Starting phenix.real_space_refine (version: dev) on Sat Apr 23 14:33:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yws_10973/04_2022/6yws_10973_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yws_10973/04_2022/6yws_10973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yws_10973/04_2022/6yws_10973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yws_10973/04_2022/6yws_10973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yws_10973/04_2022/6yws_10973_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yws_10973/04_2022/6yws_10973_trim_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 1.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 223349 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 90332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2820, 90332 Inner-chain residues flagged as termini: ['pdbres=" U A 34 "', 'pdbres=" U A 120 "', 'pdbres=" U A 645 "', 'pdbres=" U A1083 "', 'pdbres=" U A1128 "', 'pdbres=" A A1432 "', 'pdbres=" A A1655 "', 'pdbres=" U A1678 "', 'pdbres=" U A1727 "', 'pdbres=" A A1958 "', 'pdbres=" C A2145 "', 'pdbres=" A A2492 "', 'pdbres=" U A2524 "', 'pdbres=" A A2560 "', 'pdbres=" G A2694 "', 'pdbres=" A A2737 "', 'pdbres=" U A2951 "', 'pdbres=" U A3134 "', 'pdbres=" U A3193 "'] Classifications: {'RNA': 2820} Modifications used: {'rna3p_pyr': 1043, 'rna2p_pur': 307, 'rna3p_pur': 1282, 'rna2p_pyr': 188, '3*END': 20} Link IDs: {'rna3p': 2324, 'rna2p': 495} Chain breaks: 19 Chain: "B" Number of atoms: 5136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5136 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 21, 'TRANS': 304} Chain: "C" Number of atoms: 4758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4758 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 19, 'TRANS': 287} Chain: "D" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4068 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 13, 'TRANS': 240} Chain breaks: 1 Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4910 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 35, 'TRANS': 273} Chain: "F" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3253 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 15, 'TRANS': 185} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1245 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "f" Number of atoms: 3801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3801 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 22, 'TRANS': 221, 'PCIS': 1} Chain: "g" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2257 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2885 Classifications: {'peptide': 183} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 171, 'PCIS': 1} Chain: "I" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1898 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3827 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 15, 'TRANS': 227} Chain: "K" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2751 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain: "L" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3135 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain: "M" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3164 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain: "N" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2176 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "O" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4532 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 Chain: "P" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2975 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 15, 'TRANS': 164} Chain: "Q" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5829 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 24, 'TRANS': 328} Chain: "R" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4499 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 13, 'TRANS': 251, 'PCIS': 1} Chain breaks: 1 Chain: "S" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2979 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain breaks: 1 Chain: "T" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2950 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 12, 'TRANS': 167} Chain: "U" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2263 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "V" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 951 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 949 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "X" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 836 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "Y" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 777 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "0" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 797 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "1" Number of atoms: 6014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 6014 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 22, 'TRANS': 343, 'PCIS': 1} Chain: "2" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2101 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 114, 'PCIS': 1} Chain: "3" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1536 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "4" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2139 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 10, 'TRANS': 126} Chain: "5" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5429 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 28, 'TRANS': 321} Chain breaks: 1 Chain: "6" Number of atoms: 4474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4474 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain breaks: 2 Chain: "7" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1383 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "8" Number of atoms: 5374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5374 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 19, 'TRANS': 311} Chain: "h" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1577 Classifications: {'peptide': 98} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "i" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1998 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain breaks: 1 Chain: "9" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3341 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain: "a" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2671 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 15, 'TRANS': 145} Chain breaks: 1 Chain: "b" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2693 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 15, 'TRANS': 145} Chain: "c" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1700 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "d" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3797 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain breaks: 1 Chain: "e" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3821 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 14, 'TRANS': 227} Chain: "j" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3133 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 14, 'TRANS': 180} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 186 Unusual residues: {' K': 12, ' MG': 160, 'SPM': 1} Classifications: {'undetermined': 173} Link IDs: {None: 172} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' MG': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A1FRQ SG CYS W 94 149.235 238.218 116.914 1.00 33.12 S ATOM A1FSO SG CYS W 97 146.139 239.890 115.446 1.00 38.50 S ATOM A1FXA SG CYS W 107 147.048 236.393 114.365 1.00 32.80 S ATOM A1FY9 SG CYS W 110 149.233 239.479 113.361 1.00 38.04 S ATOM A1HHL SG CYS 0 89 138.631 140.988 176.021 1.00 30.16 S ATOM A1HIR SG CYS 0 92 137.303 143.888 173.944 1.00 26.12 S ATOM A1HS8 SG CYS 0 111 140.815 144.053 175.573 1.00 25.57 S Time building chain proxies: 76.67, per 1000 atoms: 0.34 Number of scatterers: 223349 At special positions: 0 Unit cell: (225.78, 289.38, 257.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 K 12 19.00 S 254 16.00 P 2822 15.00 Mg 163 11.99 O 31164 8.00 N 23064 7.00 C 68398 6.00 H 97470 1.00 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: 145.74 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 0 201 " pdb="ZN ZN 0 201 " - pdb=" ND1 HIS 0 117 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 89 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 111 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 92 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" SG CYS W 97 " pdb="ZN ZN W 201 " - pdb=" SG CYS W 110 " pdb="ZN ZN W 201 " - pdb=" SG CYS W 94 " pdb="ZN ZN W 201 " - pdb=" SG CYS W 107 " Number of angles added : 9 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15240 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 289 helices and 78 sheets defined 43.5% alpha, 12.8% beta 770 base pairs and 1593 stacking pairs defined. Time for finding SS restraints: 123.92 Creating SS restraints... Processing helix chain 'B' and resid 72 through 79 removed outlier: 5.077A pdb=" N HIS B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.773A pdb=" N THR B 96 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.312A pdb=" N GLY B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 106' Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.661A pdb=" N SER B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.730A pdb=" N ALA B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.589A pdb=" N ILE B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.878A pdb=" N SER B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.756A pdb=" N MET B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 323' Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.679A pdb=" N ASN C 80 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 81' Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 162 through 167 removed outlier: 4.910A pdb=" N GLY C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 4.133A pdb=" N LYS C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.756A pdb=" N PHE C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 209' Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 321 through 337 removed outlier: 3.586A pdb=" N ASN C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) Proline residue: C 337 - end of helix Processing helix chain 'C' and resid 338 through 360 Processing helix chain 'C' and resid 361 through 369 removed outlier: 3.786A pdb=" N LEU C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 93 through 109 removed outlier: 3.521A pdb=" N SER D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 185 removed outlier: 3.500A pdb=" N ARG D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 212 through 232 Processing helix chain 'D' and resid 248 through 259 removed outlier: 3.599A pdb=" N GLY D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 removed outlier: 3.819A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.612A pdb=" N GLN D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 removed outlier: 3.832A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLU E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.054A pdb=" N ALA E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Proline residue: E 59 - end of helix No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 62 through 70 removed outlier: 5.588A pdb=" N ARG E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.604A pdb=" N ALA E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 133 through 142 removed outlier: 4.188A pdb=" N TYR E 142 " --> pdb=" O MET E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 213 removed outlier: 4.649A pdb=" N LEU E 210 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS E 211 " --> pdb=" O PRO E 207 " (cutoff:3.500A) Proline residue: E 213 - end of helix Processing helix chain 'E' and resid 214 through 228 Processing helix chain 'E' and resid 259 through 277 removed outlier: 4.784A pdb=" N LEU E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 299 through 306 removed outlier: 4.529A pdb=" N LEU E 305 " --> pdb=" O GLU E 301 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 313 removed outlier: 4.728A pdb=" N ASN E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 346 Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.680A pdb=" N ALA E 169 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN E 170 " --> pdb=" O TYR E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 58 removed outlier: 3.957A pdb=" N THR F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 126 through 149 removed outlier: 3.597A pdb=" N GLY F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 231 removed outlier: 4.461A pdb=" N TRP F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG F 230 " --> pdb=" O ILE F 226 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 102 through 110 removed outlier: 3.574A pdb=" N GLN G 107 " --> pdb=" O PRO G 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 89 removed outlier: 3.584A pdb=" N LEU f 79 " --> pdb=" O LYS f 75 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER f 84 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR f 89 " --> pdb=" O MET f 85 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 119 removed outlier: 3.679A pdb=" N ASN f 118 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL f 119 " --> pdb=" O ALA f 115 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 132 removed outlier: 4.963A pdb=" N LYS f 131 " --> pdb=" O ASP f 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 138 through 151 removed outlier: 3.723A pdb=" N VAL f 144 " --> pdb=" O ARG f 140 " (cutoff:3.500A) Processing helix chain 'f' and resid 179 through 192 removed outlier: 4.777A pdb=" N ASN f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 200 removed outlier: 3.882A pdb=" N LYS f 198 " --> pdb=" O GLU f 194 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL f 200 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing helix chain 'f' and resid 201 through 209 Proline residue: f 206 - end of helix removed outlier: 4.404A pdb=" N VAL f 209 " --> pdb=" O ALA f 205 " (cutoff:3.500A) Processing helix chain 'f' and resid 221 through 233 removed outlier: 3.653A pdb=" N ALA f 227 " --> pdb=" O ALA f 223 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL f 231 " --> pdb=" O ALA f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 247 through 252 removed outlier: 4.198A pdb=" N TYR f 251 " --> pdb=" O ASN f 247 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP f 252 " --> pdb=" O PRO f 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 247 through 252' Processing helix chain 'f' and resid 253 through 263 removed outlier: 3.723A pdb=" N GLN f 260 " --> pdb=" O GLN f 256 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS f 261 " --> pdb=" O SER f 257 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU f 263 " --> pdb=" O LEU f 259 " (cutoff:3.500A) Processing helix chain 'f' and resid 275 through 285 removed outlier: 3.700A pdb=" N LYS f 280 " --> pdb=" O TYR f 276 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP f 281 " --> pdb=" O ASP f 277 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 298 removed outlier: 3.553A pdb=" N GLN f 295 " --> pdb=" O GLY f 291 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS f 298 " --> pdb=" O ALA f 294 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 35 removed outlier: 4.021A pdb=" N ALA g 34 " --> pdb=" O PRO g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 54 removed outlier: 3.723A pdb=" N ALA g 51 " --> pdb=" O LYS g 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA g 54 " --> pdb=" O ASN g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 92 Processing helix chain 'g' and resid 116 through 130 removed outlier: 3.975A pdb=" N LYS g 127 " --> pdb=" O ILE g 123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN g 128 " --> pdb=" O ALA g 124 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU g 130 " --> pdb=" O ILE g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.548A pdb=" N ARG g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL g 145 " --> pdb=" O LEU g 141 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE g 146 " --> pdb=" O CYS g 142 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG g 150 " --> pdb=" O ILE g 146 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER g 151 " --> pdb=" O TYR g 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 6 removed outlier: 3.504A pdb=" N VAL H 5 " --> pdb=" O MET H 1 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLY H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1 through 6' Processing helix chain 'H' and resid 8 through 13 Processing helix chain 'H' and resid 42 through 56 removed outlier: 3.537A pdb=" N THR H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 114 Processing helix chain 'H' and resid 115 through 129 removed outlier: 3.847A pdb=" N VAL H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Proline residue: H 129 - end of helix Processing helix chain 'H' and resid 133 through 142 removed outlier: 3.883A pdb=" N LEU H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 181 removed outlier: 3.654A pdb=" N ALA H 171 " --> pdb=" O GLY H 167 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU H 181 " --> pdb=" O GLU H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 removed outlier: 3.892A pdb=" N LYS I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 119' Processing helix chain 'I' and resid 120 through 128 removed outlier: 3.642A pdb=" N MET I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA I 127 " --> pdb=" O ILE I 123 " (cutoff:3.500A) Proline residue: I 128 - end of helix Processing helix chain 'J' and resid 48 through 53 removed outlier: 3.602A pdb=" N LEU J 53 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.853A pdb=" N TYR J 60 " --> pdb=" O ASN J 56 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 61' Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 101 through 107 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 143 through 151 removed outlier: 3.908A pdb=" N GLY J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.561A pdb=" N PHE J 171 " --> pdb=" O GLY J 167 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS J 172 " --> pdb=" O LYS J 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 167 through 172' Processing helix chain 'J' and resid 183 through 194 removed outlier: 3.527A pdb=" N GLU J 188 " --> pdb=" O ALA J 184 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY J 194 " --> pdb=" O ILE J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 213 removed outlier: 3.522A pdb=" N LYS J 208 " --> pdb=" O LYS J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 240 removed outlier: 3.978A pdb=" N VAL J 229 " --> pdb=" O GLY J 225 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU J 230 " --> pdb=" O LYS J 226 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU J 231 " --> pdb=" O GLU J 227 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU J 239 " --> pdb=" O GLN J 235 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS J 240 " --> pdb=" O ALA J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.618A pdb=" N ASP J 260 " --> pdb=" O GLU J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 4.389A pdb=" N LEU J 271 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA J 272 " --> pdb=" O SER J 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 267 through 272' Processing helix chain 'K' and resid 109 through 125 Processing helix chain 'K' and resid 178 through 194 removed outlier: 3.504A pdb=" N ALA K 185 " --> pdb=" O VAL K 181 " (cutoff:3.500A) Proline residue: K 194 - end of helix Processing helix chain 'K' and resid 218 through 224 removed outlier: 3.561A pdb=" N LEU K 222 " --> pdb=" O THR K 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 33 Processing helix chain 'L' and resid 39 through 59 removed outlier: 4.002A pdb=" N ARG L 47 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L 48 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP L 59 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 72 removed outlier: 3.695A pdb=" N ARG L 64 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR L 72 " --> pdb=" O GLN L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 83 Proline residue: L 79 - end of helix Processing helix chain 'L' and resid 84 through 90 removed outlier: 3.526A pdb=" N ALA L 90 " --> pdb=" O ARG L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 141 Processing helix chain 'L' and resid 145 through 159 removed outlier: 3.549A pdb=" N THR L 156 " --> pdb=" O MET L 152 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE L 158 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG L 159 " --> pdb=" O VAL L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 177 removed outlier: 4.925A pdb=" N ALA L 165 " --> pdb=" O ASP L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 192 removed outlier: 3.700A pdb=" N TRP L 188 " --> pdb=" O ASN L 184 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS L 189 " --> pdb=" O PRO L 185 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS L 190 " --> pdb=" O LYS L 186 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP L 192 " --> pdb=" O TRP L 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 192' Processing helix chain 'M' and resid 103 through 118 removed outlier: 4.585A pdb=" N LEU M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) Proline residue: M 118 - end of helix Processing helix chain 'M' and resid 120 through 127 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 206 through 212 Proline residue: M 212 - end of helix Processing helix chain 'N' and resid 89 through 102 removed outlier: 3.541A pdb=" N LEU N 95 " --> pdb=" O GLN N 91 " (cutoff:3.500A) Proline residue: N 97 - end of helix removed outlier: 3.832A pdb=" N GLN N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 166 removed outlier: 4.263A pdb=" N PHE N 165 " --> pdb=" O ASP N 161 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 161 through 166' Processing helix chain 'O' and resid 44 through 51 removed outlier: 4.533A pdb=" N GLY O 49 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS O 50 " --> pdb=" O PHE O 46 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 71 removed outlier: 3.756A pdb=" N THR O 71 " --> pdb=" O GLU O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 130 removed outlier: 4.540A pdb=" N ALA O 126 " --> pdb=" O ALA O 122 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS O 127 " --> pdb=" O ALA O 123 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP O 128 " --> pdb=" O ALA O 124 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN O 129 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 122 through 130' Processing helix chain 'O' and resid 137 through 142 Processing helix chain 'O' and resid 148 through 170 removed outlier: 3.700A pdb=" N ARG O 154 " --> pdb=" O ARG O 150 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP O 169 " --> pdb=" O GLN O 165 " (cutoff:3.500A) Proline residue: O 170 - end of helix Processing helix chain 'O' and resid 175 through 184 removed outlier: 3.871A pdb=" N ARG O 182 " --> pdb=" O GLU O 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR O 183 " --> pdb=" O ARG O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 209 removed outlier: 4.640A pdb=" N HIS O 203 " --> pdb=" O LYS O 199 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU O 204 " --> pdb=" O LYS O 200 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 223 Processing helix chain 'O' and resid 225 through 245 removed outlier: 4.367A pdb=" N LYS O 229 " --> pdb=" O LYS O 225 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU O 230 " --> pdb=" O LYS O 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 260 Processing helix chain 'O' and resid 326 through 345 removed outlier: 4.162A pdb=" N ARG O 330 " --> pdb=" O GLU O 326 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY O 345 " --> pdb=" O LYS O 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 65 Processing helix chain 'P' and resid 116 through 121 removed outlier: 5.132A pdb=" N GLU P 121 " --> pdb=" O GLU P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 148 removed outlier: 3.618A pdb=" N GLY P 148 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 175 Processing helix chain 'Q' and resid 1 through 63 removed outlier: 3.581A pdb=" N ARG Q 7 " --> pdb=" O LYS Q 3 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA Q 41 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN Q 57 " --> pdb=" O VAL Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 73 removed outlier: 3.979A pdb=" N ASP Q 72 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 68 through 73' Processing helix chain 'Q' and resid 86 through 92 Processing helix chain 'Q' and resid 97 through 106 removed outlier: 3.541A pdb=" N VAL Q 105 " --> pdb=" O ARG Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 removed outlier: 4.072A pdb=" N GLN Q 164 " --> pdb=" O PRO Q 160 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN Q 165 " --> pdb=" O GLN Q 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 160 through 165' Processing helix chain 'Q' and resid 179 through 184 removed outlier: 4.124A pdb=" N VAL Q 183 " --> pdb=" O PRO Q 179 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG Q 184 " --> pdb=" O ILE Q 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 179 through 184' Processing helix chain 'Q' and resid 250 through 256 Processing helix chain 'Q' and resid 269 through 277 removed outlier: 4.130A pdb=" N LEU Q 273 " --> pdb=" O PRO Q 269 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP Q 274 " --> pdb=" O GLN Q 270 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) Processing helix chain 'Q' and resid 288 through 313 removed outlier: 3.584A pdb=" N GLU Q 299 " --> pdb=" O LYS Q 295 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA Q 309 " --> pdb=" O LYS Q 305 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS Q 310 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA Q 311 " --> pdb=" O SER Q 307 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N MET Q 312 " --> pdb=" O ALA Q 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU Q 313 " --> pdb=" O ALA Q 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 314 through 331 removed outlier: 3.742A pdb=" N GLU Q 325 " --> pdb=" O ARG Q 321 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY Q 331 " --> pdb=" O ARG Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 336 through 352 removed outlier: 3.749A pdb=" N VAL Q 346 " --> pdb=" O LYS Q 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 286 Processing helix chain 'R' and resid 300 through 308 removed outlier: 5.017A pdb=" N ILE R 308 " --> pdb=" O ILE R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 382 removed outlier: 3.714A pdb=" N TYR R 355 " --> pdb=" O ARG R 351 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN R 365 " --> pdb=" O GLU R 361 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG R 370 " --> pdb=" O ARG R 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU R 372 " --> pdb=" O VAL R 368 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 95 removed outlier: 4.251A pdb=" N ASN S 92 " --> pdb=" O TYR S 88 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR S 93 " --> pdb=" O HIS S 89 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY S 94 " --> pdb=" O GLN S 90 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU S 95 " --> pdb=" O SER S 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 88 through 95' Processing helix chain 'S' and resid 142 through 153 Processing helix chain 'S' and resid 154 through 161 removed outlier: 3.786A pdb=" N GLY S 161 " --> pdb=" O GLU S 157 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 171 removed outlier: 3.824A pdb=" N GLY S 171 " --> pdb=" O VAL S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 185 removed outlier: 3.535A pdb=" N GLN S 183 " --> pdb=" O TRP S 179 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR S 184 " --> pdb=" O ARG S 180 " (cutoff:3.500A) Proline residue: S 185 - end of helix Processing helix chain 'S' and resid 186 through 199 removed outlier: 3.766A pdb=" N GLU S 196 " --> pdb=" O ALA S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 211 through 225 removed outlier: 3.592A pdb=" N GLN S 220 " --> pdb=" O LEU S 216 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN S 225 " --> pdb=" O VAL S 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 107 removed outlier: 4.410A pdb=" N ASP T 104 " --> pdb=" O HIS T 100 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE T 105 " --> pdb=" O GLY T 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE T 106 " --> pdb=" O LEU T 102 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR T 107 " --> pdb=" O TRP T 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 100 through 107' Processing helix chain 'T' and resid 115 through 122 removed outlier: 4.003A pdb=" N LYS T 121 " --> pdb=" O LEU T 117 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 