Starting phenix.real_space_refine on Sun Mar 3 20:41:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nac_24269/03_2024/7nac_24269_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2905 5.49 5 S 281 5.16 5 C 88740 2.51 5 N 28624 2.21 5 O 37694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 158246 Number of models: 1 Model: "" Number of chains: 61 Chain: "1" Number of atoms: 56944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2661, 56944 Inner-chain residues flagged as termini: ['pdbres=" A 12404 "'] Classifications: {'RNA': 2661} Modifications used: {'5*END': 1, 'rna2p_pur': 265, 'rna2p_pyr': 183, 'rna3p': 3, 'rna3p_pur': 1208, 'rna3p_pyr': 1001} Link IDs: {'rna2p': 448, 'rna3p': 2212} Chain breaks: 16 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 32, 'rna3p': 125} Chain: "7" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1048 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2174 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain: "B" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2661 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2731 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Chain: "E" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1309 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Chain breaks: 1 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1510 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "J" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1215 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "L" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 991 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "N" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1621 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1442 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "S" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "X" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1068 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "b" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4066 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 3 Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "e" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1009 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 628 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain breaks: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'TRANS': 71} Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5377 Classifications: {'peptide': 666} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 618} Chain breaks: 3 Chain: "q" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2799 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 16, 'TRANS': 341} Chain: "r" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1438 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "u" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1183 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "v" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1087 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Chain: "y" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "8" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3567 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "I" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4247 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 19, 'TRANS': 513} Chain: "K" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2274 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 2 Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "G" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1549 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain breaks: 1 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "n" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3470 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 402} Chain breaks: 3 Chain: "p" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2628 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Chain: "t" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2293 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 2 Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 19, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 28, 'rna3p': 58} Chain breaks: 1 Chain: "D" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3451 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 21, 'TRANS': 410} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "w" Number of atoms: 5451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5451 Classifications: {'peptide': 672} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 651} Chain breaks: 7 Chain: "a" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1695 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain: "5" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1208 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 1, 'TRANS': 139} Chain breaks: 3 Chain: "x" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4340 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 96631 SG CYS j 19 153.992 179.472 171.335 1.00 3.96 S ATOM 96656 SG CYS j 22 156.903 179.785 168.922 1.00 3.96 S ATOM 96756 SG CYS j 34 154.974 176.514 169.262 1.00 3.96 S ATOM 96774 SG CYS j 37 157.290 177.575 172.012 1.00 3.96 S ATOM A0MU2 SG CYS g 44 98.694 173.444 191.483 1.00 3.96 S ATOM A0MUK SG CYS g 47 96.741 171.504 188.884 1.00 1.64 S ATOM A0N1M SG CYS g 81 94.903 173.886 191.241 1.00 3.96 S ATOM A0N25 SG CYS g 84 96.136 170.715 192.565 1.00 5.29 S Residues with excluded nonbonded symmetry interactions: 205 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 193 not shown) Time building chain proxies: 61.50, per 1000 atoms: 0.39 Number of scatterers: 158246 At special positions: 0 Unit cell: (270, 264.6, 325.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 281 16.00 P 2905 15.00 O 37694 8.00 N 28624 7.00 C 88740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.60 Conformation dependent library (CDL) restraints added in 13.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " Number of angles added : 12 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22798 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 439 helices and 106 sheets defined 49.5% alpha, 13.2% beta 852 base pairs and 1451 stacking pairs defined. Time for finding SS restraints: 92.03 Creating SS restraints... Processing helix chain '7' and resid 23 through 30 Processing helix chain '7' and resid 46 through 60 removed outlier: 3.563A pdb=" N LYS 7 51 " --> pdb=" O LYS 7 47 " (cutoff:3.500A) Processing helix chain '7' and resid 104 through 122 removed outlier: 4.124A pdb=" N LEU 7 108 " --> pdb=" O ASP 7 104 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP 7 117 " --> pdb=" O THR 7 113 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LYS 7 118 " --> pdb=" O THR 7 114 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR 7 119 " --> pdb=" O ILE 7 115 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASP 7 120 " --> pdb=" O GLY 7 116 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP 7 121 " --> pdb=" O ASP 7 117 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE 7 122 " --> pdb=" O LYS 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 125 through 148 removed outlier: 3.534A pdb=" N ILE 7 136 " --> pdb=" O ARG 7 132 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU 7 148 " --> pdb=" O ILE 7 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 57 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.784A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 5.338A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 146' Processing helix chain 'A' and resid 147 through 160 Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.975A pdb=" N GLU A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 278 removed outlier: 3.573A pdb=" N VAL A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 5.608A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 290 " --> pdb=" O ASN A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.561A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.826A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.681A pdb=" N GLU B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.996A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.966A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.868A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.553A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.681A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.624A pdb=" N GLY C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.900A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.692A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.872A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.729A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 262 removed outlier: 4.391A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.841A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.569A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 removed outlier: 3.636A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 4.012A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 85' Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.629A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 107' Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.506A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.391A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 73 removed outlier: 4.826A pdb=" N ARG F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.502A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.725A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.944A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.175A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 5.171A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.746A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.748A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.834A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 5.198A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 209 removed outlier: 4.458A pdb=" N MET J 201 " --> pdb=" O ASN J 197 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 207 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 216 removed outlier: 3.658A pdb=" N HIS J 215 " --> pdb=" O PRO J 211 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER J 216 " --> pdb=" O TRP J 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 211 through 216' Processing helix chain 'J' and resid 238 through 265 removed outlier: 6.473A pdb=" N ARG J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU J 243 " --> pdb=" O ASP J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 315 removed outlier: 3.822A pdb=" N LYS J 287 " --> pdb=" O GLU J 283 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN J 310 " --> pdb=" O ARG J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 340 removed outlier: 3.583A pdb=" N LEU J 340 " --> pdb=" O LYS J 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.309A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.735A pdb=" N LYS L 45 " --> pdb=" O THR L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.963A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 93 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 123 removed outlier: 3.658A pdb=" N LYS L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 3.928A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 90 through 98 removed outlier: 3.593A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 removed outlier: 3.503A pdb=" N LEU M 112 " --> pdb=" O ARG M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 138 removed outlier: 3.502A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.843A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.648A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 111 Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.213A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 153 removed outlier: 4.643A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 148 through 153' Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.773A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 177 through 182 removed outlier: 4.235A pdb=" N ASN N 181 " --> pdb=" O GLY N 177 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASN N 182 " --> pdb=" O HIS N 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 177 through 182' Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.859A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.507A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 removed outlier: 4.035A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.677A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.876A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 4.034A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 7.905A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.591A pdb=" N VAL O 145 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 183 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 4.020A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN P 37 " --> pdb=" O ALA P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 3.631A pdb=" N GLU P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP P 53 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 169 through 183 removed outlier: 3.627A pdb=" N ILE P 182 " --> pdb=" O ALA P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.724A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.648A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 55 removed outlier: 4.054A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.858A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 4.333A pdb=" N HIS S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 57 removed outlier: 4.799A pdb=" N GLU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 122 removed outlier: 3.842A pdb=" N ILE S 121 " --> pdb=" O ARG S 117 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 117 through 122' Processing helix chain 'S' and resid 137 through 145 removed outlier: 4.770A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 121 removed outlier: 3.724A pdb=" N GLU T 107 " --> pdb=" O GLN T 103 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA T 114 " --> pdb=" O LYS T 110 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.652A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.884A pdb=" N LEU W 53 " --> pdb=" O ARG W 49 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 removed outlier: 3.513A pdb=" N ALA W 76 " --> pdb=" O VAL W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 96 removed outlier: 4.872A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 3.692A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 168 removed outlier: 4.413A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix removed outlier: 3.779A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 207 removed outlier: 3.651A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 16 removed outlier: 3.580A pdb=" N THR X 8 " --> pdb=" O SER X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.756A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.590A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 103 removed outlier: 3.649A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 138 removed outlier: 3.537A pdb=" N ARG X 138 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.547A pdb=" N ALA Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 32 removed outlier: 4.002A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.727A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'b' and resid 13 through 29 removed outlier: 3.697A pdb=" N THR b 29 " --> pdb=" O THR b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 66 removed outlier: 3.678A pdb=" N LYS b 49 " --> pdb=" O PHE b 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 119 removed outlier: 3.546A pdb=" N LYS b 117 " --> pdb=" O VAL b 113 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.795A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.663A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) Proline residue: b 161 - end of helix Processing helix chain 'b' and resid 179 through 188 removed outlier: 3.599A pdb=" N CYS b 186 " --> pdb=" O SER b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 245 removed outlier: 3.511A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 removed outlier: 3.633A pdb=" N GLN b 267 " --> pdb=" O THR b 263 " (cutoff:3.500A) Proline residue: b 276 - end of helix Processing helix chain 'b' and resid 301 through 312 removed outlier: 3.937A pdb=" N LEU b 305 " --> pdb=" O GLU b 301 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU b 306 " --> pdb=" O ARG b 302 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU b 307 " --> pdb=" O ALA b 303 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS b 310 " --> pdb=" O LEU b 306 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 342 removed outlier: 4.270A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU b 340 " --> pdb=" O CYS b 336 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.720A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 Processing helix chain 'b' and resid 424 through 429 removed outlier: 4.199A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.900A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 3.594A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 512 removed outlier: 5.370A pdb=" N SER b 512 " --> pdb=" O ARG b 508 " (cutoff:3.500A) Processing helix chain 'b' and resid 520 through 525 removed outlier: 4.975A pdb=" N THR b 525 " --> pdb=" O ARG b 521 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 539 removed outlier: 3.670A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR b 537 " --> pdb=" O GLU b 533 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU b 538 " --> pdb=" O HIS b 534 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 539 " --> pdb=" O MET b 535 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 21 Processing helix chain 'd' and resid 24 through 44 removed outlier: 3.772A pdb=" N ARG d 28 " --> pdb=" O SER d 24 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA d 29 " --> pdb=" O PHE d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 3.851A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 61 removed outlier: 3.938A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 26 removed outlier: 3.545A pdb=" N TYR e 25 " --> pdb=" O HIS e 21 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 21 through 26' Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 78 through 87 removed outlier: 3.670A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.707A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.685A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.092A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 37 removed outlier: 3.883A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 71 removed outlier: 4.524A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.684A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 