weight: 3.9990 chunk 1112 optimal weight: 9.9990 chunk 1186 optimal weight: 10.0000 chunk 714 optimal weight: 9.9990 chunk 516 optimal weight: 8.9990 chunk 931 optimal weight: 6.9990 chunk 364 optimal weight: 40.0000 chunk 1072 optimal weight: 0.9990 chunk 1122 optimal weight: 8.9990 chunk 1182 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN X 19 HIS ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 91 HIS ** 5 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 48 ASN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.122 144045 Z= 0.376 Angle : 0.957 106.100 205224 Z= 0.467 Chirality : 0.041 0.608 24721 Planarity : 0.007 0.174 18046 Dihedral : 14.057 175.218 39096 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 1.35 % Allowed : 12.29 % Favored : 86.36 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 1.62 % Twisted Proline : 3.98 % Twisted General : 1.03 % 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: -2.10 (0.08), residues: 11091 helix: 0.37 (0.08), residues: 4348 sheet: -0.87 (0.14), residues: 1368 loop : -3.20 (0.07), residues: 5375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1270 time to evaluate : 8.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 1273 average time/residue: 1.2701 time to fit residues: 2841.2628 Evaluate side-chains 1270 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1267 time to evaluate : 8.827 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 1.1019 time to fit residues: 17.8625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 779 optimal weight: 9.9990 chunk 1254 optimal weight: 3.9990 chunk 765 optimal weight: 9.9990 chunk 595 optimal weight: 0.0870 chunk 872 optimal weight: 5.9990 chunk 1316 optimal weight: 2.9990 chunk 1211 optimal weight: 6.9990 chunk 1047 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 809 optimal weight: 5.9990 chunk 642 optimal weight: 0.9980 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN X 19 HIS ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.122 144045 Z= 0.407 Angle : 0.961 106.100 205224 Z= 0.471 Chirality : 0.041 0.608 24721 Planarity : 0.007 0.174 18046 Dihedral : 14.057 175.218 39096 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 1.35 % Allowed : 12.29 % Favored : 86.36 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 1.62 % Twisted Proline : 3.98 % Twisted General : 1.03 % 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: -2.10 (0.08), residues: 11091 helix: 0.37 (0.08), residues: 4348 sheet: -0.87 (0.14), residues: 1368 loop : -3.20 (0.07), residues: 5375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22182 Ramachandran restraints generated. 11091 Oldfield, 0 Emsley, 11091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1269 time to evaluate : 8.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 1270 average time/residue: 1.2683 time to fit residues: 2827.1221 Evaluate side-chains 1269 residues out of total 9633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1267 time to evaluate : 8.735 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET n 341 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 1.1436 time to fit residues: 15.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1321 random chunks: chunk 832 optimal weight: 0.7980 chunk 1116 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 966 optimal weight: 0.3980 chunk 154 optimal weight: 20.0000 chunk 291 optimal weight: 40.0000 chunk 1049 optimal weight: 20.0000 chunk 439 optimal weight: 20.0000 chunk 1077 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN X 19 HIS ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 91 HIS ** 5 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 ASN c 16 ASN ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 48 ASN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.193346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176245 restraints weight = 244078.137| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 0.96 r_work: 0.4089 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work: 0.4060 rms_B_bonded: 1.43 restraints_weight: 0.1250 r_work: 0.4042 rms_B_bonded: 1.84 restraints_weight: 0.0625 r_work: 0.4016 rms_B_bonded: 2.43 restraints_weight: 0.0312 r_work: 0.3978 rms_B_bonded: 3.34 restraints_weight: 0.0156 r_work: 0.3919 rms_B_bonded: 4.81 restraints_weight: 0.0078 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.122 144045 Z= 0.409 Angle : 0.963 106.100 205224 Z= 0.473 Chirality : 0.041 0.608 24721 Planarity : 0.007 0.174 18046 Dihedral : 14.057 175.218 39096 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 1.35 % Allowed : 12.29 % Favored : 86.36 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 1.62 % Twisted Proline : 3.98 % Twisted General : 1.03 % 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: -2.10 (0.08), residues: 11091 helix: 0.37 (0.08), residues: 4348 sheet: -0.87 (0.14), residues: 1368 loop : -3.20 (0.07), residues: 5375 =============================================================================== Job complete usr+sys time: 49979.87 seconds wall clock time: 853 minutes 59.67 seconds (51239.67 seconds total)