135 removed outlier: 4.209A pdb=" N LYS T 133 " --> pdb=" O SER T 129 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS T 134 " --> pdb=" O GLU T 130 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER T 135 " --> pdb=" O LEU T 131 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 164 removed outlier: 3.511A pdb=" N TRP T 144 " --> pdb=" O HIS T 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 205 removed outlier: 3.559A pdb=" N GLU T 174 " --> pdb=" O ALA T 170 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS T 202 " --> pdb=" O GLU T 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 27 removed outlier: 3.629A pdb=" N HIS U 20 " --> pdb=" O PRO U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 51 removed outlier: 3.878A pdb=" N MET U 46 " --> pdb=" O GLN U 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS U 49 " --> pdb=" O GLY U 45 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL U 50 " --> pdb=" O MET U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 74 removed outlier: 3.584A pdb=" N LYS U 69 " --> pdb=" O LYS U 65 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU U 71 " --> pdb=" O GLU U 67 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG U 72 " --> pdb=" O LEU U 68 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS U 73 " --> pdb=" O LYS U 69 " (cutoff:3.500A) Proline residue: U 74 - end of helix Processing helix chain 'U' and resid 133 through 138 removed outlier: 3.596A pdb=" N LEU U 137 " --> pdb=" O ARG U 133 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY U 138 " --> pdb=" O ALA U 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 133 through 138' Processing helix chain 'U' and resid 141 through 152 removed outlier: 5.159A pdb=" N LYS U 152 " --> pdb=" O ILE U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 97 Proline residue: V 97 - end of helix Processing helix chain 'V' and resid 99 through 104 removed outlier: 3.660A pdb=" N LYS V 103 " --> pdb=" O ASP V 99 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN V 104 " --> pdb=" O LYS V 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 99 through 104' Processing helix chain 'W' and resid 71 through 83 removed outlier: 6.210A pdb=" N GLY W 82 " --> pdb=" O ARG W 78 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS W 83 " --> pdb=" O GLN W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 122 removed outlier: 3.783A pdb=" N ASP W 119 " --> pdb=" O LYS W 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN W 121 " --> pdb=" O PHE W 117 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLY W 122 " --> pdb=" O MET W 118 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 112 removed outlier: 3.695A pdb=" N GLN Y 108 " --> pdb=" O THR Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 120 removed outlier: 3.755A pdb=" N ARG Y 117 " --> pdb=" O GLY Y 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Y 119 " --> pdb=" O LEU Y 115 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR Y 120 " --> pdb=" O SER Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 134 removed outlier: 3.705A pdb=" N LYS Y 125 " --> pdb=" O LYS Y 121 " (cutoff:3.500A) Processing helix chain '1' and resid 89 through 99 removed outlier: 3.732A pdb=" N ALA 1 97 " --> pdb=" O ARG 1 93 " (cutoff:3.500A) Processing helix chain '1' and resid 109 through 149 removed outlier: 3.540A pdb=" N ALA 1 125 " --> pdb=" O GLN 1 121 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP 1 144 " --> pdb=" O ILE 1 140 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N SER 1 146 " --> pdb=" O ALA 1 142 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU 1 147 " --> pdb=" O ARG 1 143 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE 1 148 " --> pdb=" O ASP 1 144 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU 1 149 " --> pdb=" O ALA 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 151 through 176 removed outlier: 3.622A pdb=" N ARG 1 158 " --> pdb=" O ALA 1 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 1 161 " --> pdb=" O THR 1 157 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE 1 171 " --> pdb=" O GLU 1 167 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP 1 174 " --> pdb=" O LYS 1 170 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN 1 176 " --> pdb=" O LEU 1 172 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 187 Processing helix chain '1' and resid 193 through 208 removed outlier: 3.856A pdb=" N MET 1 207 " --> pdb=" O ARG 1 203 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 220 Processing helix chain '1' and resid 251 through 257 removed outlier: 5.231A pdb=" N VAL 1 257 " --> pdb=" O ARG 1 253 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 316 removed outlier: 3.908A pdb=" N VAL 1 315 " --> pdb=" O SER 1 311 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY 1 316 " --> pdb=" O LEU 1 312 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 311 through 316' Processing helix chain '1' and resid 355 through 366 removed outlier: 4.083A pdb=" N LEU 1 363 " --> pdb=" O LEU 1 359 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 1 364 " --> pdb=" O LYS 1 360 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN 1 365 " --> pdb=" O LYS 1 361 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG 1 366 " --> pdb=" O HIS 1 362 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 379 removed outlier: 3.659A pdb=" N PHE 1 378 " --> pdb=" O PHE 1 374 " (cutoff:3.500A) Processing helix chain '1' and resid 395 through 404 Processing helix chain '1' and resid 428 through 434 removed outlier: 3.709A pdb=" N ARG 1 433 " --> pdb=" O TRP 1 429 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN 1 434 " --> pdb=" O GLU 1 430 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 440 removed outlier: 4.283A pdb=" N LYS 1 439 " --> pdb=" O LYS 1 435 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER 1 440 " --> pdb=" O PRO 1 436 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 435 through 440' Processing helix chain '1' and resid 441 through 446 removed outlier: 3.574A pdb=" N VAL 1 445 " --> pdb=" O LEU 1 441 " (cutoff:3.500A) Processing helix chain '1' and resid 221 through 226 removed outlier: 3.539A pdb=" N LEU 1 226 " --> pdb=" O VAL 1 221 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 221 through 226' Processing helix chain '2' and resid 248 through 262 removed outlier: 3.890A pdb=" N LEU 2 261 " --> pdb=" O HIS 2 257 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER 2 262 " --> pdb=" O PHE 2 258 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 319 removed outlier: 3.623A pdb=" N ASN 2 318 " --> pdb=" O GLU 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 328 through 336 removed outlier: 3.940A pdb=" N LEU 2 336 " --> pdb=" O ARG 2 332 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 354 removed outlier: 4.164A pdb=" N ARG 2 353 " --> pdb=" O GLU 2 349 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ALA 2 354 " --> pdb=" O TYR 2 350 " (cutoff:3.500A) Processing helix chain '3' and resid 10 through 15 removed outlier: 4.107A pdb=" N LYS 3 14 " --> pdb=" O LEU 3 10 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU 3 15 " --> pdb=" O LYS 3 11 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 10 through 15' Processing helix chain '3' and resid 18 through 23 removed outlier: 3.786A pdb=" N VAL 3 22 " --> pdb=" O THR 3 18 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN 3 23 " --> pdb=" O THR 3 19 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 18 through 23' Processing helix chain '3' and resid 47 through 52 removed outlier: 5.561A pdb=" N ARG 3 52 " --> pdb=" O TYR 3 48 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 100 removed outlier: 3.576A pdb=" N SER 3 98 " --> pdb=" O ALA 3 94 " (cutoff:3.500A) Processing helix chain '4' and resid 14 through 19 removed outlier: 5.455A pdb=" N GLY 4 18 " --> pdb=" O ARG 4 14 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA 4 19 " --> pdb=" O ASN 4 15 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 14 through 19' Processing helix chain '4' and resid 35 through 47 removed outlier: 4.208A pdb=" N ARG 4 39 " --> pdb=" O ALA 4 35 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY 4 40 " --> pdb=" O GLY 4 36 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N MET 4 41 " --> pdb=" O SER 4 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY 4 43 " --> pdb=" O ARG 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 57 Proline residue: 4 57 - end of helix Processing helix chain '4' and resid 91 through 105 Processing helix chain '5' and resid 67 through 72 Proline residue: 5 72 - end of helix Processing helix chain '5' and resid 75 through 83 removed outlier: 3.931A pdb=" N ALA 5 79 " --> pdb=" O LEU 5 75 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU 5 80 " --> pdb=" O PRO 5 76 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR 5 81 " --> pdb=" O GLU 5 77 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER 5 82 " --> pdb=" O ARG 5 78 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA 5 83 " --> pdb=" O ALA 5 79 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 75 through 83' Processing helix chain '5' and resid 84 through 93 removed outlier: 3.571A pdb=" N ASN 5 93 " --> pdb=" O HIS 5 89 " (cutoff:3.500A) Processing helix chain '5' and resid 99 through 109 removed outlier: 3.954A pdb=" N LEU 5 107 " --> pdb=" O LEU 5 103 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL 5 108 " --> pdb=" O ALA 5 104 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP 5 109 " --> pdb=" O ARG 5 105 " (cutoff:3.500A) Processing helix chain '5' and resid 121 through 143 Processing helix chain '5' and resid 147 through 159 Processing helix chain '5' and resid 160 through 172 removed outlier: 3.735A pdb=" N GLY 5 172 " --> pdb=" O ALA 5 168 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 215 Processing helix chain '5' and resid 220 through 227 removed outlier: 3.994A pdb=" N ARG 5 224 " --> pdb=" O GLY 5 220 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL 5 225 " --> pdb=" O MET 5 221 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL 5 226 " --> pdb=" O ALA 5 222 " (cutoff:3.500A) Processing helix chain '5' and resid 281 through 307 removed outlier: 3.604A pdb=" N ALA 5 286 " --> pdb=" O PRO 5 282 " (cutoff:3.500A) Processing helix chain '5' and resid 308 through 320 Processing helix chain '5' and resid 326 through 331 removed outlier: 4.116A pdb=" N LEU 5 330 " --> pdb=" O ASP 5 326 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE 5 331 " --> pdb=" O ILE 5 327 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 326 through 331' Processing helix chain '5' and resid 335 through 348 Processing helix chain '5' and resid 387 through 406 removed outlier: 3.642A pdb=" N TYR 5 406 " --> pdb=" O ALA 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 414 through 421 removed outlier: 4.449A pdb=" N MET 5 418 " --> pdb=" O VAL 5 414 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU 5 419 " --> pdb=" O PRO 5 415 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU 5 420 " --> pdb=" O SER 5 416 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU 5 421 " --> pdb=" O ASP 5 417 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 414 through 421' Processing helix chain '6' and resid 105 through 123 removed outlier: 3.593A pdb=" N LEU 6 118 " --> pdb=" O TYR 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 127 through 132 removed outlier: 4.203A pdb=" N TYR 6 131 " --> pdb=" O ARG 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 136 through 150 Processing helix chain '6' and resid 176 through 181 removed outlier: 4.407A pdb=" N SER 6 180 " --> pdb=" O SER 6 176 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ARG 6 181 " --> pdb=" O GLN 6 177 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 176 through 181' Processing helix chain '6' and resid 182 through 193 removed outlier: 3.842A pdb=" N GLU 6 193 " --> pdb=" O LEU 6 189 " (cutoff:3.500A) Processing helix chain '6' and resid 219 through 225 Processing helix chain '6' and resid 267 through 280 Processing helix chain '6' and resid 345 through 353 removed outlier: 4.146A pdb=" N SER 6 351 " --> pdb=" O GLU 6 347 " (cutoff:3.500A) Processing helix chain '6' and resid 354 through 363 removed outlier: 3.631A pdb=" N VAL 6 361 " --> pdb=" O TYR 6 357 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY 6 363 " --> pdb=" O HIS 6 359 " (cutoff:3.500A) Processing helix chain '7' and resid 118 through 131 Processing helix chain '7' and resid 133 through 138 removed outlier: 3.618A pdb=" N VAL 7 137 " --> pdb=" O GLU 7 133 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG 7 138 " --> pdb=" O VAL 7 134 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 133 through 138' Processing helix chain '7' and resid 152 through 164 Processing helix chain '8' and resid 127 through 132 removed outlier: 5.981A pdb=" N ARG 8 132 " --> pdb=" O PRO 8 128 " (cutoff:3.500A) Processing helix chain '8' and resid 157 through 162 removed outlier: 4.354A pdb=" N PHE 8 161 " --> pdb=" O LYS 8 157 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ARG 8 162 " --> pdb=" O PRO 8 158 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 157 through 162' Processing helix chain '8' and resid 165 through 170 removed outlier: 3.689A pdb=" N GLU 8 169 " --> pdb=" O GLY 8 165 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR 8 170 " --> pdb=" O LYS 8 166 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 165 through 170' Processing helix chain '8' and resid 182 through 203 removed outlier: 3.964A pdb=" N VAL 8 187 " --> pdb=" O ARG 8 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG 8 190 " --> pdb=" O LYS 8 186 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS 8 201 " --> pdb=" O LEU 8 197 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE 8 202 " --> pdb=" O ALA 8 198 " (cutoff:3.500A) Processing helix chain '8' and resid 211 through 216 removed outlier: 5.418A pdb=" N ILE 8 216 " --> pdb=" O MET 8 212 " (cutoff:3.500A) Processing helix chain '8' and resid 219 through 228 removed outlier: 4.329A pdb=" N GLN 8 223 " --> pdb=" O GLY 8 219 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL 8 228 " --> pdb=" O ARG 8 224 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 277 removed outlier: 4.242A pdb=" N LEU 8 246 " --> pdb=" O ASN 8 242 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN 8 247 " --> pdb=" O GLU 8 243 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS 8 248 " --> pdb=" O SER 8 244 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN 8 271 " --> pdb=" O GLN 8 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 8 272 " --> pdb=" O GLU 8 268 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER 8 275 " --> pdb=" O ASN 8 271 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU 8 276 " --> pdb=" O ARG 8 272 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY 8 277 " --> pdb=" O LEU 8 273 " (cutoff:3.500A) Processing helix chain '8' and resid 278 through 293 removed outlier: 3.517A pdb=" N ALA 8 282 " --> pdb=" O GLU 8 278 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS 8 283 " --> pdb=" O LYS 8 279 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN 8 284 " --> pdb=" O GLU 8 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU 8 285 " --> pdb=" O GLN 8 281 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU 8 288 " --> pdb=" O GLN 8 284 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS 8 290 " --> pdb=" O LEU 8 286 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS 8 291 " --> pdb=" O GLU 8 287 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU 8 292 " --> pdb=" O GLU 8 288 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY 8 293 " --> pdb=" O GLY 8 289 " (cutoff:3.500A) Processing helix chain '8' and resid 307 through 318 removed outlier: 3.611A pdb=" N GLU 8 313 " --> pdb=" O ASP 8 309 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS 8 316 " --> pdb=" O VAL 8 312 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER 8 317 " --> pdb=" O GLU 8 313 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP 8 318 " --> pdb=" O LEU 8 314 " (cutoff:3.500A) Processing helix chain '8' and resid 320 through 326 removed outlier: 4.564A pdb=" N GLU 8 324 " --> pdb=" O ASN 8 320 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA 8 325 " --> pdb=" O ASP 8 321 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE 8 326 " --> pdb=" O TRP 8 322 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 320 through 326' Processing helix chain '8' and resid 329 through 344 Processing helix chain '8' and resid 349 through 357 removed outlier: 5.176A pdb=" N GLN 8 357 " --> pdb=" O LEU 8 353 " (cutoff:3.500A) Processing helix chain '8' and resid 358 through 368 Processing helix chain '8' and resid 374 through 383 removed outlier: 3.638A pdb=" N GLN 8 381 " --> pdb=" O GLU 8 377 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER 8 383 " --> pdb=" O ILE 8 379 " (cutoff:3.500A) Processing helix chain '8' and resid 399 through 408 Processing helix chain '8' and resid 409 through 421 removed outlier: 3.763A pdb=" N LYS 8 415 " --> pdb=" O LYS 8 411 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU 8 416 " --> pdb=" O VAL 8 412 " (cutoff:3.500A) Processing helix chain '8' and resid 434 through 440 removed outlier: 3.642A pdb=" N LEU 8 439 " --> pdb=" O GLU 8 435 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 31 removed outlier: 4.028A pdb=" N SER h 28 " --> pdb=" O ARG h 24 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE h 29 " --> pdb=" O LEU h 25 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU h 30 " --> pdb=" O PHE h 26 " (cutoff:3.500A) Proline residue: h 31 - end of helix Processing helix chain 'h' and resid 33 through 38 Processing helix chain 'h' and resid 74 through 97 removed outlier: 3.507A pdb=" N GLU h 81 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL h 82 " --> pdb=" O ILE h 78 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS h 85 " --> pdb=" O GLU h 81 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN h 90 " --> pdb=" O SER h 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 108 removed outlier: 3.797A pdb=" N TYR i 107 " --> pdb=" O PRO i 103 " (cutoff:3.500A) Proline residue: i 108 - end of helix No H-bonds generated for 'chain 'i' and resid 103 through 108' Processing helix chain 'i' and resid 109 through 115 removed outlier: 4.076A pdb=" N ARG i 113 " --> pdb=" O GLU i 109 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU i 115 " --> pdb=" O LEU i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 138 through 156 removed outlier: 4.403A pdb=" N ARG i 148 " --> pdb=" O MET i 144 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA i 149 " --> pdb=" O LYS i 145 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS i 153 " --> pdb=" O ALA i 149 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA i 156 " --> pdb=" O ALA i 152 " (cutoff:3.500A) Processing helix chain 'i' and resid 159 through 164 removed outlier: 4.504A pdb=" N LEU i 163 " --> pdb=" O ASP i 159 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA i 164 " --> pdb=" O LEU i 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 159 through 164' Processing helix chain 'i' and resid 183 through 218 removed outlier: 3.754A pdb=" N LYS i 193 " --> pdb=" O LEU i 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA i 200 " --> pdb=" O GLU i 196 