92 removed outlier: 6.040A pdb=" N LEU h 92 " --> pdb=" O LEU h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 34 through 49 removed outlier: 4.135A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.980A pdb=" N SER i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 99 removed outlier: 3.891A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.927A pdb=" N LYS j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG j 56 " --> pdb=" O LYS j 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 77 removed outlier: 4.025A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 20 removed outlier: 4.167A pdb=" N TYR l 19 " --> pdb=" O LYS l 15 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 30 removed outlier: 4.086A pdb=" N LEU l 27 " --> pdb=" O ASN l 23 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL l 28 " --> pdb=" O ILE l 24 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP l 29 " --> pdb=" O SER l 25 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN l 30 " --> pdb=" O PHE l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 23 through 30' Processing helix chain 'l' and resid 48 through 56 removed outlier: 3.514A pdb=" N LEU l 54 " --> pdb=" O HIS l 50 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR l 56 " --> pdb=" O ALA l 52 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 93 removed outlier: 4.457A pdb=" N LEU l 86 " --> pdb=" O HIS l 82 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR l 87 " --> pdb=" O ILE l 83 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL l 88 " --> pdb=" O THR l 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS l 91 " --> pdb=" O THR l 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS l 92 " --> pdb=" O VAL l 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 110 removed outlier: 4.216A pdb=" N MET l 105 " --> pdb=" O PRO l 101 " (cutoff:3.500A) Proline residue: l 106 - end of helix removed outlier: 3.518A pdb=" N GLY l 110 " --> pdb=" O PRO l 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 119 removed outlier: 5.399A pdb=" N GLY l 119 " --> pdb=" O LYS l 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 149 through 156 removed outlier: 4.483A pdb=" N ASN l 155 " --> pdb=" O SER l 151 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N MET l 156 " --> pdb=" O GLU l 152 " (cutoff:3.500A) Processing helix chain 'l' and resid 169 through 176 removed outlier: 4.298A pdb=" N LEU l 173 " --> pdb=" O ILE l 169 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP l 175 " --> pdb=" O GLU l 171 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU l 176 " --> pdb=" O TYR l 172 " (cutoff:3.500A) Processing helix chain 'm' and resid 161 through 167 removed outlier: 4.860A pdb=" N TYR m 165 " --> pdb=" O PRO m 161 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP m 166 " --> pdb=" O LEU m 162 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU m 167 " --> pdb=" O SER m 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 161 through 167' Processing helix chain 'm' and resid 187 through 198 removed outlier: 3.666A pdb=" N LEU m 198 " --> pdb=" O ASP m 194 " (cutoff:3.500A) Processing helix chain 'm' and resid 217 through 230 removed outlier: 3.540A pdb=" N ILE m 227 " --> pdb=" O LEU m 223 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 268 removed outlier: 4.821A pdb=" N PHE m 266 " --> pdb=" O PRO m 262 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL m 267 " --> pdb=" O LYS m 263 " (cutoff:3.500A) Proline residue: m 268 - end of helix No H-bonds generated for 'chain 'm' and resid 262 through 268' Processing helix chain 'm' and resid 269 through 286 Processing helix chain 'm' and resid 290 through 299 removed outlier: 3.535A pdb=" N LYS m 295 " --> pdb=" O PRO m 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU m 296 " --> pdb=" O LYS m 292 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS m 298 " --> pdb=" O LEU m 294 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU m 299 " --> pdb=" O LYS m 295 " (cutoff:3.500A) Processing helix chain 'm' and resid 347 through 358 removed outlier: 3.679A pdb=" N THR m 357 " --> pdb=" O ALA m 353 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU m 358 " --> pdb=" O TRP m 354 " (cutoff:3.500A) Processing helix chain 'm' and resid 382 through 396 removed outlier: 3.820A pdb=" N GLU m 386 " --> pdb=" O GLU m 382 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG m 387 " --> pdb=" O SER m 383 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR m 395 " --> pdb=" O SER m 391 " (cutoff:3.500A) Processing helix chain 'm' and resid 408 through 413 removed outlier: 4.336A pdb=" N LEU m 412 " --> pdb=" O ASP m 408 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE m 413 " --> pdb=" O PRO m 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 408 through 413' Processing helix chain 'm' and resid 418 through 423 removed outlier: 4.016A pdb=" N LEU m 422 " --> pdb=" O SER m 418 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG m 423 " --> pdb=" O PRO m 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 418 through 423' Processing helix chain 'm' and resid 519 through 538 removed outlier: 3.678A pdb=" N ASN m 525 " --> pdb=" O ASP m 521 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY m 533 " --> pdb=" O LYS m 529 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE m 534 " --> pdb=" O ILE m 530 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY m 535 " --> pdb=" O GLU m 531 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TYR m 536 " --> pdb=" O ASP m 532 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP m 537 " --> pdb=" O GLY m 533 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR m 538 " --> pdb=" O PHE m 534 " (cutoff:3.500A) Processing helix chain 'm' and resid 579 through 586 removed outlier: 4.273A pdb=" N GLU m 584 " --> pdb=" O GLN m 580 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS m 585 " --> pdb=" O LYS m 581 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP m 586 " --> pdb=" O GLN m 582 " (cutoff:3.500A) Processing helix chain 'q' and resid 196 through 214 removed outlier: 4.193A pdb=" N THR q 200 " --> pdb=" O ASN q 196 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG q 201 " --> pdb=" O LEU q 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL q 208 " --> pdb=" O MET q 204 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU q 212 " --> pdb=" O VAL q 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN q 213 " --> pdb=" O LYS q 209 " (cutoff:3.500A) Processing helix chain 'q' and resid 224 through 239 removed outlier: 4.204A pdb=" N VAL q 228 " --> pdb=" O ARG q 224 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP q 229 " --> pdb=" O GLY q 225 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS q 233 " --> pdb=" O ASP q 229 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS q 236 " --> pdb=" O LEU q 232 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU q 237 " --> pdb=" O LYS q 233 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 254 removed outlier: 4.002A pdb=" N LEU q 252 " --> pdb=" O LYS q 248 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE q 253 " --> pdb=" O LEU q 249 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER q 254 " --> pdb=" O PHE q 250 " (cutoff:3.500A) Processing helix chain 'q' and resid 255 through 266 removed outlier: 3.664A pdb=" N MET q 259 " --> pdb=" O PRO q 255 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN q 265 " --> pdb=" O PHE q 261 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU q 266 " --> pdb=" O PHE q 262 " (cutoff:3.500A) Processing helix chain 'q' and resid 281 through 293 removed outlier: 3.507A pdb=" N ARG q 292 " --> pdb=" O THR q 288 " (cutoff:3.500A) Processing helix chain 'q' and resid 319 through 325 removed outlier: 3.512A pdb=" N GLY q 325 " --> pdb=" O GLU q 321 " (cutoff:3.500A) Processing helix chain 'q' and resid 331 through 342 removed outlier: 3.529A pdb=" N PHE q 335 " --> pdb=" O ALA q 331 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU q 336 " --> pdb=" O ALA q 332 " (cutoff:3.500A) Proline residue: q 337 - end of helix removed outlier: 3.702A pdb=" N LEU q 341 " --> pdb=" O PRO q 337 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP q 342 " --> pdb=" O VAL q 338 " (cutoff:3.500A) Processing helix chain 'q' and resid 357 through 368 Processing helix chain 'q' and resid 379 through 394 removed outlier: 4.290A pdb=" N LYS q 384 " --> pdb=" O LYS q 380 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N SER q 385 " --> pdb=" O SER q 381 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU q 386 " --> pdb=" O ARG q 382 " (cutoff:3.500A) Processing helix chain 'q' and resid 404 through 412 Proline residue: q 409 - end of helix Processing helix chain 'q' and resid 429 through 434 removed outlier: 3.882A pdb=" N GLN q 434 " --> pdb=" O ILE q 430 " (cutoff:3.500A) Processing helix chain 'q' and resid 435 through 440 removed outlier: 4.033A pdb=" N SER q 439 " --> pdb=" O SER q 435 " (cutoff:3.500A) Processing helix chain 'q' and resid 441 through 463 removed outlier: 3.819A pdb=" N PHE q 445 " --> pdb=" O THR q 441 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE q 446 " --> pdb=" O GLU q 442 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 3.973A pdb=" N VAL q 463 " --> pdb=" O ALA q 459 " (cutoff:3.500A) Processing helix chain 'q' and resid 481 through 497 removed outlier: 4.320A pdb=" N ALA q 487 " --> pdb=" O GLU q 483 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL q 488 " --> pdb=" O GLU q 484 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU q 493 " --> pdb=" O ILE q 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS q 495 " --> pdb=" O TYR q 491 " (cutoff:3.500A) Proline residue: q 497 - end of helix Processing helix chain 'q' and resid 532 through 537 Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 20 through 38 removed outlier: 4.601A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 3.654A pdb=" N VAL r 73 " --> pdb=" O GLU r 69 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 174 through 179 removed outlier: 3.848A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN r 179 " --> pdb=" O SER r 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 174 through 179' Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 248 through 253 removed outlier: 3.571A pdb=" N ASP r 252 " --> pdb=" O GLU r 248 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY r 253 " --> pdb=" O PRO r 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 248 through 253' Processing helix chain 's' and resid 12 through 36 removed outlier: 3.567A pdb=" N LYS s 35 " --> pdb=" O LYS s 31 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS s 36 " --> pdb=" O LYS s 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 45 through 50 removed outlier: 5.259A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 removed outlier: 3.653A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY u 60 " --> pdb=" O ARG u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 71 removed outlier: 3.829A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.513A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL u 127 " --> pdb=" O ASP u 123 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN u 130 " --> pdb=" O LEU u 126 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 140 removed outlier: 4.064A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU u 140 " --> pdb=" O ILE u 136 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 13 removed outlier: 3.505A pdb=" N ARG v 11 " --> pdb=" O ARG v 7 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER v 13 " --> pdb=" O MET v 9 " (cutoff:3.500A) Processing helix chain 'v' and resid 21 through 28 removed outlier: 4.005A pdb=" N GLN v 25 " --> pdb=" O ASN v 21 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG v 26 " --> pdb=" O LYS v 22 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS v 27 " --> pdb=" O ASP v 23 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE v 28 " --> pdb=" O LYS v 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 21 through 28' Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 155 through 167 removed outlier: 4.471A pdb=" N LYS v 160 " --> pdb=" O THR v 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU v 164 " --> pdb=" O LYS v 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU v 165 " --> pdb=" O LYS v 161 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 192 removed outlier: 3.738A pdb=" N GLU v 183 " --> pdb=" O GLU v 179 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS v 187 " --> pdb=" O GLU v 183 " (cutoff:3.500A) Processing helix chain 'v' and resid 195 through 202 removed outlier: 3.779A pdb=" N PHE v 201 " --> pdb=" O LYS v 197 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP v 202 " --> pdb=" O LYS v 198 " (cutoff:3.500A) Processing helix chain 'v' and resid 211 through 227 removed outlier: 3.569A pdb=" N ARG v 225 " --> pdb=" O ARG v 221 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.924A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.737A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.660A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 132 removed outlier: 3.821A pdb=" N GLU y 126 " --> pdb=" O ASP y 122 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU y 127 " --> pdb=" O ARG y 123 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU y 128 " --> pdb=" O GLU y 124 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 removed outlier: 3.530A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 removed outlier: 3.614A pdb=" N VAL y 217 " --> pdb=" O PRO y 213 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 3.628A pdb=" N ARG z 19 " --> pdb=" O SER z 15 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU z 47 " --> pdb=" O LYS z 43 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP z 48 " --> pdb=" O GLN z 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY z 56 " --> pdb=" O LYS z 52 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 14 Processing helix chain '8' and resid 15 through 35 removed outlier: 5.068A pdb=" N GLY 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 41 through 50 Processing helix chain '8' and resid 51 through 64 removed outlier: 3.891A pdb=" N GLU 8 63 " --> pdb=" O LYS 8 59 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU 8 64 " --> pdb=" O SER 8 60 " (cutoff:3.500A) Processing helix chain '8' and resid 70 through 77 removed outlier: 3.729A pdb=" N GLU 8 76 " --> pdb=" O GLU 8 72 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 8 77 " --> pdb=" O THR 8 73 " (cutoff:3.500A) Processing helix chain '8' and resid 267 through 287 removed outlier: 4.183A pdb=" N VAL 8 274 " --> pdb=" O VAL 8 270 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS 8 275 " --> pdb=" O SER 8 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS 8 277 " --> pdb=" O ILE 8 273 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY 8 279 " --> pdb=" O LYS 8 275 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 8 283 " --> pdb=" O GLY 8 279 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU 8 284 " --> pdb=" O SER 8 280 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN 8 286 " --> pdb=" O LEU 8 282 " (cutoff:3.500A) Processing helix chain '8' and resid 292 through 308 removed outlier: 4.005A pdb=" N LEU 8 296 " --> pdb=" O GLU 8 292 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS 8 299 " --> pdb=" O ALA 8 295 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU 8 304 " --> pdb=" O SER 8 300 " (cutoff:3.500A) Proline residue: 8 306 - end of helix Processing helix chain '8' and resid 312 through 329 removed outlier: 3.812A pdb=" N VAL 8 325 " --> pdb=" O SER 8 321 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP 8 326 " --> pdb=" O ILE 8 322 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 350 removed outlier: 4.315A pdb=" N PHE 8 339 " --> pdb=" O GLN 8 335 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE 8 341 " --> pdb=" O ALA 8 337 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU 8 342 " --> pdb=" O SER 8 338 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN 8 344 " --> pdb=" O ALA 8 340 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR 8 346 " --> pdb=" O LEU 8 342 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS 8 347 " --> pdb=" O ILE 8 343 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS 8 350 " --> pdb=" O THR 8 346 " (cutoff:3.500A) Processing helix chain '8' and resid 353 through 368 removed outlier: 4.505A pdb=" N THR 8 357 " --> pdb=" O MET 8 353 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR 8 361 " --> pdb=" O THR 8 357 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR 8 362 " --> pdb=" O LEU 8 358 " (cutoff:3.500A) Processing helix chain '8' and resid 376 through 393 removed outlier: 3.777A pdb=" N GLY 8 392 " --> pdb=" O ALA 8 388 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE 8 393 " --> pdb=" O GLU 8 389 " (cutoff:3.500A) Processing helix chain '8' and resid 396 through 421 removed outlier: 3.904A pdb=" N GLU 8 404 " --> pdb=" O GLN 8 400 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG 8 407 " --> pdb=" O PHE 8 403 " (cutoff:3.500A) Processing helix chain '8' and resid 430 through 438 removed outlier: 5.159A pdb=" N LYS 8 434 " --> pdb=" O ALA 8 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE 8 435 " --> pdb=" O GLU 8 431 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL 8 436 " --> pdb=" O ALA 8 432 " (cutoff:3.500A) Processing helix chain '8' and resid 439 through 457 removed outlier: 3.579A pdb=" N SER 8 449 " --> pdb=" O LEU 8 445 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN 8 457 " --> pdb=" O SER 8 453 " (cutoff:3.500A) Processing helix chain '8' and resid 469 through 487 removed outlier: 4.689A pdb=" N TYR 8 473 " --> pdb=" O ARG 8 469 " (cutoff:3.500A) Proline residue: 8 474 - end of helix removed outlier: 3.587A pdb=" N ILE 8 483 " --> pdb=" O THR 8 479 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE 8 486 " --> pdb=" O VAL 8 482 " (cutoff:3.500A) Proline residue: 8 487 - end of helix Processing helix chain '8' and resid 488 through 510 removed outlier: 3.621A pdb=" N PHE 8 492 " --> pdb=" O THR 8 488 " (cutoff:3.500A) Proline residue: 8 493 - end of helix Processing helix chain '8' and resid 515 through 530 removed outlier: 3.809A pdb=" N LEU 8 519 " --> pdb=" O ILE 8 515 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE 8 522 " --> pdb=" O LEU 8 518 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU 8 523 " --> pdb=" O LEU 8 519 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR 8 524 " --> pdb=" O SER 8 520 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR 8 526 " --> pdb=" O ILE 8 522 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA 8 527 " --> pdb=" O LEU 8 523 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE 8 528 " --> pdb=" O THR 8 524 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR 8 529 " --> pdb=" O SER 8 525 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS 8 530 " --> pdb=" O THR 8 526 " (cutoff:3.500A) Processing helix chain '8' and resid 556 through 579 removed outlier: 4.056A pdb=" N LEU 8 577 " --> pdb=" O ASP 8 573 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR 8 578 " --> pdb=" O TYR 8 574 " (cutoff:3.500A) Processing helix chain '8' and resid 583 through 602 Proline residue: 8 590 - end of helix removed outlier: 3.506A pdb=" N LYS 8 600 " --> pdb=" O ARG 8 596 " (cutoff:3.500A) Processing helix chain '8' and resid 605 through 629 removed outlier: 3.739A pdb=" N LYS 8 609 " --> pdb=" O VAL 8 605 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG 8 610 " --> pdb=" O LYS 8 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN 8 626 " --> pdb=" O SER 8 622 " (cutoff:3.500A) Processing helix chain '8' and resid 640 through 646 removed outlier: 4.286A pdb=" N PHE 8 645 " --> pdb=" O GLU 8 641 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU 8 646 " --> pdb=" O VAL 8 642 " (cutoff:3.500A) Processing helix chain '8' and resid 654 through 678 Processing helix chain 'I' and resid 130 through 151 removed outlier: 3.720A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 169 removed outlier: 3.726A pdb=" N VAL I 166 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU I 167 " --> pdb=" O CYS I 163 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER I 168 " --> pdb=" O LYS I 164 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS I 169 " --> pdb=" O MET I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 189 removed outlier: 3.742A pdb=" N LEU I 179 " --> pdb=" O LYS I 175 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA I 180 " --> pdb=" O PHE I 176 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 182 " --> pdb=" O MET I 178 " (cutoff:3.500A) Proline residue: I 183 - end of helix Processing helix chain 'I' and resid 198 through 203 Processing helix chain 'I' and resid 208 through 237 removed outlier: 3.571A pdb=" N LYS I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 263 removed outlier: 3.931A pdb=" N SER I 261 " --> pdb=" O LYS I 257 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 282 removed outlier: 3.892A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 305 removed outlier: 4.862A pdb=" N ILE I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN I 293 " --> pdb=" O PRO I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 326 removed outlier: 3.533A pdb=" N GLU I 313 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 345 removed outlier: 3.950A pdb=" N MET I 336 " --> pdb=" O SER I 332 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU I 337 " --> pdb=" O VAL I 333 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU I 338 " --> pdb=" O LEU I 334 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER I 339 " --> pdb=" O ASN I 335 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU I 340 " --> pdb=" O MET I 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP I 341 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL I 342 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU I 343 " --> pdb=" O SER I 339 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS I 344 " --> pdb=" O LEU I 340 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP I 345 " --> pdb=" O ASP I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 421 Processing helix chain 'I' and resid 422 through 441 removed outlier: 4.884A pdb=" N GLY I 427 " --> pdb=" O LYS I 423 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER I 428 " --> pdb=" O THR I 424 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASN I 438 " --> pdb=" O THR I 434 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET I 439 " --> pdb=" O LYS I 435 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA I 440 " --> pdb=" O PHE I 436 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN I 441 " --> pdb=" O GLY I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 442 through 463 removed outlier: 5.416A pdb=" N GLY I 446 " --> pdb=" O PHE I 442 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP I 447 " --> pdb=" O ASP I 443 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE I 461 " --> pdb=" O SER I 457 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN I 463 " --> pdb=" O THR I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 486 removed outlier: 5.954A pdb=" N VAL I 469 " --> pdb=" O SER I 465 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR I 486 " --> pdb=" O LEU I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 512 Proline residue: I 507 - end of helix removed outlier: 3.997A pdb=" N LEU I 511 " --> pdb=" O PRO I 507 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP I 512 " --> pdb=" O TYR I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 524 removed outlier: 4.437A pdb=" N LEU I 522 " --> pdb=" O SER I 518 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG I 523 " --> pdb=" O TYR I 519 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU I 524 " --> pdb=" O ARG I 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 518 through 524' Processing helix chain 'I' and resid 541 through 555 Processing helix chain 'I' and resid 561 through 579 removed outlier: 3.775A pdb=" N SER I 577 " --> pdb=" O TYR I 573 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS I 578 " --> pdb=" O MET I 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 598 removed outlier: 3.564A pdb=" N ALA I 586 " --> pdb=" O LYS I 582 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN I 596 " --> pdb=" O ASP I 592 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG I 597 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 606 removed outlier: 4.563A pdb=" N LEU I 604 " --> pdb=" O GLU I 600 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR I 605 " --> pdb=" O ILE I 601 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER I 606 " --> pdb=" O SER I 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 600 through 606' Processing helix chain 'I' and resid 622 through 627 removed outlier: 3.694A pdb=" N SER I 626 " --> pdb=" O ASN I 622 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN I 627 " --> pdb=" O PRO I 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 622 through 627' Processing helix chain 'I' and resid 633 through 640 removed outlier: 4.881A pdb=" N ALA I 637 " --> pdb=" O LEU I 633 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU I 638 " --> pdb=" O TRP I 634 " (cutoff:3.500A) Processing helix chain 'I' and resid 644 through 662 removed outlier: 3.877A pdb=" N SER I 658 " --> pdb=" O LEU I 654 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 659 " --> pdb=" O SER I 655 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU I 660 " --> pdb=" O SER I 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 50 removed outlier: 3.656A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 75 Processing helix chain 'K' and resid 105 through 117 Proline residue: K 109 - end of helix removed outlier: 3.756A pdb=" N ALA K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 removed outlier: 5.288A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS K 134 " --> pdb=" O SER K 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL K 135 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.777A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 163 removed outlier: 3.638A pdb=" N LEU K 160 " --> pdb=" O CYS K 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 177 removed outlier: 4.355A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 191 removed outlier: 4.886A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER K 189 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU K 190 " --> pdb=" O ILE K 186 " (cutoff:3.500A) Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 195 through 201 removed outlier: 4.163A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 250 through 255 removed outlier: 4.449A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 250 through 255' Processing helix chain 'K' and resid 256 through 274 removed outlier: 3.521A pdb=" N GLN K 269 " --> pdb=" O LEU K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 338 removed outlier: 3.847A pdb=" N GLU K 335 " --> pdb=" O LYS K 331 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE K 336 " --> pdb=" O GLY K 332 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 337 " --> pdb=" O LEU K 333 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASN K 338 " --> pdb=" O MET K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 301 removed outlier: 3.623A pdb=" N VAL K 297 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU K 298 " --> pdb=" O GLN K 295 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU K 300 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 301 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 72 removed outlier: 3.558A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS V 72 " --> pdb=" O GLU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 127 removed outlier: 3.569A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 4.031A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 4.074A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 90 through 113 Processing helix chain 'R' and resid 116 through 130 removed outlier: 3.688A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.522A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 162 Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.708A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 4.677A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.544A pdb=" N LEU G 93 " --> pdb=" O GLU G 89 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 160 through 174 removed outlier: 4.889A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 191 removed outlier: 3.726A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 227 removed outlier: 4.808A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 223 " --> pdb=" O ASP G 219 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 removed outlier: 4.350A pdb=" N LYS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 52 removed outlier: 4.093A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.080A pdb=" N VAL Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.590A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 97 through 104 removed outlier: 3.848A pdb=" N PHE Z 101 " --> pdb=" O SER Z 97 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) Proline residue: Z 104 - end of helix Processing helix chain 'Z' and resid 105 through 125 Processing helix chain 'Z' and resid 127 through 133 removed outlier: 5.471A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 26 removed outlier: 3.851A pdb=" N THR U 23 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY U 26 " --> pdb=" O PRO U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 Processing helix chain 'U' and resid 72 through 88 removed outlier: 3.535A pdb=" N LYS U 86 " --> pdb=" O LYS U 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.814A pdb=" N LYS c 13 " --> pdb=" O SER c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'c' and resid 99 through 104 Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.642A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 112 removed outlier: 3.816A pdb=" N ALA g 112 " --> pdb=" O GLN g 108 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.685A pdb=" N ARG k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 54 removed outlier: 4.781A pdb=" N LYS n 54 " --> pdb=" O LYS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 64 through 74 removed outlier: 3.834A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU n 74 " --> pdb=" O TYR n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 removed outlier: 3.704A pdb=" N GLY n 97 " --> pdb=" O ALA n 93 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 109 removed outlier: 3.585A pdb=" N GLU n 106 " --> pdb=" O ALA n 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG n 109 " --> pdb=" O LEU n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 123 Proline residue: n 123 - end of helix Processing helix chain 'n' and resid 124 through 146 removed outlier: 3.581A pdb=" N ASP n 131 " --> pdb=" O ASP n 127 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Proline residue: n 146 - end of helix Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 241 removed outlier: 3.562A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 removed outlier: 4.187A pdb=" N LYS n 254 " --> pdb=" O LEU n 250 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE n 255 " --> pdb=" O LYS n 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE n 256 " --> pdb=" O LYS n 252 " (cutoff:3.500A) Processing helix chain 'n' and resid 354 through 359 removed outlier: 4.440A pdb=" N SER n 358 " --> pdb=" O SER n 354 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 384 removed outlier: 4.222A pdb=" N PHE n 378 " --> pdb=" O ASP n 374 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU n 379 " --> pdb=" O ILE n 375 " (cutoff:3.500A) Processing helix chain 'n' and resid 389 through 394 removed outlier: 3.736A pdb=" N MET n 393 " --> pdb=" O SER n 389 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP n 394 " --> pdb=" O GLU n 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 389 through 394' Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.543A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'n' and resid 550 through 559 removed outlier: 3.897A pdb=" N LEU n 554 " --> pdb=" O GLU n 550 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS n 555 " --> pdb=" O GLU n 551 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET n 558 " --> pdb=" O LEU n 554 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET n 559 " --> pdb=" O LYS n 555 " (cutoff:3.500A) Processing helix chain 'n' and resid 561 through 594 removed outlier: 4.123A pdb=" N GLN n 594 " --> pdb=" O GLN n 590 " (cutoff:3.500A) Processing helix chain 'p' and resid 237 through 242 removed outlier: 4.607A pdb=" N MET p 241 " --> pdb=" O ILE p 237 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR p 242 " --> pdb=" O TYR p 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 237 through 242' Processing helix chain 'p' and resid 245 through 254 removed outlier: 3.968A pdb=" N ASP p 249 " --> pdb=" O ASP p 245 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE p 250 " --> pdb=" O PRO p 246 " (cutoff:3.500A) Proline residue: p 253 - end of helix Processing helix chain 'p' and resid 258 through 271 removed outlier: 3.534A pdb=" N LYS p 266 " --> pdb=" O ARG p 262 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR p 268 " --> pdb=" O ARG p 264 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET p 269 " --> pdb=" O ARG p 265 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS p 270 " --> pdb=" O LYS p 266 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP p 271 " --> pdb=" O LEU p 267 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 54 removed outlier: 3.514A pdb=" N ASN t 51 " --> pdb=" O LYS t 47 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS t 52 " --> pdb=" O LYS t 48 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN t 53 " --> pdb=" O ARG t 49 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS t 54 " --> pdb=" O SER t 50 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 removed outlier: 3.506A pdb=" N ARG t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 167 removed outlier: 3.849A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 180 through 191 Proline residue: t 185 - end of helix removed outlier: 3.567A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 removed outlier: 3.552A pdb=" N LYS t 210 " --> pdb=" O SER t 206 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG t 211 " --> pdb=" O LEU t 207 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 239 removed outlier: 4.362A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 removed outlier: 4.421A pdb=" N MET t 257 " --> pdb=" O GLU t 253 " (cutoff:3.500A) Processing helix chain 't' and resid 260 through 269 removed outlier: 3.501A pdb=" N LEU t 268 " --> pdb=" O CYS t 264 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN t 269 " --> pdb=" O ASN t 265 " (cutoff:3.500A) Processing helix chain 't' and resid 281 through 299 removed outlier: 3.555A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG t 297 " --> pdb=" O GLU t 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR t 298 " --> pdb=" O ALA t 294 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.730A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.051A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 48' Processing helix chain 'D' and resid 50 through 61 removed outlier: 3.622A pdb=" N LYS D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 79 removed outlier: 3.760A pdb=" N ARG D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Proline residue: D 74 - end of helix Processing helix chain 'D' and resid 91 through 108 removed outlier: 3.811A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 123 through 139 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.537A pdb=" N LEU D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.565A pdb=" N GLY D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.560A pdb=" N GLU D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.542A pdb=" N SER D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 324 through 338 Processing helix chain 'D' and resid 346 through 354 removed outlier: 5.012A pdb=" N GLY D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 removed outlier: 5.266A pdb=" N GLY D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG D 379 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA D 381 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 409 removed outlier: 4.275A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 437 through 457 removed outlier: 3.552A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.907A pdb=" N LEU D 468 " --> pdb=" O GLN D 464 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP D 469 " --> pdb=" O ILE D 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 464 through 469' Processing helix chain 'D' and resid 470 through 478 removed outlier: 3.610A pdb=" N TYR D 477 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 4.417A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE o 114 " --> pdb=" O TYR o 110 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY o 115 " --> pdb=" O PHE o 111 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 153 removed outlier: 3.985A pdb=" N ALA o 145 " --> pdb=" O ASN o 141 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET o 146 " --> pdb=" O LYS o 142 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE o 147 " --> pdb=" O GLU o 143 " (cutoff:3.500A) Processing helix chain 'o' and resid 192 through 215 removed outlier: 3.543A pdb=" N LYS o 201 " --> pdb=" O LYS o 197 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN o 202 " --> pdb=" O ASP o 198 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU o 211 " --> pdb=" O ARG o 207 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS o 213 " --> pdb=" O LYS o 209 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER o 214 " --> pdb=" O LYS o 210 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'w' and resid 14 through 24 removed outlier: 3.679A pdb=" N LYS w 21 " --> pdb=" O TYR w 17 " (cutoff:3.500A) Processing helix chain 'w' and resid 27 through 41 removed outlier: 4.859A pdb=" N PHE w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS w 32 " --> pdb=" O ARG w 28 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE w 33 " --> pdb=" O SER w 29 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE w 34 " --> pdb=" O SER w 30 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY w 41 " --> pdb=" O ASN w 37 " (cutoff:3.500A) Processing helix chain 'w' and resid 42 through 48 removed outlier: 4.085A pdb=" N LYS w 46 " --> pdb=" O HIS w 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER w 47 " --> pdb=" O PHE w 43 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS w 48 " --> pdb=" O LEU w 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 42 through 48' Processing helix chain 'w' and resid 58 through 68 Processing helix chain 'w' and resid 97 through 109 removed outlier: 3.737A pdb=" N ARG w 101 " --> pdb=" O THR w 97 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR w 107 " --> pdb=" O LYS w 103 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS w 109 " --> pdb=" O ARG w 105 " (cutoff:3.500A) Processing helix chain 'w' and resid 127 through 150 removed outlier: 5.964A pdb=" N ASP w 131 " --> pdb=" O GLY w 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE w 133 " --> pdb=" O VAL w 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU w 145 " --> pdb=" O GLN w 141 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU w 148 " --> pdb=" O LYS w 144 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN w 149 " --> pdb=" O LEU w 145 " (cutoff:3.500A) Processing helix chain 'w' and resid 165 through 177 removed outlier: 3.905A pdb=" N LEU w 169 " --> pdb=" O ASP w 165 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU w 176 " --> pdb=" O VAL w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 209 through 215 removed outlier: 4.038A pdb=" N LEU w 213 " --> pdb=" O ASP w 209 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP w 214 " --> pdb=" O PRO w 210 " (cutoff:3.500A) Proline residue: w 215 - end of helix No H-bonds generated for 'chain 'w' and resid 209 through 215' Processing helix chain 'w' and resid 229 through 235 removed outlier: 3.511A pdb=" N ILE w 233 " --> pdb=" O MET w 229 " (cutoff:3.500A) Processing helix chain 'w' and resid 258 through 265 removed outlier: 3.613A pdb=" N PHE w 262 " --> pdb=" O SER w 258 " (cutoff:3.500A) Processing helix chain 'w' and resid 267 through 275 removed outlier: 4.003A pdb=" N MET w 275 " --> pdb=" O MET w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 284 through 293 removed outlier: 3.839A pdb=" N LYS w 292 " --> pdb=" O LYS w 288 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU w 293 " --> pdb=" O ILE w 289 " (cutoff:3.500A) Processing helix chain 'w' and resid 299 through 307 removed outlier: 4.386A pdb=" N CYS w 303 " --> pdb=" O GLU w 299 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP w 306 " --> pdb=" O SER w 302 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU w 307 " --> pdb=" O CYS w 303 " (cutoff:3.500A) Processing helix chain 'w' and resid 311 through 329 removed outlier: 3.922A pdb=" N MET w 317 " --> pdb=" O LYS w 313 " (cutoff:3.500A) Processing helix chain 'w' and resid 348 through 388 removed outlier: 3.565A pdb=" N GLN w 379 " --> pdb=" O ASN w 375 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN w 388 " --> pdb=" O ARG w 384 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 417 removed outlier: 3.634A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY w 417 " --> pdb=" O ALA w 413 " (cutoff:3.500A) Processing helix chain 'w' and resid 418 through 425 removed outlier: 4.186A pdb=" N LEU w 422 " --> pdb=" O ILE w 418 " (cutoff:3.500A) Processing helix chain 'w' and resid 455 through 480 removed outlier: 4.690A pdb=" N ALA w 459 " --> pdb=" O SER w 455 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG w 480 " --> pdb=" O ARG w 476 " (cutoff:3.500A) Processing helix chain 'w' and resid 481 through 492 removed outlier: 3.910A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA w 489 " --> pdb=" O ARG w 485 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG w 490 " --> pdb=" O ALA w 486 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY w 491 " --> pdb=" O LYS w 487 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY w 492 " --> pdb=" O GLN w 488 " (cutoff:3.500A) Processing helix chain 'w' and resid 552 through 561 removed outlier: 3.507A pdb=" N ASN w 560 " --> pdb=" O ARG w 556 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP w 561 " --> pdb=" O MET w 557 " (cutoff:3.500A) Processing helix chain 'w' and resid 619 through 627 removed outlier: 3.515A pdb=" N ILE w 623 " --> pdb=" O SER w 619 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP w 627 " --> pdb=" O ILE w 623 " (cutoff:3.500A) Processing helix chain 'w' and resid 638 through 656 removed outlier: 3.579A pdb=" N THR w 646 " --> pdb=" O GLU w 642 " (cutoff:3.500A) Processing helix chain 'w' and resid 659 through 672 Processing helix chain 'w' and resid 675 through 685 removed outlier: 3.960A pdb=" N PHE w 684 " --> pdb=" O VAL w 680 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN w 685 " --> pdb=" O ASP w 681 " (cutoff:3.500A) Processing helix chain 'w' and resid 696 through 708 removed outlier: 4.512A pdb=" N ASP w 702 " --> pdb=" O TRP w 698 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU w 705 " --> pdb=" O GLU w 701 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS w 706 " --> pdb=" O ASP w 702 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS w 708 " --> pdb=" O LYS w 704 " (cutoff:3.500A) Processing helix chain 'w' and resid 714 through 726 removed outlier: 3.764A pdb=" N GLU w 723 " --> pdb=" O MET w 719 " (cutoff:3.500A) Processing helix chain 'w' and resid 732 through 759 Processing helix chain 'w' and resid 820 through 838 removed outlier: 3.507A pdb=" N ASN w 825 " --> pdb=" O GLY w 821 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 22 removed outlier: 3.574A pdb=" N VAL a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS a 14 " --> pdb=" O ARG a 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU a 15 " --> pdb=" O GLU a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 81 removed outlier: 3.622A pdb=" N CYS a 80 " --> pdb=" O ARG a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 92 removed outlier: 4.733A pdb=" N LYS a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 108 removed outlier: 3.789A pdb=" N TYR a 107 " --> pdb=" O LEU a 103 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN a 108 " --> pdb=" O SER a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 123 removed outlier: 3.736A pdb=" N ILE a 117 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LYS a 118 " --> pdb=" O GLU a 114 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN a 119 " --> pdb=" O VAL a 115 " (cutoff:3.500A) Proline residue: a 121 - end of helix Processing helix chain 'a' and resid 126 through 132 Processing helix chain 'a' and resid 143 through 154 removed outlier: 3.671A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR a 154 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 195 removed outlier: 3.811A pdb=" N LEU a 179 " --> pdb=" O GLU a 175 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN a 181 " --> pdb=" O ASP a 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU a 193 " --> pdb=" O PHE a 189 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU a 194 " --> pdb=" O PHE a 190 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 93 removed outlier: 4.276A pdb=" N PHE 5 43 " --> pdb=" O TYR 5 39 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N HIS 5 44 " --> pdb=" O LEU 5 40 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS 5 45 " --> pdb=" O THR 5 41 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG 5 46 " --> pdb=" O GLY 5 42 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS 5 47 " --> pdb=" O PHE 5 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS 5 53 " --> pdb=" O GLN 5 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG 5 63 " --> pdb=" O LYS 5 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN 5 84 " --> pdb=" O VAL 5 80 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE 5 88 " --> pdb=" O GLN 5 84 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS 5 89 " --> pdb=" O LEU 5 85 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU 5 90 " --> pdb=" O LYS 5 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER 5 91 " --> pdb=" O THR 5 87 " (cutoff:3.500A) Processing helix chain '5' and resid 163 through 180 removed outlier: 4.283A pdb=" N GLU 5 167 " --> pdb=" O ASN 5 163 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS 5 176 " --> pdb=" O LEU 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 217 through 232 removed outlier: 3.529A pdb=" N ILE 5 223 " --> pdb=" O ASN 5 219 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS 5 232 " --> pdb=" O ALA 5 228 " (cutoff:3.500A) Processing helix chain 'x' and resid 15 through 26 Processing helix chain 'x' and resid 31 through 44 removed outlier: 3.528A pdb=" N ILE x 38 " --> pdb=" O GLN x 34 " (cutoff:3.500A) Proline residue: x 39 - end of helix removed outlier: 3.777A pdb=" N GLY x 43 " --> pdb=" O PRO x 39 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN x 44 " --> pdb=" O MET x 40 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 73 Proline residue: x 64 - end of helix removed outlier: 3.732A pdb=" N GLU x 73 " --> pdb=" O VAL x 69 " (cutoff:3.500A) Processing helix chain 'x' and resid 92 through 109 removed outlier: 4.552A pdb=" N HIS x 109 " --> pdb=" O SER x 105 " (cutoff:3.500A) Processing helix chain 'x' and resid 129 through 141 Processing helix chain 'x' and resid 148 through 158 Processing helix chain 'x' and resid 173 through 179 Processing helix chain 'x' and resid 180 through 194 removed outlier: 4.563A pdb=" N LYS x 184 " --> pdb=" O MET x 180 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP x 185 " --> pdb=" O SER x 181 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS x 188 " --> pdb=" O LYS x 184 " (cutoff:3.500A) Proline residue: x 194 - end of helix Processing helix chain 'x' and resid 205 through 210 removed outlier: 4.202A pdb=" N ALA x 209 " --> pdb=" O THR x 205 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY x 210 " --> pdb=" O MET x 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 205 through 210' Processing helix chain 'x' and resid 211 through 217 removed outlier: 4.566A pdb=" N LYS x 215 " --> pdb=" O SER x 211 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR x 216 " --> pdb=" O ASP x 212 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY x 217 " --> pdb=" O ILE x 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 211 through 217' Processing helix chain 'x' and resid 244 through 258 removed outlier: 3.630A pdb=" N LYS x 248 " --> pdb=" O ASN x 244 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU x 249 " --> pdb=" O PRO x 245 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN x 250 " --> pdb=" O ALA x 246 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN x 258 " --> pdb=" O SER x 254 " (cutoff:3.500A) Processing helix chain 'x' and resid 270 through 288 Processing helix chain 'x' and resid 304 through 317 Processing helix chain 'x' and resid 327 through 332 removed outlier: 4.303A pdb=" N ALA x 331 " --> pdb=" O THR x 327 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG x 332 " --> pdb=" O ASP x 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 327 through 332' Processing helix chain 'x' and resid 350 through 360 removed outlier: 3.882A pdb=" N PHE x 354 " --> pdb=" O ASN x 350 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET x 355 " --> pdb=" O THR x 351 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS x 356 " --> pdb=" O ASP x 352 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG x 360 " --> pdb=" O HIS x 356 " (cutoff:3.500A) Processing helix chain 'x' and resid 378 through 390 removed outlier: 4.140A pdb=" N PHE x 382 " --> pdb=" O ARG x 378 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE x 383 " --> pdb=" O GLU x 379 " (cutoff:3.500A) Proline residue: x 384 - end of helix Processing helix chain 'x' and resid 406 through 419 removed outlier: 3.876A pdb=" N GLU x 417 " --> pdb=" O ASN x 413 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP x 418 " --> pdb=" O TRP x 414 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG x 419 " --> pdb=" O ILE x 415 " (cutoff:3.500A) Processing helix chain 'x' and resid 420 through 439 removed outlier: 4.196A pdb=" N HIS x 439 " --> pdb=" O TYR x 435 " (cutoff:3.500A) Processing helix chain 'x' and resid 441 through 446 removed outlier: 3.793A pdb=" N ARG x 446 " --> pdb=" O THR x 442 " (cutoff:3.500A) Processing helix chain 'x' and resid 451 through 460 Processing helix chain 'x' and resid 467 through 473 Processing helix chain 'x' and resid 494 through 499 removed outlier: 3.907A pdb=" N TYR x 498 " --> pdb=" O ASN x 494 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS x 499 " --> pdb=" O MET x 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 494 through 499' Processing helix chain 'x' and resid 502 through 516 removed outlier: 3.722A pdb=" N LYS x 507 " --> pdb=" O LYS x 503 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU x 508 " --> pdb=" O LYS x 504 " (cutoff:3.500A) Processing helix chain 'x' and resid 517 through 534 Processing helix chain 'x' and resid 536 through 560 removed outlier: 3.815A pdb=" N LYS x 556 " --> pdb=" O LYS x 552 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA x 559 " --> pdb=" O LEU x 555 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 58 through 62 removed outlier: 4.737A pdb=" N SER A 37 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA A 91 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 97 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 111 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 220 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN A 116 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.014A pdb=" N ASP A 174 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 180 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= 4, first strand: chain 'A' and resid 190 through 196 removed outlier: 7.407A pdb=" N THR A 190 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 209 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.855A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 51 through 55 Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.806A pdb=" N THR B 95 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 274 through 278 removed outlier: 4.104A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'B' and resid 215 through 219 Processing sheet with id= 11, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.226A pdb=" N GLN C 87 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.307A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 37 through 43 removed outlier: 3.957A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.597A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 152 through 155 removed outlier: 6.745A pdb=" N GLY F 152 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.344A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 18, first strand: chain 'H' and resid 100 through 105 removed outlier: 5.500A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 132 through 137 removed outlier: 5.263A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 21, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.166A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.451A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.800A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 25, first strand: chain 'P' and resid 13 through 20 removed outlier: 6.863A pdb=" N LYS P 13 " --> pdb=" O GLU P 152 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS P 111 " --> pdb=" O LYS P 153 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 27, first strand: chain 'P' and resid 124 through 128 removed outlier: 3.756A pdb=" N GLN P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 29, first strand: chain 'S' and resid 24 through 31 removed outlier: 4.396A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 88 through 96 removed outlier: 4.918A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'W' and resid 63 through 67 removed outlier: 9.010A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'W' and resid 120 through 123 Processing sheet with id= 33, first strand: chain 'W' and resid 173 through 176 Processing sheet with id= 34, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.916A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Y' and resid 55 through 58 removed outlier: 4.582A pdb=" N GLN Y 66 " --> pdb=" O VAL Y 58 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.981A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'b' and resid 203 through 210 removed outlier: 6.671A pdb=" N SER b 203 " --> pdb=" O PRO b 222 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR b 205 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU b 171 " --> pdb=" O CYS b 249 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS b 173 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE b 253 " --> pdb=" O CYS b 173 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER b 282 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL b 250 " --> pdb=" O SER b 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL b 283 " --> pdb=" O GLY b 314 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.256A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL d 8 " --> pdb=" O ARG d 77 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL d 107 " --> pdb=" O GLU d 11 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 40, first strand: chain 'f' and resid 11 through 14 removed outlier: 6.618A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'f' and resid 8 through 14 removed outlier: 4.233A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 15 through 18 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'l' and resid 36 through 39 removed outlier: 6.856A pdb=" N VAL l 44 " --> pdb=" O LEU l 70 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'l' and resid 95 through 99 removed outlier: 4.663A pdb=" N TYR l 95 " --> pdb=" O GLY l 130 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'm' and resid 123 through 127 Processing sheet with id= 46, first strand: chain 'm' and resid 171 through 174 removed outlier: 3.690A pdb=" N GLY