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA i 207 " --> pdb=" O LYS i 203 " (cutoff:3.500A) Processing helix chain '9' and resid 64 through 69 removed outlier: 3.941A pdb=" N TYR 9 68 " --> pdb=" O PRO 9 64 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N THR 9 69 " --> pdb=" O ARG 9 65 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 64 through 69' Processing helix chain '9' and resid 85 through 90 removed outlier: 4.381A pdb=" N LYS 9 89 " --> pdb=" O ASP 9 85 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN 9 90 " --> pdb=" O PRO 9 86 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 85 through 90' Processing helix chain '9' and resid 96 through 109 removed outlier: 3.587A pdb=" N PHE 9 103 " --> pdb=" O LYS 9 99 " (cutoff:3.500A) Processing helix chain '9' and resid 111 through 116 removed outlier: 3.670A pdb=" N MET 9 115 " --> pdb=" O GLY 9 111 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU 9 116 " --> pdb=" O GLY 9 112 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 111 through 116' Processing helix chain '9' and resid 117 through 126 removed outlier: 3.773A pdb=" N TRP 9 122 " --> pdb=" O GLU 9 118 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 9 125 " --> pdb=" O LYS 9 121 " (cutoff:3.500A) Processing helix chain '9' and resid 129 through 134 removed outlier: 5.738A pdb=" N GLY 9 133 " --> pdb=" O SER 9 129 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG 9 134 " --> pdb=" O PHE 9 130 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 129 through 134' Processing helix chain '9' and resid 139 through 160 removed outlier: 3.553A pdb=" N GLN 9 147 " --> pdb=" O PHE 9 143 " (cutoff:3.500A) Processing helix chain '9' and resid 179 through 190 removed outlier: 3.524A pdb=" N ASN 9 183 " --> pdb=" O ALA 9 179 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE 9 184 " --> pdb=" O ALA 9 180 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU 9 187 " --> pdb=" O ASN 9 183 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE 9 188 " --> pdb=" O ILE 9 184 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR 9 189 " --> pdb=" O ASP 9 185 " (cutoff:3.500A) Processing helix chain '9' and resid 191 through 197 removed outlier: 3.961A pdb=" N ILE 9 195 " --> pdb=" O GLN 9 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP 9 197 " --> pdb=" O LEU 9 193 " (cutoff:3.500A) Processing helix chain '9' and resid 198 through 209 removed outlier: 3.542A pdb=" N GLY 9 205 " --> pdb=" O ILE 9 201 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 9 206 " --> pdb=" O ALA 9 202 " (cutoff:3.500A) Processing helix chain '9' and resid 223 through 248 removed outlier: 4.322A pdb=" N VAL 9 229 " --> pdb=" O GLU 9 225 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL 9 230 " --> pdb=" O SER 9 226 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL 9 231 " --> pdb=" O SER 9 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 9 241 " --> pdb=" O LEU 9 237 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 9 246 " --> pdb=" O GLY 9 242 " (cutoff:3.500A) Processing helix chain '9' and resid 249 through 266 removed outlier: 3.555A pdb=" N GLU 9 259 " --> pdb=" O ARG 9 255 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU 9 262 " --> pdb=" O ARG 9 258 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS 9 263 " --> pdb=" O GLU 9 259 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG 9 264 " --> pdb=" O LYS 9 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 52 Processing helix chain 'a' and resid 56 through 62 removed outlier: 3.660A pdb=" N LEU a 60 " --> pdb=" O HIS a 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN a 61 " --> pdb=" O GLU a 57 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL a 62 " --> pdb=" O SER a 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 56 through 62' Processing helix chain 'a' and resid 84 through 89 removed outlier: 3.508A pdb=" N LEU a 88 " --> pdb=" O PRO a 84 " (cutoff:3.500A) Proline residue: a 89 - end of helix No H-bonds generated for 'chain 'a' and resid 84 through 89' Processing helix chain 'a' and resid 98 through 103 Processing helix chain 'a' and resid 143 through 157 removed outlier: 3.784A pdb=" N GLU a 148 " --> pdb=" O PRO a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 171 Processing helix chain 'a' and resid 173 through 181 removed outlier: 3.532A pdb=" N MET a 178 " --> pdb=" O LYS a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 202 removed outlier: 3.602A pdb=" N GLN a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS a 191 " --> pdb=" O HIS a 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN a 201 " --> pdb=" O ARG a 197 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP a 202 " --> pdb=" O THR a 198 " (cutoff:3.500A) Processing helix chain 'a' and resid 203 through 223 removed outlier: 3.539A pdb=" N LYS a 217 " --> pdb=" O ALA a 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU a 218 " --> pdb=" O ARG a 214 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 14 removed outlier: 3.628A pdb=" N LEU b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 26 Proline residue: b 26 - end of helix Processing helix chain 'b' and resid 27 through 32 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 36 through 41 removed outlier: 4.391A pdb=" N HIS b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS b 41 " --> pdb=" O PRO b 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 36 through 41' Processing helix chain 'b' and resid 42 through 49 Proline residue: b 49 - end of helix Processing helix chain 'b' and resid 69 through 84 removed outlier: 3.682A pdb=" N HIS b 83 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 95 through 106 Processing helix chain 'b' and resid 122 through 143 removed outlier: 3.689A pdb=" N LEU b 128 " --> pdb=" O HIS b 124 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL b 129 " --> pdb=" O GLU b 125 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA b 130 " --> pdb=" O ARG b 126 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA b 141 " --> pdb=" O GLU b 137 " (cutoff:3.500A) Proline residue: b 143 - end of helix Processing helix chain 'b' and resid 144 through 153 Processing helix chain 'c' and resid 24 through 53 removed outlier: 3.863A pdb=" N LYS c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 66 removed outlier: 3.507A pdb=" N ALA c 64 " --> pdb=" O GLU c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 68 through 73 removed outlier: 5.671A pdb=" N LEU c 73 " --> pdb=" O GLU c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 79 Processing helix chain 'd' and resid 65 through 71 removed outlier: 3.676A pdb=" N LEU d 69 " --> pdb=" O SER d 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER d 71 " --> pdb=" O LEU d 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 65 through 71' Processing helix chain 'd' and resid 106 through 113 removed outlier: 3.837A pdb=" N LEU d 110 " --> pdb=" O SER d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 132 removed outlier: 5.876A pdb=" N ARG d 132 " --> pdb=" O LYS d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 165 removed outlier: 4.005A pdb=" N GLY d 148 " --> pdb=" O GLN d 144 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP d 165 " --> pdb=" O ARG d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 172 removed outlier: 3.616A pdb=" N ALA d 170 " --> pdb=" O TRP d 166 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU d 171 " --> pdb=" O ALA d 167 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU d 172 " --> pdb=" O ASN d 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 166 through 172' Processing helix chain 'd' and resid 175 through 180 removed outlier: 3.808A pdb=" N LYS d 179 " --> pdb=" O LYS d 175 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER d 180 " --> pdb=" O LEU d 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 175 through 180' Processing helix chain 'd' and resid 181 through 191 removed outlier: 3.576A pdb=" N ASP d 190 " --> pdb=" O GLN d 186 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 205 Processing helix chain 'd' and resid 256 through 263 removed outlier: 4.092A pdb=" N LYS d 260 " --> pdb=" O ASN d 256 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE d 261 " --> pdb=" O GLU d 257 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS d 262 " --> pdb=" O GLN d 258 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA d 263 " --> pdb=" O ASP d 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 256 through 263' Processing helix chain 'd' and resid 278 through 283 removed outlier: 3.657A pdb=" N LYS d 282 " --> pdb=" O GLY d 278 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 90 removed outlier: 3.626A pdb=" N TYR e 84 " --> pdb=" O ASP e 80 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA e 87 " --> pdb=" O ARG e 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL e 88 " --> pdb=" O TYR e 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL e 90 " --> pdb=" O ARG e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 98 removed outlier: 5.082A pdb=" N LYS e 98 " --> pdb=" O PRO e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 148 removed outlier: 3.879A pdb=" N GLU e 142 " --> pdb=" O SER e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 153 through 164 removed outlier: 4.092A pdb=" N LEU e 157 " --> pdb=" O GLY e 153 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY e 164 " --> pdb=" O ALA e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 185 removed outlier: 3.636A pdb=" N LEU e 181 " --> pdb=" O SER e 177 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG e 182 " --> pdb=" O GLU e 178 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS e 183 " --> pdb=" O