m 172 " --> pdb=" O ILE m 180 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS m 178 " --> pdb=" O ASP m 174 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'm' and resid 430 through 434 removed outlier: 3.518A pdb=" N THR m 431 " --> pdb=" O LEU m 804 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR m 801 " --> pdb=" O GLY m 797 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TRP m 792 " --> pdb=" O HIS m 787 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 442 through 446 removed outlier: 3.812A pdb=" N THR m 442 " --> pdb=" O GLY m 455 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TRP m 451 " --> pdb=" O ASP m 446 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR m 460 " --> pdb=" O SER m 456 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL m 463 " --> pdb=" O VAL m 472 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG m 470 " --> pdb=" O GLU m 465 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'm' and resid 490 through 494 removed outlier: 5.594A pdb=" N ILE m 501 " --> pdb=" O ASN m 494 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE m 589 " --> pdb=" O LEU m 512 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN m 574 " --> pdb=" O SER m 592 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'm' and resid 598 through 603 removed outlier: 3.521A pdb=" N LYS m 599 " --> pdb=" O VAL m 612 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR m 608 " --> pdb=" O HIS m 603 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ASP m 607 " --> pdb=" O VAL m 626 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER m 620 " --> pdb=" O GLN m 613 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 643 through 648 removed outlier: 5.145A pdb=" N GLN m 653 " --> pdb=" O HIS m 648 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR m 661 " --> pdb=" O SER m 658 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE m 664 " --> pdb=" O VAL m 673 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'm' and resid 685 through 689 removed outlier: 5.619A pdb=" N ASN m 694 " --> pdb=" O HIS m 689 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU m 695 " --> pdb=" O TRP m 706 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP m 706 " --> pdb=" O LEU m 695 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA m 697 " --> pdb=" O VAL m 704 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL m 704 " --> pdb=" O ALA m 697 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER m 699 " --> pdb=" O LYS m 702 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'm' and resid 728 through 732 removed outlier: 5.307A pdb=" N LEU m 737 " --> pdb=" O HIS m 732 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE m 747 " --> pdb=" O LYS m 769 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS m 769 " --> pdb=" O ILE m 747 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL m 749 " --> pdb=" O LEU m 767 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'm' and resid 460 through 463 Processing sheet with id= 55, first strand: chain 'm' and resid 661 through 664 Processing sheet with id= 56, first strand: chain 'q' and resid 305 through 309 removed outlier: 6.209A pdb=" N VAL q 305 " --> pdb=" O THR q 275 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE q 271 " --> pdb=" O ILE q 309 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR q 272 " --> pdb=" O GLN q 330 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS q 326 " --> pdb=" O ASN q 276 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 397 through 403 removed outlier: 6.530A pdb=" N ASN q 397 " --> pdb=" O GLY q 371 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR q 403 " --> pdb=" O ASP q 377 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG q 417 " --> pdb=" O ARG q 348 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP q 421 " --> pdb=" O MET q 352 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY q 471 " --> pdb=" O LYS q 548 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR q 475 " --> pdb=" O ALA q 544 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS q 545 " --> pdb=" O VAL q 502 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN q 498 " --> pdb=" O ILE q 549 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'q' and resid 528 through 531 removed outlier: 4.847A pdb=" N TYR q 531 " --> pdb=" O PHE q 541 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE q 541 " --> pdb=" O TYR q 531 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'r' and resid 190 through 195 removed outlier: 3.694A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA r 243 " --> pdb=" O ILE r 221 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.711A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 18 through 23 removed outlier: 3.969A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 63, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 64, first strand: chain 'y' and resid 114 through 117 Processing sheet with id= 65, first strand: chain 'y' and resid 158 through 162 Processing sheet with id= 66, first strand: chain 'K' and resid 97 through 101 Processing sheet with id= 67, first strand: chain 'K' and resid 122 through 126 removed outlier: 3.561A pdb=" N LEU K 179 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'K' and resid 242 through 248 removed outlier: 5.727A pdb=" N THR K 242 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'V' and resid 79 through 82 removed outlier: 3.772A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN V 98 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'V' and resid 84 through 88 Processing sheet with id= 71, first strand: chain 'V' and resid 75 through 78 Processing sheet with id= 72, first strand: chain 'G' and resid 176 through 181 removed outlier: 3.599A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Z' and resid 9 through 14 removed outlier: 3.815A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 75, first strand: chain 'U' and resid 54 through 58 removed outlier: 6.227A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.354A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.496A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.422A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG k 46 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'n' and resid 177 through 182 removed outlier: 3.541A pdb=" N GLY n 185 " --> pdb=" O SER n 182 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'n' and resid 385 through 388 Processing sheet with id= 81, first strand: chain 'p' and resid 94 through 97 removed outlier: 6.481A pdb=" N SER p 95 " --> pdb=" O LYS p 453 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE p 451 " --> pdb=" O LEU p 97 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS p 447 " --> pdb=" O ASN p 102 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN p 98 " --> pdb=" O ILE p 451 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'p' and resid 107 through 111 removed outlier: 3.542A pdb=" N SER p 122 " --> pdb=" O ILE p 126 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE p 126 " --> pdb=" O SER p 122 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS p 138 " --> pdb=" O THR p 129 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'p' and resid 148 through 153 removed outlier: 3.519A pdb=" N ILE p 153 " --> pdb=" O ARG p 157 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG p 157 " --> pdb=" O ILE p 153 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR p 156 " --> pdb=" O THR p 172 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU p 169 " --> pdb=" O LEU p 201 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'p' and resid 213 through 217 removed outlier: 4.414A pdb=" N ARG p 221 " --> pdb=" O SER p 217 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER p 220 " --> pdb=" O THR p 236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER p 281 " --> pdb=" O PHE p 233 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'p' and resid 292 through 296 removed outlier: 6.019A pdb=" N VAL p 302 " --> pdb=" O ASP p 296 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR p 301 " --> pdb=" O LEU p 317 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP p 315 " --> pdb=" O GLY p 303 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR p 314 " --> pdb=" O ILE p 323 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG p 321 " --> pdb=" O ASP p 316 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'p' and resid 334 through 339 removed outlier: 4.202A pdb=" N GLN p 369 " --> pdb=" O LEU p 355 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'p' and resid 379 through 384 removed outlier: 6.102A pdb=" N ILE p 390 " --> pdb=" O CYS p 384 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N TYR p 389 " --> pdb=" O VAL p 405 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR p 399 " --> pdb=" O SER p 395 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL p 402 " --> pdb=" O TYR p 412 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR p 412 " --> pdb=" O VAL p 402 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'p' and resid 431 through 435 Processing sheet with id= 89, first strand: chain 'p' and resid 166 through 169 Processing sheet with id= 90, first strand: chain 'p' and resid 310 through 314 removed outlier: 5.479A pdb=" N HIS p 310 " --> pdb=" O THR p 328 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP p 324 " --> pdb=" O THR p 314 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'p' and resid 439 through 443 Processing sheet with id= 92, first strand: chain 't' and resid 128 through 134 Processing sheet with id= 93, first strand: chain 't' and resid 193 through 198 removed outlier: 5.480A pdb=" N TYR t 193 " --> pdb=" O VAL t 147 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN t 172 " --> pdb=" O LEU t 273 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 't' and resid 213 through 216 Processing sheet with id= 95, first strand: chain 'D' and resid 81 through 86 removed outlier: 3.980A pdb=" N ILE D 250 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL D 252 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'D' and resid 144 through 148 removed outlier: 3.607A pdb=" N ILE D 118 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'D' and resid 292 through 296 removed outlier: 4.667A pdb=" N SER D 390 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL D 270 " --> pdb=" O TYR D 415 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'D' and resid 316 through 319 Processing sheet with id= 99, first strand: chain 'o' and resid 118 through 123 removed outlier: 3.540A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'w' and resid 88 through 92 removed outlier: 3.652A pdb=" N VAL w 50 " --> pdb=" O LEU w 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR w 115 " --> pdb=" O VAL w 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP w 119 " --> pdb=" O LEU w 53 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'w' and resid 793 through 797 removed outlier: 3.605A pdb=" N THR w 794 " --> pdb=" O LYS w 815 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'a' and resid 65 through 68 No H-bonds generated for sheet with id=102 Processing sheet with id=103, first strand: chain 'a' and resid 164 through 169 removed outlier: 3.843A pdb=" N LEU a 165 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU a 34 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL a 32 " --> pdb=" O VAL a 169 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER a 203 " --> pdb=" O GLY a 37 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU a 204 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU a 216 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL a 206 " --> pdb=" O PHE a 214 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain '5' and resid 145 through 148 removed outlier: 3.880A pdb=" N VAL 5 155 " --> pdb=" O GLU 5 147 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'x' and resid 118 through 122 removed outlier: 5.645A pdb=" N THR x 199 " --> pdb=" O LYS x 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER x 51 " --> pdb=" O SER x 203 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'x' and resid 294 through 299 removed outlier: 3.567A pdb=" N TYR x 240 " --> pdb=" O GLU x 394 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL x 242 " --> pdb=" O LEU x 396 " (cutoff:3.500A) 4273 hydrogen bonds defined for protein. 12687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2120 hydrogen bonds 3422 hydrogen bond angles 0 basepair planarities 852 basepair parallelities 1451 stacking parallelities Total time for adding SS restraints: 174.86 Time building geometry restraints manager: 62.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 32536 1.33 - 1.46: 58480 1.46 - 1.58: 70010 1.58 - 1.71: 5788 1.71 - 1.84: 466 Bond restraints: 167280 Sorted by residual: bond pdb=" C2' A2M 12946 " pdb=" C1' A2M 12946 " ideal model delta sigma weight residual 1.305 1.565 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" O4' A2M 12946 " pdb=" C1' A2M 12946 " ideal model delta sigma weight residual 1.615 1.406 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" P A2M 12946 " pdb=" O5' A2M 12946 " ideal model delta sigma weight residual 1.647 1.836 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C5 OMU 12921 " pdb=" C6 OMU 12921 " ideal model delta sigma weight residual 1.480 1.355 0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C5 OMG 12922 " pdb=" C6 OMG 12922 " ideal model delta sigma weight residual 1.548 1.426 0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 167275 not shown) Histogram of bond angle deviations from ideal: 90.71 - 99.78: 12 99.78 - 108.85: 39634 108.85 - 117.92: 104941 117.92 - 126.99: 87489 126.99 - 136.06: 7707 Bond angle restraints: 239783 Sorted by residual: angle pdb=" C1' A2M 12946 " pdb=" N9 A2M 12946 " pdb=" C8 A2M 12946 " ideal model delta sigma weight residual 88.50 127.21 -38.71 3.00e+00 1.11e-01 1.67e+02 angle pdb=" N6 A2M 12946 " pdb=" C6 A2M 12946 " pdb=" N1 A2M 12946 " ideal model delta sigma weight residual 92.14 118.95 -26.81 3.00e+00 1.11e-01 7.99e+01 angle pdb=" O3' C 12600 " pdb=" C3' C 12600 " pdb=" C2' C 12600 " ideal model delta sigma weight residual 109.50 121.26 -11.76 1.50e+00 4.44e-01 6.14e+01 angle pdb=" O3' A 1 906 " pdb=" C3' A 1 906 " pdb=" C2' A 1 906 " ideal model delta sigma weight residual 113.70 124.49 -10.79 1.50e+00 4.44e-01 5.17e+01 angle pdb=" C3' A 1 906 " pdb=" C2' A 1 906 " pdb=" O2' A 1 906 " ideal model delta sigma weight residual 110.70 120.71 -10.01 1.50e+00 4.44e-01 4.45e+01 ... (remaining 239778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 97475 35.88 - 71.77: 7261 71.77 - 107.65: 772 107.65 - 143.53: 32 143.53 - 179.42: 50 Dihedral angle restraints: 105590 sinusoidal: 70500 harmonic: 35090 Sorted by residual: dihedral pdb=" O4' U 11124 " pdb=" C1' U 11124 " pdb=" N1 U 11124 " pdb=" C2 U 11124 " ideal model delta sinusoidal sigma weight residual -160.00 16.21 -176.21 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 13306 " pdb=" C1' U 13306 " pdb=" N1 U 13306 " pdb=" C2 U 13306 " ideal model delta sinusoidal sigma weight residual 200.00 24.04 175.96 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C 11201 " pdb=" C1' C 11201 " pdb=" N1 C 11201 " pdb=" C2 C 11201 " ideal model delta sinusoidal sigma weight residual 200.00 24.66 175.34 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 105587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 29078 0.142 - 0.283: 156 0.283 - 0.425: 2 0.425 - 0.566: 1 0.566 - 0.708: 1 Chirality restraints: 29238 Sorted by residual: chirality pdb=" C3' C 12600 " pdb=" C4' C 12600 " pdb=" O3' C 12600 " pdb=" C2' C 12600 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C3' A 1 906 " pdb=" C4' A 1 906 " pdb=" O3' A 1 906 " pdb=" C2' A 1 906 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C2' A2M 12946 " pdb=" C3' A2M 12946 " pdb=" O2' A2M 12946 " pdb=" C1' A2M 12946 " both_signs ideal model delta sigma weight residual False -2.39 -2.69 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 29235 not shown) Planarity restraints: 19630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12922 " -0.045 2.00e-02 2.50e+03 5.51e-01 6.84e+03 pdb=" C4' OMG 12922 " -0.420 2.00e-02 2.50e+03 pdb=" O4' OMG 12922 " -0.550 2.00e-02 2.50e+03 pdb=" C3' OMG 12922 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMG 12922 " 0.555 2.00e-02 2.50e+03 pdb=" C2' OMG 12922 " 0.215 2.00e-02 2.50e+03 pdb=" O2' OMG 12922 " -0.925 2.00e-02 2.50e+03 pdb=" C1' OMG 12922 " -0.225 2.00e-02 2.50e+03 pdb=" N9 OMG 12922 " 0.800 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG n 414 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO n 415 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO n 415 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO n 415 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA q 355 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO q 356 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO q 356 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO q 356 " -0.054 5.00e-02 4.00e+02 ... (remaining 19627 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 8778 2.71 - 3.26: 143385 3.26 - 3.80: 280876 3.80 - 4.35: 380889 4.35 - 4.90: 549537 Nonbonded interactions: 1363465 Sorted by model distance: nonbonded pdb=" N2 G 12393 " pdb=" O6 G 12394 " model vdw 2.159 2.520 nonbonded pdb=" OD2 ASP V 97 " pdb=" OH TYR w 246 " model vdw 2.197 2.440 nonbonded pdb=" OP1 G 1 331 " pdb=" OG SER v 3 " model vdw 2.199 2.440 nonbonded pdb=" O2' C 12496 " pdb=" OP1 U 12497 " model vdw 2.199 2.440 nonbonded pdb=" OP1 A 11504 " pdb=" NH1 ARG P 23 " model vdw 2.202 2.520 ... (remaining 1363460 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 max=1.00 mean=0.99 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 21.770 Check model and map are aligned: 1.890 Set scattering table: 1.100 Process input model: 533.550 Find NCS groups from input model: 4.150 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 569.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.004 0.260 167280 Z= 0.236 Angle : 0.579 38.713 239783 Z= 0.301 Chirality : 0.040 0.708 29238 Planarity : 0.006 0.551 19630 Dihedral : 20.817 179.415 82792 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 0.12 % Allowed : 0.49 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.07), residues: 11810 helix: -0.77 (0.07), residues: 4815 sheet: -0.04 (0.13), residues: 1592 loop : -0.84 (0.08), residues: 5403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 427 HIS 0.007 0.001 HIS A 148 PHE 0.032 0.002 PHE o 102 TYR 0.027 0.002 TYR m 338 ARG 0.009 0.000 ARG b 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1371 time to evaluate : 10.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 300 ARG cc_start: 0.7249 (mmt90) cc_final: 0.7037 (mmt90) REVERT: J 336 LYS cc_start: 0.7932 (mmtp) cc_final: 0.7409 (pttt) REVERT: L 41 THR cc_start: 0.8730 (m) cc_final: 0.8453 (m) REVERT: O 52 LEU cc_start: 0.8700 (tp) cc_final: 0.8392 (tp) REVERT: O 56 ASP cc_start: 0.7820 (t70) cc_final: 0.7479 (t0) REVERT: b 530 LYS cc_start: 0.6942 (mttm) cc_final: 0.6560 (mmtt) REVERT: d 6 ASP cc_start: 0.6704 (m-30) cc_final: 0.6193 (m-30) REVERT: e 15 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8203 (mmtm) REVERT: u 128 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5990 (pt0) REVERT: 8 431 GLU cc_start: 0.5209 (tp30) cc_final: 0.4927 (tt0) REVERT: U 61 THR cc_start: 0.6885 (p) cc_final: 0.6659 (p) REVERT: k 21 LYS cc_start: 0.6315 (mmtt) cc_final: 0.5938 (tppt) REVERT: k 64 LYS cc_start: 0.8230 (mtpp) cc_final: 0.8006 (mtpp) REVERT: n 144 ASN cc_start: 0.7571 (t0) cc_final: 0.7217 (t0) REVERT: D 135 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7183 (mtp85) REVERT: o 209 LYS cc_start: 0.6485 (tptm) cc_final: 0.6134 (mttt) REVERT: w 719 MET cc_start: 0.8677 (ptp) cc_final: 0.8403 (ptm) REVERT: a 53 LEU cc_start: 0.2482 (tp) cc_final: 0.2227 (mt) REVERT: x 168 MET cc_start: 0.7696 (tpt) cc_final: 0.7479 (tpt) REVERT: x 470 ILE cc_start: 0.4261 (mm) cc_final: 0.3620 (tp) outliers start: 12 outliers final: 4 residues processed: 1378 average time/residue: 1.4580 time to fit residues: 3414.4015 Evaluate side-chains 1029 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1025 time to evaluate : 9.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 400 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 1237 optimal weight: 0.9980 chunk 1110 optimal weight: 0.9990 chunk 616 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 749 optimal weight: 0.0270 chunk 593 optimal weight: 20.0000 chunk 1148 optimal weight: 8.9990 chunk 444 optimal weight: 9.9990 chunk 698 optimal weight: 3.9990 chunk 854 optimal weight: 20.0000 chunk 1330 optimal weight: 6.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 11 ASN 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 317 GLN M 41 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN W 148 GLN W 205 GLN X 137 ASN j 30 GLN l 137 ASN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 276 ASN v 39 ASN z 23 GLN 8 381 ASN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN U 88 GLN p 308 GLN t 182 ASN t 300 GLN D 330 ASN w 386 GLN w 420 ASN ** x 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 167280 Z= 0.162 Angle : 0.544 16.955 239783 Z= 0.287 Chirality : 0.037 0.242 29238 Planarity : 0.004 0.123 19630 Dihedral : 21.941 179.731 58183 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.94 % Rotamer: Outliers : 0.68 % Allowed : 6.59 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.08), residues: 11810 helix: 0.65 (0.07), residues: 4954 sheet: 0.08 (0.13), residues: 1605 loop : -0.81 (0.08), residues: 5251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP b 427 HIS 0.006 0.001 HIS A 175 PHE 0.029 0.001 PHE D 96 TYR 0.016 0.001 TYR x 436 ARG 0.005 0.000 ARG O 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1133 time to evaluate : 10.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6616 (pp20) cc_final: 0.6395 (pp20) REVERT: H 152 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7397 (mp0) REVERT: J 295 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: J 336 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7420 (pttt) REVERT: O 56 ASP cc_start: 0.7771 (t70) cc_final: 0.7563 (t70) REVERT: S 110 MET cc_start: 0.8821 (mmp) cc_final: 0.8391 (mmm) REVERT: W 85 TYR cc_start: 0.5560 (t80) cc_final: 0.5271 (t80) REVERT: b 107 GLN cc_start: 0.7406 (pt0) cc_final: 0.7159 (pt0) REVERT: b 530 LYS cc_start: 0.6566 (mttm) cc_final: 0.6169 (mmtt) REVERT: d 6 ASP cc_start: 0.6575 (m-30) cc_final: 0.6039 (m-30) REVERT: e 15 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8173 (mmtm) REVERT: m 580 GLN cc_start: 0.5929 (tm-30) cc_final: 0.5683 (tp40) REVERT: r 241 LYS cc_start: 0.6038 (tptp) cc_final: 0.5563 (ttpt) REVERT: u 128 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6127 (pt0) REVERT: 8 40 LYS cc_start: 0.6094 (ttmm) cc_final: 0.5769 (ttmt) REVERT: 8 431 GLU cc_start: 0.5072 (tp30) cc_final: 0.4862 (tt0) REVERT: I 154 GLU cc_start: 0.6280 (mt-10) cc_final: 0.6070 (mt-10) REVERT: R 92 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: U 61 THR cc_start: 0.6884 (p) cc_final: 0.6677 (p) REVERT: D 96 PHE cc_start: 0.6704 (p90) cc_final: 0.6420 (p90) REVERT: D 135 ARG cc_start: 0.7348 (mtm180) cc_final: 0.7036 (mtp180) REVERT: o 209 LYS cc_start: 0.6477 (tptm) cc_final: 0.6059 (mttt) REVERT: w 386 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6429 (mp-120) REVERT: w 719 MET cc_start: 0.8278 (ptp) cc_final: 0.8012 (ptm) REVERT: 5 7 ARG cc_start: 0.5917 (mtm-85) cc_final: 0.5625 (mtm110) REVERT: x 168 MET cc_start: 0.7666 (tpt) cc_final: 0.7449 (tpt) REVERT: x 328 ASP cc_start: 0.5493 (m-30) cc_final: 0.5288 (m-30) REVERT: x 470 ILE cc_start: 0.4284 (mm) cc_final: 0.4072 (tp) outliers start: 71 outliers final: 48 residues processed: 1181 average time/residue: 1.4256 time to fit residues: 2888.8004 Evaluate side-chains 1080 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1029 time to evaluate : 10.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 386 GLN Chi-restraints excluded: chain x residue 24 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 517 SER Chi-restraints excluded: chain x residue 521 ASP Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 739 optimal weight: 10.0000 chunk 412 optimal weight: 9.9990 chunk 1107 optimal weight: 10.0000 chunk 905 optimal weight: 0.9990 chunk 366 optimal weight: 8.9990 chunk 1332 optimal weight: 10.0000 chunk 1439 optimal weight: 30.0000 chunk 1186 optimal weight: 20.0000 chunk 1321 optimal weight: 20.0000 chunk 454 optimal weight: 7.9990 chunk 1069 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN C 116 ASN C 320 ASN L 103 ASN M 62 GLN ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN X 137 ASN Y 26 GLN Y 81 GLN b 120 GLN b 534 HIS d 57 GLN i 100 HIS ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 447 GLN z 23 GLN I 293 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN R 118 HIS t 51 ASN o 199 ASN w 141 GLN w 386 GLN w 677 HIS ** x 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 167280 Z= 0.356 Angle : 0.661 15.528 239783 Z= 0.341 Chirality : 0.044 0.302 29238 Planarity : 0.005 0.124 19630 Dihedral : 21.984 179.382 58182 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 1.67 % Allowed : 9.53 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.08), residues: 11810 helix: 0.75 (0.07), residues: 4962 sheet: -0.09 (0.13), residues: 1608 loop : -0.97 (0.08), residues: 5240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP b 427 HIS 0.009 0.002 HIS 8 18 PHE 0.035 0.002 PHE F 229 TYR 0.025 0.002 TYR P 4 ARG 0.010 0.001 ARG O 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1046 time to evaluate : 9.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6710 (pp20) cc_final: 0.6383 (pp20) REVERT: H 106 LYS cc_start: 0.7657 (pptt) cc_final: 0.7434 (ptpt) REVERT: J 285 MET cc_start: 0.8938 (mmm) cc_final: 0.8664 (mmm) REVERT: J 295 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: S 90 MET cc_start: 0.8127 (mtt) cc_final: 0.7830 (mtt) REVERT: S 110 MET cc_start: 0.8807 (mmp) cc_final: 0.8265 (mmm) REVERT: W 10 VAL cc_start: 0.6921 (OUTLIER) cc_final: 0.6659 (t) REVERT: b 503 MET cc_start: 0.6800 (mtm) cc_final: 0.6174 (mtt) REVERT: b 530 LYS cc_start: 0.6594 (mttm) cc_final: 0.6134 (mmtt) REVERT: d 6 ASP cc_start: 0.6981 (m-30) cc_final: 0.6383 (m-30) REVERT: e 15 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8230 (mmtm) REVERT: r 179 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7363 (mt0) REVERT: r 241 LYS cc_start: 0.6217 (tptp) cc_final: 0.5802 (ttpt) REVERT: I 154 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5945 (mt-10) REVERT: K 158 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7991 (ttmt) REVERT: K 326 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6292 (pp) REVERT: R 92 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: g 109 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6300 (m) REVERT: k 21 LYS cc_start: 0.6611 (mmtt) cc_final: 0.6391 (mmtp) REVERT: n 144 ASN cc_start: 0.7846 (t0) cc_final: 0.7396 (t0) REVERT: D 135 ARG cc_start: 0.7349 (mtm180) cc_final: 0.6959 (mtp85) REVERT: D 138 MET cc_start: 0.7287 (mtm) cc_final: 0.7017 (mtp) REVERT: o 209 LYS cc_start: 0.6514 (tptm) cc_final: 0.6141 (mttt) REVERT: w 377 MET cc_start: 0.6041 (ttm) cc_final: 0.5431 (ttm) REVERT: w 719 MET cc_start: 0.8448 (ptp) cc_final: 0.8139 (ptm) REVERT: x 98 GLN cc_start: 0.5187 (tt0) cc_final: 0.4845 (mt0) REVERT: x 168 MET cc_start: 0.7734 (tpt) cc_final: 0.7500 (tpt) REVERT: x 470 ILE cc_start: 0.4482 (mm) cc_final: 0.4254 (tp) REVERT: x 557 ARG cc_start: 0.1098 (mmp80) cc_final: 0.0250 (ttp-110) outliers start: 174 outliers final: 125 residues processed: 1165 average time/residue: 1.3901 time to fit residues: 2782.9741 Evaluate side-chains 1126 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 994 time to evaluate : 10.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 219 THR Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 124 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 68 ASP Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 648 ASP Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 557 SER Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 156 CYS Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 344 LEU Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 111 TRP Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain w residue 429 MET Chi-restraints excluded: chain w residue 542 LEU Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 199 THR Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 349 THR Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 517 SER Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 1316 optimal weight: 8.9990 chunk 1002 optimal weight: 1.9990 chunk 691 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 636 optimal weight: 2.9990 chunk 894 optimal weight: 3.9990 chunk 1337 optimal weight: 10.0000 chunk 1416 optimal weight: 6.9990 chunk 698 optimal weight: 5.9990 chunk 1267 optimal weight: 10.0000 chunk 381 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN J 317 GLN L 103 ASN M 62 GLN S 46 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 26 GLN Y 81 GLN j 30 GLN m 250 HIS ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN G 243 GLN p 308 GLN t 34 GLN ** w 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 167280 Z= 0.183 Angle : 0.541 15.570 239783 Z= 0.284 Chirality : 0.038 0.253 29238 Planarity : 0.004 0.119 19630 Dihedral : 21.898 179.168 58182 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 1.59 % Allowed : 11.29 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.08), residues: 11810 helix: 1.16 (0.07), residues: 4965 sheet: -0.09 (0.13), residues: 1637 loop : -0.89 (0.08), residues: 5208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP b 427 HIS 0.006 0.001 HIS 8 18 PHE 0.024 0.001 PHE x 61 TYR 0.016 0.001 TYR 8 497 ARG 0.005 0.000 ARG d 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1043 time to evaluate : 10.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6663 (pp20) cc_final: 0.6378 (pp20) REVERT: A 221 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8655 (ptt) REVERT: J 262 LYS cc_start: 0.7831 (tptp) cc_final: 0.7494 (ttpt) REVERT: J 295 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: S 90 MET cc_start: 0.8027 (mtt) cc_final: 0.7822 (mtt) REVERT: S 110 MET cc_start: 0.8756 (mmp) cc_final: 0.8162 (mmm) REVERT: Y 120 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: d 6 ASP cc_start: 0.6827 (m-30) cc_final: 0.6217 (m-30) REVERT: e 15 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8209 (mmtm) REVERT: q 489 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7201 (mm) REVERT: q 510 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7162 (tttt) REVERT: r 205 GLN cc_start: 0.8564 (tp40) cc_final: 0.8295 (tp40) REVERT: r 241 LYS cc_start: 0.6251 (tptp) cc_final: 0.5764 (ttpt) REVERT: u 62 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: z 43 LYS cc_start: 0.8046 (mttt) cc_final: 0.7682 (mttt) REVERT: I 154 GLU cc_start: 0.6281 (mt-10) cc_final: 0.5953 (mt-10) REVERT: K 112 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: K 235 PRO cc_start: 0.8592 (Cg_endo) cc_final: 0.8291 (Cg_exo) REVERT: R 92 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: k 10 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: n 229 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8806 (mm) REVERT: p 441 ILE cc_start: 0.5856 (pt) cc_final: 0.5521 (mt) REVERT: t 34 GLN cc_start: 0.8571 (mt0) cc_final: 0.8300 (mt0) REVERT: D 135 ARG cc_start: 0.7318 (mtm180) cc_final: 0.6976 (mtp85) REVERT: D 167 MET cc_start: 0.7583 (ttm) cc_final: 0.7186 (ttm) REVERT: o 209 LYS cc_start: 0.6476 (tptm) cc_final: 0.6145 (mttt) REVERT: w 377 MET cc_start: 0.6048 (ttm) cc_final: 0.5489 (ttm) REVERT: w 650 LYS cc_start: 0.7933 (mttt) cc_final: 0.7694 (ttpp) REVERT: a 53 LEU cc_start: 0.2113 (tp) cc_final: 0.1869 (mp) REVERT: 5 66 LYS cc_start: 0.5331 (OUTLIER) cc_final: 0.5016 (tttp) REVERT: x 50 ASP cc_start: 0.6083 (t0) cc_final: 0.5870 (t70) REVERT: x 98 GLN cc_start: 0.5306 (tt0) cc_final: 0.5010 (mt0) REVERT: x 168 MET cc_start: 0.7683 (tpt) cc_final: 0.7442 (tpt) REVERT: x 470 ILE cc_start: 0.4489 (mm) cc_final: 0.4195 (tp) REVERT: x 557 ARG cc_start: 0.0952 (mmp80) cc_final: 0.0063 (ttp-110) outliers start: 166 outliers final: 109 residues processed: 1162 average time/residue: 1.3957 time to fit residues: 2784.7996 Evaluate side-chains 1115 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 995 time to evaluate : 10.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 102 ASP Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain m residue 126 SER Chi-restraints excluded: chain m residue 450 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain y residue 124 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 68 ASP Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain w residue 542 LEU Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 361 THR Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 503 LYS Chi-restraints excluded: chain x residue 517 SER Chi-restraints excluded: chain x residue 521 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 1179 optimal weight: 4.9990 chunk 803 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 1054 optimal weight: 1.9990 chunk 584 optimal weight: 9.9990 chunk 1208 optimal weight: 30.0000 chunk 978 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 723 optimal weight: 2.9990 chunk 1271 optimal weight: 9.9990 chunk 357 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN L 103 ASN M 62 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 81 GLN Y 120 GLN l 137 ASN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 192 HIS z 23 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN p 207 HIS ** w 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 167280 Z= 0.235 Angle : 0.567 15.582 239783 Z= 0.296 Chirality : 0.039 0.269 29238 Planarity : 0.004 0.119 19630 Dihedral : 21.881 179.094 58182 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.14 % Allowed : 12.07 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.08), residues: 11810 helix: 1.22 (0.07), residues: 4969 sheet: -0.08 (0.13), residues: 1627 loop : -0.92 (0.08), residues: 5214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 427 HIS 0.008 0.001 HIS 8 18 PHE 0.028 0.002 PHE F 229 TYR 0.016 0.002 TYR o 134 ARG 0.007 0.000 ARG p 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1019 time to evaluate : 10.306 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: A 204 GLU cc_start: 0.6691 (pp20) cc_final: 0.6413 (pp20) REVERT: A 221 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8636 (ptt) REVERT: B 102 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7313 (tp) REVERT: J 262 LYS cc_start: 0.7823 (tptp) cc_final: 0.7361 (ttpt) REVERT: J 295 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: S 110 MET cc_start: 0.8752 (mmp) cc_final: 0.8177 (mmm) REVERT: W 10 VAL cc_start: 0.6935 (OUTLIER) cc_final: 0.6658 (t) REVERT: W 220 TYR cc_start: 0.5454 (t80) cc_final: 0.5239 (t80) REVERT: X 24 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7085 (mt) REVERT: b 116 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7925 (mt) REVERT: b 171 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7025 (tp) REVERT: b 287 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6332 (mp) REVERT: d 6 ASP cc_start: 0.6887 (m-30) cc_final: 0.6244 (m-30) REVERT: m 443 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8809 (pt) REVERT: m 580 GLN cc_start: 0.5541 (tm-30) cc_final: 0.5124 (mp10) REVERT: q 489 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7233 (mm) REVERT: r 179 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: r 241 LYS cc_start: 0.6185 (tptp) cc_final: 0.5775 (ttpt) REVERT: u 62 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: z 43 LYS cc_start: 0.8163 (mttt) cc_final: 0.7781 (mttt) REVERT: I 150 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5994 (mm-30) REVERT: I 154 GLU cc_start: 0.6220 (mt-10) cc_final: 0.5954 (mt-10) REVERT: K 32 ILE cc_start: 0.5781 (OUTLIER) cc_final: 0.5352 (mt) REVERT: K 112 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: R 92 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: c 74 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7190 (p0) REVERT: k 10 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: n 144 ASN cc_start: 0.7863 (t0) cc_final: 0.7396 (t0) REVERT: n 229 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8827 (mm) REVERT: p 436 GLU cc_start: 0.5103 (tp30) cc_final: 0.4167 (tm-30) REVERT: p 441 ILE cc_start: 0.5824 (pt) cc_final: 0.5494 (mt) REVERT: D 135 ARG cc_start: 0.7317 (mtm180) cc_final: 0.6972 (mtp85) REVERT: D 167 MET cc_start: 0.7650 (ttm) cc_final: 0.7327 (ttm) REVERT: o 209 LYS cc_start: 0.6503 (tptm) cc_final: 0.6173 (mttt) REVERT: w 377 MET cc_start: 0.5995 (ttm) cc_final: 0.5537 (ttm) REVERT: w 650 LYS cc_start: 0.7951 (mttt) cc_final: 0.7732 (ttpp) REVERT: 5 66 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.5069 (tttp) REVERT: x 50 ASP cc_start: 0.6144 (t0) cc_final: 0.5917 (t70) REVERT: x 98 GLN cc_start: 0.5314 (tt0) cc_final: 0.5032 (mt0) REVERT: x 168 MET cc_start: 0.7703 (tpt) cc_final: 0.7447 (tpt) REVERT: x 412 ARG cc_start: 0.4485 (mtm110) cc_final: 0.4192 (mtp-110) REVERT: x 495 MET cc_start: 0.2028 (mmp) cc_final: 0.1615 (mmt) REVERT: x 557 ARG cc_start: 0.1053 (mmp80) cc_final: 0.0298 (ttp-110) outliers start: 223 outliers final: 152 residues processed: 1177 average time/residue: 1.4493 time to fit residues: 2945.5858 Evaluate side-chains 1159 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 988 time to evaluate : 10.