GLY e 179 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 194 removed outlier: 3.537A pdb=" N GLY e 191 " --> pdb=" O GLY e 187 " (cutoff:3.500A) Proline residue: e 192 - end of helix Processing helix chain 'e' and resid 207 through 216 removed outlier: 4.457A pdb=" N THR e 211 " --> pdb=" O ASN e 207 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG e 213 " --> pdb=" O GLU e 209 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP e 214 " --> pdb=" O ALA e 210 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE e 216 " --> pdb=" O PHE e 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 238 through 261 removed outlier: 3.595A pdb=" N GLU e 244 " --> pdb=" O LYS e 240 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE e 249 " --> pdb=" O ASN e 245 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP e 261 " --> pdb=" O ILE e 257 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 16 removed outlier: 3.778A pdb=" N LEU j 14 " --> pdb=" O VAL j 10 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN j 16 " --> pdb=" O ARG j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 45 through 54 removed outlier: 4.079A pdb=" N ARG j 49 " --> pdb=" O HIS j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 64 removed outlier: 3.819A pdb=" N LEU j 59 " --> pdb=" O ASN j 55 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS j 60 " --> pdb=" O LEU j 56 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP j 62 " --> pdb=" O LYS j 58 " (cutoff:3.500A) Proline residue: j 64 - end of helix Processing helix chain 'j' and resid 128 through 141 removed outlier: 3.540A pdb=" N LYS j 139 " --> pdb=" O GLU j 135 " (cutoff:3.500A) Processing helix chain 'j' and resid 148 through 196 removed outlier: 3.561A pdb=" N ARG j 163 " --> pdb=" O GLU j 159 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG j 171 " --> pdb=" O ILE j 167 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA j 184 " --> pdb=" O LYS j 180 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP j 192 " --> pdb=" O LYS j 188 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA j 193 " --> pdb=" O ALA j 189 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER j 195 " --> pdb=" O SER j 191 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE j 196 " --> pdb=" O ASP j 192 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 58 through 61 removed outlier: 8.107A pdb=" N TYR B 58 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 143 through 146 removed outlier: 3.728A pdb=" N ARG B 143 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 156 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP B 178 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 212 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 181 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.680A pdb=" N THR B 224 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B 270 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N LYS B 267 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 228 through 231 removed outlier: 4.265A pdb=" N CYS B 228 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 288 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N CYS B 286 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 153 through 160 removed outlier: 5.156A pdb=" N HIS B 153 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 164 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 109 through 113 removed outlier: 7.524A pdb=" N VAL C 308 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE C 219 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN C 276 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 117 through 122 removed outlier: 4.203A pdb=" N ALA C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.356A pdb=" N ARG C 137 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 159 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN C 155 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP C 152 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 212 through 215 removed outlier: 4.480A pdb=" N GLN C 212 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.531A pdb=" N LEU D 80 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 111 through 115 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'D' and resid 186 through 189 removed outlier: 5.551A pdb=" N GLU D 186 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 240 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 231 through 235 removed outlier: 6.093A pdb=" N GLY E 292 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 238 through 241 removed outlier: 6.680A pdb=" N ASN E 238 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 247 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 66 through 73 removed outlier: 5.058A pdb=" N LYS F 88 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS F 86 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 106 through 111 removed outlier: 3.803A pdb=" N THR F 118 " --> pdb=" O ASP F 109 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 162 through 167 removed outlier: 5.346A pdb=" N GLN F 179 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 199 through 203 removed outlier: 5.805A pdb=" N THR F 207 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 79 through 82 removed outlier: 4.324A pdb=" N ALA G 79 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL G 64 " --> pdb=" O MET G 101 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'f' and resid 133 through 136 removed outlier: 3.732A pdb=" N HIS f 133 " --> pdb=" O THR f 216 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU f 91 " --> pdb=" O LEU f 217 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'f' and resid 159 through 164 removed outlier: 4.724A pdb=" N THR f 168 " --> pdb=" O THR f 164 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'g' and resid 14 through 20 removed outlier: 3.515A pdb=" N VAL g 20 " --> pdb=" O MET g 62 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 15 through 20 Processing sheet with id= 24, first strand: chain 'H' and resid 92 through 95 Processing sheet with id= 25, first strand: chain 'I' and resid 6 through 10 removed outlier: 4.171A pdb=" N THR I 6 " --> pdb=" O CYS I 21 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA I 17 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 72 through 75 removed outlier: 3.712A pdb=" N ARG I 73 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS I 75 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP I 90 " --> pdb=" O LYS I 75 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 77 through 80 removed outlier: 4.403A pdb=" N SER I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 119 through 122 Processing sheet with id= 29, first strand: chain 'K' and resid 105 through 108 Processing sheet with id= 30, first strand: chain 'K' and resid 130 through 134 removed outlier: 6.392A pdb=" N ILE K 170 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE K 171 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP K 96 " --> pdb=" O LYS K 202 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 141 through 144 removed outlier: 7.092A pdb=" N VAL K 141 " --> pdb=" O ASP K 158 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER K 156 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 34 through 38 removed outlier: 4.173A pdb=" N SER L 113 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TYR L 96 " --> pdb=" O VAL L 119 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'M' and resid 56 through 59 removed outlier: 6.896A pdb=" N ILE M 50 " --> pdb=" O ARG M 59 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 149 through 152 removed outlier: 6.738A pdb=" N VAL M 138 " --> pdb=" O ILE M 194 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'M' and resid 156 through 159 removed outlier: 3.979A pdb=" N ALA M 156 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'N' and resid 105 through 108 removed outlier: 4.138A pdb=" N VAL N 146 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER N 145 " --> pdb=" O GLY N 156 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU N 152 " --> pdb=" O SER N 149 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'N' and resid 121 through 127 removed outlier: 3.952A pdb=" N ASP N 122 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR N 202 " --> pdb=" O LEU N 126 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL N 203 " --> pdb=" O MET N 172 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG N 168 " --> pdb=" O ASN N 207 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS N 167 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP N 137 " --> pdb=" O VAL N 171 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'N' and resid 173 through 176 removed outlier: 3.695A pdb=" N GLY N 173 " --> pdb=" O VAL N 203 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'N' and resid 179 through 185 Processing sheet with id= 40, first strand: chain 'O' and resid 186 through 192 removed outlier: 5.072A pdb=" N MET O 320 " --> pdb=" O THR O 191 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR O 317 " --> pdb=" O GLY O 295 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'O' and resid 267 through 270 Processing sheet with id= 42, first strand: chain 'O' and resid 298 through 305 removed outlier: 3.605A pdb=" N ARG O 309 " --> pdb=" O ARG O 305 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'P' and resid 31 through 34 removed outlier: 4.541A pdb=" N THR P 46 " --> pdb=" O VAL P 34 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN P 43 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS P 99 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY P 72 " --> pdb=" O GLU P 104 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 