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 102 ASP Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 173 CYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 318 MET Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain m residue 277 MET Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 443 LEU Chi-restraints excluded: chain m residue 450 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 244 PHE Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 219 THR Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 124 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 68 ASP Chi-restraints excluded: chain 8 residue 71 VAL Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 577 LEU Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain 8 residue 648 ASP Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 557 SER Chi-restraints excluded: chain I residue 583 THR Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 183 VAL Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 238 LEU Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 361 THR Chi-restraints excluded: chain x residue 503 LYS Chi-restraints excluded: chain x residue 517 SER Chi-restraints excluded: chain x residue 521 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 476 optimal weight: 1.9990 chunk 1275 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 831 optimal weight: 20.0000 chunk 349 optimal weight: 0.4980 chunk 1417 optimal weight: 7.9990 chunk 1176 optimal weight: 4.9990 chunk 656 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 468 optimal weight: 1.9990 chunk 744 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN M 62 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 81 GLN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** 8 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN x 258 ASN x 282 GLN ** x 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 167280 Z= 0.227 Angle : 0.561 15.603 239783 Z= 0.292 Chirality : 0.039 0.266 29238 Planarity : 0.004 0.119 19630 Dihedral : 21.867 179.203 58182 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 2.25 % Allowed : 12.65 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.08), residues: 11810 helix: 1.27 (0.07), residues: 4974 sheet: -0.08 (0.13), residues: 1614 loop : -0.92 (0.08), residues: 5222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 427 HIS 0.007 0.001 HIS 8 18 PHE 0.027 0.002 PHE F 229 TYR 0.016 0.001 TYR 8 497 ARG 0.010 0.000 ARG Y 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1005 time to evaluate : 10.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6661 (pp20) cc_final: 0.6418 (pp20) REVERT: A 221 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8630 (ptt) REVERT: B 102 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7304 (tp) REVERT: B 112 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7786 (t0) REVERT: J 262 LYS cc_start: 0.7863 (tptp) cc_final: 0.7377 (ttpt) REVERT: J 295 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: S 110 MET cc_start: 0.8733 (mmp) cc_final: 0.8160 (mmm) REVERT: W 10 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6677 (t) REVERT: X 24 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7085 (mt) REVERT: Y 120 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: b 2 GLN cc_start: 0.6885 (pt0) cc_final: 0.6558 (pt0) REVERT: b 116 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7894 (mt) REVERT: b 171 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7015 (tp) REVERT: b 287 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6336 (mp) REVERT: d 6 ASP cc_start: 0.6911 (m-30) cc_final: 0.6235 (m-30) REVERT: m 443 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8783 (pt) REVERT: q 247 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.5170 (tt0) REVERT: q 489 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7223 (mm) REVERT: r 179 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: r 241 LYS cc_start: 0.6185 (tptp) cc_final: 0.5784 (ttpt) REVERT: u 62 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: z 43 LYS cc_start: 0.8163 (mttt) cc_final: 0.7731 (mttt) REVERT: I 468 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: K 32 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5545 (mt) REVERT: R 92 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: U 13 LYS cc_start: 0.7375 (ttpt) cc_final: 0.7118 (ttpt) REVERT: k 10 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: n 144 ASN cc_start: 0.7874 (t0) cc_final: 0.7402 (t0) REVERT: n 229 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8825 (mm) REVERT: p 227 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: p 436 GLU cc_start: 0.4946 (tp30) cc_final: 0.4085 (tm-30) REVERT: p 441 ILE cc_start: 0.5686 (pt) cc_final: 0.5400 (mt) REVERT: D 113 ASN cc_start: 0.6866 (m110) cc_final: 0.6623 (m110) REVERT: D 135 ARG cc_start: 0.7309 (mtm180) cc_final: 0.6984 (mtp85) REVERT: o 209 LYS cc_start: 0.6496 (tptm) cc_final: 0.6213 (mttt) REVERT: w 377 MET cc_start: 0.6004 (ttm) cc_final: 0.5543 (ttm) REVERT: w 650 LYS cc_start: 0.7948 (mttt) cc_final: 0.7723 (ttpp) REVERT: 5 66 LYS cc_start: 0.5335 (OUTLIER) cc_final: 0.4938 (tttp) REVERT: x 50 ASP cc_start: 0.5994 (t0) cc_final: 0.5774 (t70) REVERT: x 98 GLN cc_start: 0.5310 (tt0) cc_final: 0.5053 (mt0) REVERT: x 106 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5839 (t80) REVERT: x 168 MET cc_start: 0.7700 (tpt) cc_final: 0.7448 (tpt) REVERT: x 180 MET cc_start: 0.5691 (mmm) cc_final: 0.5440 (mmm) REVERT: x 363 ARG cc_start: 0.3552 (mmt-90) cc_final: 0.3171 (mmm-85) REVERT: x 412 ARG cc_start: 0.4494 (mtm110) cc_final: 0.4206 (mtp-110) REVERT: x 435 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6396 (t80) REVERT: x 495 MET cc_start: 0.2042 (mmp) cc_final: 0.1584 (mmt) REVERT: x 536 TRP cc_start: 0.5517 (m100) cc_final: 0.4699 (m100) outliers start: 234 outliers final: 168 residues processed: 1167 average time/residue: 1.3577 time to fit residues: 2731.8974 Evaluate side-chains 1169 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 977 time to evaluate : 9.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 102 ASP Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 47 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 173 CYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 318 MET Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain m residue 133 ASP Chi-restraints excluded: chain m residue 277 MET Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 443 LEU Chi-restraints excluded: chain m residue 467 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 244 PHE Chi-restraints excluded: chain q residue 247 GLU Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 219 THR Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 124 GLU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 68 ASP Chi-restraints excluded: chain 8 residue 71 VAL Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 577 LEU Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 468 GLU Chi-restraints excluded: chain I residue 557 SER Chi-restraints excluded: chain I residue 583 THR Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain n residue 582 GLU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 227 TYR Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 183 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 106 PHE Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 361 THR Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 517 SER Chi-restraints excluded: chain x residue 521 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 1366 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 807 optimal weight: 0.9990 chunk 1035 optimal weight: 3.9990 chunk 802 optimal weight: 6.9990 chunk 1193 optimal weight: 10.0000 chunk 791 optimal weight: 5.9990 chunk 1412 optimal weight: 0.0270 chunk 883 optimal weight: 4.9990 chunk 860 optimal weight: 7.9990 chunk 651 optimal weight: 10.0000 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN X 137 ASN Y 120 GLN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** 8 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN U 25 ASN c 71 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 167280 Z= 0.168 Angle : 0.533 15.523 239783 Z= 0.280 Chirality : 0.037 0.253 29238 Planarity : 0.004 0.118 19630 Dihedral : 21.869 179.044 58182 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 2.10 % Allowed : 13.22 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.08), residues: 11810 helix: 1.38 (0.07), residues: 4982 sheet: -0.06 (0.13), residues: 1623 loop : -0.89 (0.08), residues: 5205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 427 HIS 0.006 0.001 HIS 8 18 PHE 0.023 0.001 PHE x 61 TYR 0.020 0.001 TYR S 81 ARG 0.010 0.000 ARG x 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1017 time to evaluate : 10.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6636 (pp20) cc_final: 0.6417 (pp20) REVERT: A 221 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8622 (ptt) REVERT: B 102 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7277 (tp) REVERT: J 262 LYS cc_start: 0.7808 (tptp) cc_final: 0.7326 (ttpt) REVERT: J 295 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: S 110 MET cc_start: 0.8744 (mmp) cc_final: 0.8139 (mmm) REVERT: W 10 VAL cc_start: 0.6940 (OUTLIER) cc_final: 0.6680 (t) REVERT: X 24 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7087 (mt) REVERT: b 2 GLN cc_start: 0.6882 (pt0) cc_final: 0.6553 (pt0) REVERT: b 171 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6988 (tp) REVERT: b 287 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6344 (mp) REVERT: d 6 ASP cc_start: 0.6887 (m-30) cc_final: 0.6226 (m-30) REVERT: m 443 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8767 (pt) REVERT: q 247 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5133 (tt0) REVERT: q 489 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7210 (mm) REVERT: r 179 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: r 241 LYS cc_start: 0.6258 (tptp) cc_final: 0.5816 (ttpt) REVERT: u 62 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: z 43 LYS cc_start: 0.8135 (mttt) cc_final: 0.7688 (mttt) REVERT: 8 72 GLU cc_start: 0.7042 (tp30) cc_final: 0.6663 (tp30) REVERT: 8 663 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.6139 (mp10) REVERT: I 468 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: K 32 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5528 (mt) REVERT: K 112 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: R 92 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: U 13 LYS cc_start: 0.7375 (ttpt) cc_final: 0.7152 (ttpt) REVERT: k 10 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: n 144 ASN cc_start: 0.7901 (t0) cc_final: 0.7400 (t0) REVERT: n 229 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8814 (mm) REVERT: p 227 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6639 (m-10) REVERT: p 436 GLU cc_start: 0.4999 (tp30) cc_final: 0.4119 (tm-30) REVERT: p 441 ILE cc_start: 0.5727 (pt) cc_final: 0.5467 (mt) REVERT: D 113 ASN cc_start: 0.6852 (m110) cc_final: 0.6591 (m110) REVERT: D 135 ARG cc_start: 0.7309 (mtm180) cc_final: 0.6984 (mtp85) REVERT: o 209 LYS cc_start: 0.6489 (tptm) cc_final: 0.6209 (mttt) REVERT: w 377 MET cc_start: 0.5997 (ttm) cc_final: 0.5542 (ttm) REVERT: 5 66 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.4968 (tttp) REVERT: x 50 ASP cc_start: 0.5988 (t0) cc_final: 0.5763 (t70) REVERT: x 98 GLN cc_start: 0.5301 (tt0) cc_final: 0.5048 (mt0) REVERT: x 168 MET cc_start: 0.7686 (tpt) cc_final: 0.7428 (tpt) REVERT: x 180 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.5375 (mmm) REVERT: x 363 ARG cc_start: 0.3537 (mmt-90) cc_final: 0.3098 (mmm-85) REVERT: x 412 ARG cc_start: 0.4479 (mtm110) cc_final: 0.4199 (mtp-110) REVERT: x 435 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6359 (t80) outliers start: 219 outliers final: 168 residues processed: 1169 average time/residue: 1.3950 time to fit residues: 2810.6576 Evaluate side-chains 1177 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 986 time to evaluate : 10.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 102 ASP Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 173 CYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 318 MET Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain m residue 133 ASP Chi-restraints excluded: chain m residue 277 MET Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 443 LEU Chi-restraints excluded: chain m residue 450 LEU Chi-restraints excluded: chain m residue 467 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 247 GLU Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain s residue 7 GLN Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 577 LEU Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain 8 residue 648 ASP Chi-restraints excluded: chain 8 residue 663 GLN Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 468 GLU Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain n residue 582 GLU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 227 TYR Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 183 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 542 LEU Chi-restraints excluded: chain w residue 723 GLU Chi-restraints excluded: chain a residue 91 LYS Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 180 MET Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 238 LEU Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 349 THR Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 503 LYS Chi-restraints excluded: chain x residue 517 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 873 optimal weight: 0.5980 chunk 563 optimal weight: 9.9990 chunk 843 optimal weight: 0.0770 chunk 425 optimal weight: 0.4980 chunk 277 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 897 optimal weight: 6.9990 chunk 962 optimal weight: 20.0000 chunk 698 optimal weight: 0.0980 chunk 131 optimal weight: 10.0000 chunk 1109 optimal weight: 9.9990 overall best weight: 1.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN A 148 HIS ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN X 137 ASN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** 8 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 638 ASN I 245 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN x 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 167280 Z= 0.142 Angle : 0.508 15.496 239783 Z= 0.267 Chirality : 0.036 0.266 29238 Planarity : 0.004 0.116 19630 Dihedral : 21.802 179.574 58182 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.92 % Rotamer: Outliers : 1.88 % Allowed : 13.56 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.08), residues: 11810 helix: 1.54 (0.07), residues: 4991 sheet: 0.00 (0.13), residues: 1630 loop : -0.83 (0.08), residues: 5189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 427 HIS 0.005 0.001 HIS A 175 PHE 0.023 0.001 PHE x 61 TYR 0.017 0.001 TYR 8 497 ARG 0.011 0.000 ARG J 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1024 time to evaluate : 10.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6677 (pp20) cc_final: 0.6435 (pp20) REVERT: A 221 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8629 (ptt) REVERT: B 112 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7730 (t0) REVERT: H 144 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7938 (mp) REVERT: J 262 LYS cc_start: 0.7719 (tptp) cc_final: 0.7236 (ttpt) REVERT: J 295 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: J 328 LEU cc_start: 0.8735 (tp) cc_final: 0.8466 (tp) REVERT: S 110 MET cc_start: 0.8763 (mmp) cc_final: 0.8141 (mmm) REVERT: W 10 VAL cc_start: 0.6982 (OUTLIER) cc_final: 0.6733 (t) REVERT: b 2 GLN cc_start: 0.6904 (pt0) cc_final: 0.6573 (pt0) REVERT: b 171 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6949 (tp) REVERT: b 287 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6311 (mp) REVERT: d 6 ASP cc_start: 0.6735 (m-30) cc_final: 0.6069 (m-30) REVERT: m 443 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8747 (pt) REVERT: q 247 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5109 (tt0) REVERT: q 489 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7167 (mm) REVERT: q 506 LEU cc_start: 0.7437 (mt) cc_final: 0.7215 (mt) REVERT: q 510 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7021 (tmtt) REVERT: r 179 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: r 241 LYS cc_start: 0.6250 (tptp) cc_final: 0.5838 (ttpt) REVERT: u 62 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: u 128 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6095 (pt0) REVERT: z 43 LYS cc_start: 0.8118 (mttt) cc_final: 0.7661 (mttt) REVERT: 8 72 GLU cc_start: 0.6994 (tp30) cc_final: 0.6600 (tp30) REVERT: 8 663 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: I 468 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6611 (mm-30) REVERT: K 32 ILE cc_start: 0.5822 (OUTLIER) cc_final: 0.5494 (mt) REVERT: K 112 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: K 235 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8276 (Cg_exo) REVERT: R 92 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: R 105 LEU cc_start: 0.8285 (tp) cc_final: 0.8033 (tp) REVERT: R 109 TYR cc_start: 0.7015 (m-10) cc_final: 0.6585 (m-10) REVERT: U 13 LYS cc_start: 0.7389 (ttpt) cc_final: 0.7183 (ttpt) REVERT: k 10 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7381 (tp40) REVERT: k 31 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7484 (pp) REVERT: n 195 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: n 229 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8814 (mm) REVERT: p 436 GLU cc_start: 0.5042 (tp30) cc_final: 0.4158 (tm-30) REVERT: D 113 ASN cc_start: 0.6746 (m110) cc_final: 0.6482 (m110) REVERT: D 135 ARG cc_start: 0.7212 (mtm180) cc_final: 0.6885 (mtp85) REVERT: o 209 LYS cc_start: 0.6442 (tptm) cc_final: 0.6200 (mttt) REVERT: w 357 GLN cc_start: 0.4989 (OUTLIER) cc_final: 0.4667 (mt0) REVERT: w 377 MET cc_start: 0.5968 (ttm) cc_final: 0.5506 (ttm) REVERT: 5 37 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6859 (mm) REVERT: 5 66 LYS cc_start: 0.5224 (OUTLIER) cc_final: 0.4873 (tttp) REVERT: x 50 ASP cc_start: 0.5973 (t0) cc_final: 0.5763 (t70) REVERT: x 98 GLN cc_start: 0.5285 (tt0) cc_final: 0.5055 (mt0) REVERT: x 106 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5824 (t80) REVERT: x 168 MET cc_start: 0.7674 (tpt) cc_final: 0.7415 (tpt) REVERT: x 180 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5311 (mmm) REVERT: x 206 MET cc_start: 0.6903 (tpt) cc_final: 0.6230 (tpt) REVERT: x 213 ILE cc_start: 0.6306 (pt) cc_final: 0.6068 (mm) REVERT: x 412 ARG cc_start: 0.4323 (mtm110) cc_final: 0.4097 (mtp-110) REVERT: x 495 MET cc_start: 0.1908 (mmp) cc_final: 0.1633 (mmt) outliers start: 196 outliers final: 143 residues processed: 1161 average time/residue: 1.3937 time to fit residues: 2785.0557 Evaluate side-chains 1160 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 990 time to evaluate : 10.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 47 ASP Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 173 CYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 318 MET Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain m residue 133 ASP Chi-restraints excluded: chain m residue 277 MET Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 443 LEU Chi-restraints excluded: chain m residue 450 LEU Chi-restraints excluded: chain m residue 467 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 242 THR Chi-restraints excluded: chain q residue 244 PHE Chi-restraints excluded: chain q residue 247 GLU Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 71 VAL Chi-restraints excluded: chain 8 residue 511 VAL Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 577 LEU Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain 8 residue 648 ASP Chi-restraints excluded: chain 8 residue 663 GLN Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 468 GLU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 183 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 723 GLU Chi-restraints excluded: chain a residue 91 LYS Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 37 LEU Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 24 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 106 PHE Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 180 MET Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 238 LEU Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 517 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 1284 optimal weight: 10.0000 chunk 1352 optimal weight: 2.9990 chunk 1234 optimal weight: 0.9990 chunk 1315 optimal weight: 4.9990 chunk 791 optimal weight: 10.0000 chunk 573 optimal weight: 9.9990 chunk 1033 optimal weight: 7.9990 chunk 403 optimal weight: 0.9980 chunk 1189 optimal weight: 20.0000 chunk 1244 optimal weight: 8.9990 chunk 1311 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN X 137 ASN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** 8 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** x 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 167280 Z= 0.230 Angle : 0.560 15.590 239783 Z= 0.291 Chirality : 0.039 0.264 29238 Planarity : 0.004 0.118 19630 Dihedral : 21.811 178.919 58182 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.27 % Allowed : 13.46 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.08), residues: 11810 helix: 1.45 (0.07), residues: 4982 sheet: -0.02 (0.13), residues: 1631 loop : -0.88 (0.08), residues: 5197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 427 HIS 0.008 0.001 HIS 8 18 PHE 0.028 0.002 PHE F 229 TYR 0.017 0.002 TYR S 81 ARG 0.010 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 984 time to evaluate : 10.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6664 (pp20) cc_final: 0.6429 (pp20) REVERT: A 221 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8655 (ptt) REVERT: B 102 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7313 (tp) REVERT: B 112 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7781 (t0) REVERT: H 144 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7974 (mp) REVERT: J 262 LYS cc_start: 0.7767 (tptp) cc_final: 0.7268 (ttpt) REVERT: J 295 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: S 90 MET cc_start: 0.8132 (mtt) cc_final: 0.7779 (mtt) REVERT: W 10 VAL cc_start: 0.6982 (OUTLIER) cc_final: 0.6723 (t) REVERT: X 24 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7078 (mt) REVERT: Y 120 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: b 2 GLN cc_start: 0.6897 (pt0) cc_final: 0.6568 (pt0) REVERT: b 171 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6949 (tp) REVERT: b 287 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6343 (mp) REVERT: d 6 ASP cc_start: 0.6839 (m-30) cc_final: 0.6326 (m-30) REVERT: m 443 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8814 (pt) REVERT: q 247 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5114 (tt0) REVERT: q 489 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7215 (mm) REVERT: r 179 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: r 241 LYS cc_start: 0.6170 (tptp) cc_final: 0.5780 (ttpt) REVERT: u 62 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: z 43 LYS cc_start: 0.8164 (mttt) cc_final: 0.7712 (mttt) REVERT: 8 72 GLU cc_start: 0.7041 (tp30) cc_final: 0.6685 (tp30) REVERT: 8 663 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.6173 (mp10) REVERT: I 468 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: K 32 ILE cc_start: 0.5983 (OUTLIER) cc_final: 0.5580 (mt) REVERT: K 112 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: R 92 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: R 105 LEU cc_start: 0.8310 (tp) cc_final: 0.8026 (tp) REVERT: R 109 TYR cc_start: 0.7101 (m-10) cc_final: 0.6663 (m-10) REVERT: U 13 LYS cc_start: 0.7442 (ttpt) cc_final: 0.7214 (ttpt) REVERT: k 10 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: n 195 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: n 229 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8826 (mm) REVERT: p 241 MET cc_start: 0.5437 (OUTLIER) cc_final: 0.5222 (mtp) REVERT: p 436 GLU cc_start: 0.5037 (tp30) cc_final: 0.4160 (tm-30) REVERT: D 113 ASN cc_start: 0.6772 (m110) cc_final: 0.6496 (m110) REVERT: D 135 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6883 (mtp85) REVERT: o 209 LYS cc_start: 0.6450 (tptm) cc_final: 0.6217 (mttt) REVERT: w 357 GLN cc_start: 0.4811 (OUTLIER) cc_final: 0.4531 (mt0) REVERT: w 377 MET cc_start: 0.5892 (ttm) cc_final: 0.5440 (ttm) REVERT: 5 66 LYS cc_start: 0.5285 (OUTLIER) cc_final: 0.4896 (tttp) REVERT: x 98 GLN cc_start: 0.5320 (tt0) cc_final: 0.5112 (mt0) REVERT: x 106 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5827 (t80) REVERT: x 168 MET cc_start: 0.7666 (tpt) cc_final: 0.7420 (tpt) REVERT: x 180 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5303 (mmm) REVERT: x 206 MET cc_start: 0.6869 (tpt) cc_final: 0.6173 (tpt) REVERT: x 213 ILE cc_start: 0.6371 (pt) cc_final: 0.6125 (mm) REVERT: x 363 ARG cc_start: 0.3785 (mmm160) cc_final: 0.2909 (mtt-85) REVERT: x 366 ARG cc_start: 0.4013 (ptt90) cc_final: 0.2519 (ttt-90) REVERT: x 412 ARG cc_start: 0.4341 (mtm110) cc_final: 0.4131 (mtp-110) REVERT: x 435 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6335 (t80) REVERT: x 495 MET cc_start: 0.1981 (mmp) cc_final: 0.1629 (mmt) outliers start: 237 outliers final: 178 residues processed: 1158 average time/residue: 1.4110 time to fit residues: 2814.3871 Evaluate side-chains 1180 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 973 time to evaluate : 9.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 43 LEU Chi-restraints excluded: chain W residue 47 ASP Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 173 CYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 318 MET Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 126 SER Chi-restraints excluded: chain m residue 133 ASP Chi-restraints excluded: chain m residue 277 MET Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 443 LEU Chi-restraints excluded: chain m residue 450 LEU Chi-restraints excluded: chain m residue 467 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 242 THR Chi-restraints excluded: chain q residue 244 PHE Chi-restraints excluded: chain q residue 247 GLU Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 71 VAL Chi-restraints excluded: chain 8 residue 511 VAL Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 577 LEU Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain 8 residue 648 ASP Chi-restraints excluded: chain 8 residue 663 GLN Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 468 GLU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain n residue 582 GLU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 241 MET Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 183 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain w residue 169 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain w residue 429 MET Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 723 GLU Chi-restraints excluded: chain a residue 31 THR Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 24 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 106 PHE Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 180 MET Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 238 LEU Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 349 THR Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 517 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 864 optimal weight: 3.9990 chunk 1391 optimal weight: 6.9990 chunk 849 optimal weight: 9.9990 chunk 660 optimal weight: 0.9980 chunk 967 optimal weight: 6.9990 chunk 1459 optimal weight: 0.8980 chunk 1343 optimal weight: 6.9990 chunk 1162 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 897 optimal weight: 4.9990 chunk 712 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN X 137 ASN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** 8 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN U 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 167280 Z= 0.172 Angle : 0.538 15.552 239783 Z= 0.281 Chirality : 0.037 0.324 29238 Planarity : 0.004 0.117 19630 Dihedral : 21.823 178.916 58182 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.03 % Allowed : 13.70 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.08), residues: 11810 helix: 1.51 (0.07), residues: 4975 sheet: -0.02 (0.13), residues: 1627 loop : -0.86 (0.08), residues: 5208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 427 HIS 0.006 0.001 HIS C 311 PHE 0.023 0.001 PHE x 61 TYR 0.020 0.001 TYR x 436 ARG 0.019 0.000 ARG w 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23620 Ramachandran restraints generated. 11810 Oldfield, 0 Emsley, 11810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 989 time to evaluate : 9.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6652 (pp20) cc_final: 0.6428 (pp20) REVERT: A 221 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8632 (ptt) REVERT: B 102 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7289 (tp) REVERT: B 112 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7789 (t0) REVERT: H 144 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7968 (mp) REVERT: J 262 LYS cc_start: 0.7738 (tptp) cc_final: 0.7247 (ttpt) REVERT: J 295 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: W 10 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6731 (t) REVERT: W 85 TYR cc_start: 0.5381 (t80) cc_final: 0.4999 (t80) REVERT: X 24 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7084 (mt) REVERT: Y 120 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: b 2 GLN cc_start: 0.6886 (pt0) cc_final: 0.6563 (pt0) REVERT: b 171 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6944 (tp) REVERT: b 287 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6328 (mp) REVERT: d 6 ASP cc_start: 0.6602 (m-30) cc_final: 0.6068 (m-30) REVERT: m 443 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8766 (pt) REVERT: q 247 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.5106 (tt0) REVERT: q 489 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7201 (mm) REVERT: r 179 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: r 241 LYS cc_start: 0.6159 (tptp) cc_final: 0.5776 (ttpt) REVERT: u 62 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: z 43 LYS cc_start: 0.8176 (mttt) cc_final: 0.7782 (mttt) REVERT: 8 72 GLU cc_start: 0.7019 (tp30) cc_final: 0.6652 (tp30) REVERT: 8 659 TYR cc_start: 0.6150 (t80) cc_final: 0.5882 (t80) REVERT: 8 663 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6106 (mp10) REVERT: I 468 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: K 32 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5565 (mt) REVERT: K 112 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: K 260 VAL cc_start: 0.7737 (m) cc_final: 0.7413 (m) REVERT: R 92 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: R 105 LEU cc_start: 0.8283 (tp) cc_final: 0.8005 (tp) REVERT: R 109 TYR cc_start: 0.7081 (m-10) cc_final: 0.6645 (m-10) REVERT: U 13 LYS cc_start: 0.7438 (ttpt) cc_final: 0.7214 (ttpt) REVERT: k 10 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: n 195 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: n 229 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8816 (mm) REVERT: p 436 GLU cc_start: 0.5041 (tp30) cc_final: 0.4159 (tm-30) REVERT: D 113 ASN cc_start: 0.6752 (m110) cc_final: 0.6477 (m110) REVERT: D 135 ARG cc_start: 0.7241 (mtm180) cc_final: 0.6905 (mtp85) REVERT: o 209 LYS cc_start: 0.6438 (tptm) cc_final: 0.6185 (mttt) REVERT: w 357 GLN cc_start: 0.4821 (OUTLIER) cc_final: 0.4527 (mt0) REVERT: w 377 MET cc_start: 0.5887 (ttm) cc_final: 0.5433 (ttm) REVERT: 5 37 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6838 (mm) REVERT: 5 66 LYS cc_start: 0.5251 (OUTLIER) cc_final: 0.4881 (tttp) REVERT: x 98 GLN cc_start: 0.5315 (tt0) cc_final: 0.5103 (mt0) REVERT: x 106 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5819 (t80) REVERT: x 168 MET cc_start: 0.7656 (tpt) cc_final: 0.7411 (tpt) REVERT: x 206 MET cc_start: 0.6700 (tpt) cc_final: 0.6167 (tpt) REVERT: x 213 ILE cc_start: 0.6366 (pt) cc_final: 0.6120 (mm) REVERT: x 363 ARG cc_start: 0.3691 (mmm160) cc_final: 0.2877 (mtt-85) REVERT: x 366 ARG cc_start: 0.3962 (ptt90) cc_final: 0.2507 (ttt-90) REVERT: x 412 ARG cc_start: 0.4329 (mtm110) cc_final: 0.4122 (mtp-110) REVERT: x 435 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6307 (t80) REVERT: x 495 MET cc_start: 0.1958 (mmp) cc_final: 0.1624 (mmt) outliers start: 212 outliers final: 175 residues processed: 1140 average time/residue: 1.3088 time to fit residues: 2570.8945 Evaluate side-chains 1181 residues out of total 10501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 978 time to evaluate : 9.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 113 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 248 LYS Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 29 GLU Chi-restraints excluded: chain W residue 43 LEU Chi-restraints excluded: chain W residue 47 ASP Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 173 CYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 240 ILE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 318 MET Chi-restraints excluded: chain b residue 324 LEU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 126 SER Chi-restraints excluded: chain m residue 133 ASP Chi-restraints excluded: chain m residue 277 MET Chi-restraints excluded: chain m residue 357 THR Chi-restraints excluded: chain m residue 443 LEU Chi-restraints excluded: chain m residue 450 LEU Chi-restraints excluded: chain m residue 467 LEU Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 756 ASP Chi-restraints excluded: chain q residue 242 THR Chi-restraints excluded: chain q residue 244 PHE Chi-restraints excluded: chain q residue 247 GLU Chi-restraints excluded: chain q residue 338 VAL Chi-restraints excluded: chain q residue 344 HIS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 510 LYS Chi-restraints excluded: chain q residue 526 LYS Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 179 GLN Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain 8 residue 41 THR Chi-restraints excluded: chain 8 residue 71 VAL Chi-restraints excluded: chain 8 residue 511 VAL Chi-restraints excluded: chain 8 residue 529 THR Chi-restraints excluded: chain 8 residue 566 GLN Chi-restraints excluded: chain 8 residue 577 LEU Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 642 VAL Chi-restraints excluded: chain 8 residue 648 ASP Chi-restraints excluded: chain 8 residue 663 GLN Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 349 ASN Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 468 GLU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 646 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 92 GLN Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 88 ASP Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 10 GLN Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain n residue 154 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 556 MET Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 267 LEU Chi-restraints excluded: chain p residue 274 ILE Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 354 THR Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 297 ARG Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 392 MET Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 183 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain w residue 49 VAL Chi-restraints excluded: chain w residue 117 LEU Chi-restraints excluded: chain w residue 152 VAL Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 199 CYS Chi-restraints excluded: chain w residue 279 THR Chi-restraints excluded: chain w residue 357 GLN Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 723 GLU Chi-restraints excluded: chain a residue 31 THR Chi-restraints excluded: chain a residue 91 LYS Chi-restraints excluded: chain 5 residue 24 PHE Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 37 LEU Chi-restraints excluded: chain 5 residue 66 LYS Chi-restraints excluded: chain 5 residue 169 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 52 VAL Chi-restraints excluded: chain x residue 106 PHE Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 179 ASP Chi-restraints excluded: chain x residue 205 THR Chi-restraints excluded: chain x residue 238 LEU Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 339 VAL Chi-restraints excluded: chain x residue 349 THR Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 517 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1465 random chunks: chunk 923 optimal weight: 3.9990 chunk 1238 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 1071 optimal weight: 0.0060 chunk 171 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 1164 optimal weight: 6.9990 chunk 487 optimal weight: 0.8980 chunk 1195 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 317 GLN ** L 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN X 137 ASN m 625 GLN ** m 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 GLN ** 8 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.161386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135544 restraints weight = 174858.054| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.12 r_work: 0.3272 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 167280 Z= 0.173 Angle : 0.532 15.523 239783 Z= 0.278 Chirality : 0.037 0.274 29238 Planarity : 0.004 0.117 19630 Dihedral : 21.801 178.935 58182 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 2.04 % Allowed : 13.82 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.08), residues: 11810 helix: 1.52 (0.07), residues: 4980 sheet: 0.01 (0.13), residues: 1632 loop : -0.85 (0.08), residues: 5198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 427 HIS 0.006 0.001 HIS 8 18 PHE 0.024 0.001 PHE x 61 TYR 0.023 0.001 TYR x 436 ARG 0.016 0.000 ARG J 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41123.87 seconds wall clock time: 720 minutes 56.72 seconds (43256.72 seconds total)