122 through 125 removed outlier: 4.141A pdb=" N LEU Q 132 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 138 through 141 removed outlier: 4.046A pdb=" N LYS Q 138 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 153 through 158 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'Q' and resid 209 through 214 removed outlier: 5.101A pdb=" N ASN Q 209 " --> pdb=" O ARG Q 222 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG Q 222 " --> pdb=" O ASN Q 209 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'R' and resid 111 through 114 removed outlier: 4.141A pdb=" N THR R 118 " --> pdb=" O GLY R 114 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 126 through 130 Processing sheet with id= 50, first strand: chain 'R' and resid 189 through 192 Processing sheet with id= 51, first strand: chain 'S' and resid 101 through 108 removed outlier: 4.709A pdb=" N THR S 115 " --> pdb=" O ASN S 106 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE S 113 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'S' and resid 125 through 131 removed outlier: 3.687A pdb=" N VAL S 135 " --> pdb=" O SER S 130 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'U' and resid 32 through 38 removed outlier: 4.303A pdb=" N GLN U 33 " --> pdb=" O LEU U 8 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 85 through 88 removed outlier: 5.218A pdb=" N VAL U 127 " --> pdb=" O ASP U 95 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 70 through 75 removed outlier: 4.475A pdb=" N SER V 70 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA V 81 " --> pdb=" O THR V 61 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 91 through 94 removed outlier: 4.368A pdb=" N ASN W 99 " --> pdb=" O CYS W 94 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'X' and resid 22 through 27 removed outlier: 5.963A pdb=" N TYR X 22 " --> pdb=" O SER X 16 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU X 49 " --> pdb=" O MET X 17 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET X 35 " --> pdb=" O GLU X 52 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain '0' and resid 79 through 82 removed outlier: 3.617A pdb=" N LEU 0 107 " --> pdb=" O GLN 0 121 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain '1' and resid 233 through 238 Processing sheet with id= 60, first strand: chain '1' and resid 282 through 285 Processing sheet with id= 61, first strand: chain '1' and resid 296 through 299 removed outlier: 3.535A pdb=" N PHE 1 296 " --> pdb=" O VAL 1 277 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '1' and resid 380 through 383 removed outlier: 6.637A pdb=" N VAL 1 345 " --> pdb=" O VAL 1 383 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '1' and resid 272 through 279 removed outlier: 4.782A pdb=" N LEU 1 272 " --> pdb=" O GLN 1 348 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '3' and resid 36 through 39 removed outlier: 4.561A pdb=" N THR 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '4' and resid 59 through 66 removed outlier: 3.519A pdb=" N TYR 4 31 " --> pdb=" O SER 4 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE 4 72 " --> pdb=" O HIS 4 30 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER 4 32 " --> pdb=" O HIS 4 70 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N HIS 4 70 " --> pdb=" O SER 4 32 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG 4 81 " --> pdb=" O TYR 4 77 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '5' and resid 353 through 357 removed outlier: 6.872A pdb=" N VAL 5 370 " --> pdb=" O LEU 5 357 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY 5 381 " --> pdb=" O ILE 5 373 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '6' and resid 253 through 257 removed outlier: 3.640A pdb=" N LYS 6 254 " --> pdb=" O LYS 6 244 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU 6 94 " --> pdb=" O LEU 6 240 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL 6 242 " --> pdb=" O VAL 6 92 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N VAL 6 92 " --> pdb=" O VAL 6 242 " (cutoff:3.500A) removed outlier: 14.308A pdb=" N LYS 6 244 " --> pdb=" O SER 6 90 " (cutoff:3.500A) removed outlier: 16.751A pdb=" N SER 6 90 " --> pdb=" O LYS 6 244 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '6' and resid 85 through 94 Processing sheet with id= 69, first strand: chain '6' and resid 239 through 244 removed outlier: 3.890A pdb=" N ASP 6 340 " --> pdb=" O LYS 6 243 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '7' and resid 96 through 102 Processing sheet with id= 71, first strand: chain 'h' and resid 39 through 46 removed outlier: 3.981A pdb=" N LEU h 56 " --> pdb=" O LEU h 68 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'b' and resid 53 through 57 removed outlier: 6.865A pdb=" N MET b 53 " --> pdb=" O PRO b 66 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS b 62 " --> pdb=" O HIS b 57 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'd' and resid 96 through 100 removed outlier: 4.305A pdb=" N GLN d 96 " --> pdb=" O HIS d 91 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP d 84 " --> pdb=" O LEU d 139 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ARG d 249 " --> pdb=" O ALA d 140 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'd' and resid 250 through 255 Processing sheet with id= 75, first strand: chain 'e' and resid 114 through 119 removed outlier: 5.002A pdb=" N VAL e 114 " --> pdb=" O GLU e 223 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP e 116 " --> pdb=" O TYR e 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR e 221 " --> pdb=" O ASP e 116 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'e' and resid 129 through 134 Processing sheet with id= 77, first strand: chain 'e' and resid 266 through 269 removed outlier: 4.038A pdb=" N MET e 267 " --> pdb=" O ARG e 106 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS e 104 " --> pdb=" O GLU e 269 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS e 102 " --> pdb=" O VAL e 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU e 270 " --> pdb=" O LYS e 104 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL e 271 " --> pdb=" O LEU e 283 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'j' and resid 67 through 73 removed outlier: 3.647A pdb=" N VAL j 69 " --> pdb=" O VAL j 33 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS j 32 " --> pdb=" O TYR j 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN j 36 " --> pdb=" O VAL j 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL j 81 " --> pdb=" O GLN j 36 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA j 80 " --> pdb=" O MET j 124 " (cutoff:3.500A) 2448 hydrogen bonds defined for protein. 7254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1799 hydrogen bonds 2922 hydrogen bond angles 0 basepair planarities 770 basepair parallelities 1593 stacking parallelities Total time for adding SS restraints: 198.51 Time building geometry restraints manager: 154.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 97428 1.03 - 1.22: 894 1.22 - 1.42: 60790 1.42 - 1.62: 72213 1.62 - 1.81: 459 Bond restraints: 231784 Sorted by residual: bond pdb=" O3 NAD 24301 " pdb=" PA NAD 24301 " ideal model delta sigma weight residual 1.653 1.601 0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" C6A NAD 24301 " pdb=" N6A NAD 24301 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1D NAD 24301 " pdb=" O4D NAD 24301 " ideal model delta sigma weight residual 1.376 1.419 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C8A NAD 24301 " pdb=" N7A NAD 24301 " ideal model delta sigma weight residual 1.298 1.338 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C2B NAD 24301 " pdb=" O2B NAD 24301 " ideal model delta sigma weight residual 1.394 1.430 -0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 231779 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.11: 17855 106.11 - 113.13: 250353 113.13 - 120.14: 79907 120.14 - 127.15: 62978 127.15 - 134.16: 7079 Bond angle restraints: 418172 Sorted by residual: angle pdb=" C11 SPM A3661 " pdb=" N10 SPM A3661 " pdb=" C9 SPM A3661 " ideal model delta sigma weight residual 109.47 121.42 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O1A NAD 24301 " pdb=" PA NAD 24301 " pdb=" O2A NAD 24301 " ideal model delta sigma weight residual 122.64 111.08 11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C4 SPM A3661 " pdb=" N5 SPM A3661 " pdb=" C6 SPM A3661 " ideal model delta sigma weight residual 109.47 118.66 -9.19 3.00e+00 1.11e-01 9.38e+00 angle pdb=" O1N NAD 24301 " pdb=" PN NAD 24301 " pdb=" O2N NAD 24301 " ideal model delta sigma weight residual 120.02 111.06 8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" CA ARG M 145 " pdb=" CB ARG M 145 " pdb=" CG ARG M 145 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.94e+00 ... (remaining 418167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 86747 36.00 - 72.00: 3938 72.00 - 108.00: 646 108.00 - 144.00: 10 144.00 - 180.00: 569 Dihedral angle restraints: 91910 sinusoidal: 64828 harmonic: 27082 Sorted by residual: dihedral pdb=" O4' U A1109 " pdb=" C1' U A1109 " pdb=" N1 U A1109 " pdb=" C2 U A1109 " ideal model delta sinusoidal sigma weight residual 200.00 42.32 157.68 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" O4' U A2759 " pdb=" C1' U A2759 " pdb=" N1 U A2759 " pdb=" C2 U A2759 " ideal model delta sinusoidal sigma weight residual 232.00 56.56 175.44 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U A2648 " pdb=" C1' U A2648 " pdb=" N1 U A2648 " pdb=" C2 U A2648 " ideal model delta sinusoidal sigma weight residual 200.00 88.32 111.68 1 1.50e+01 4.44e-03 5.84e+01 ... (remaining 91907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 22199 0.050 - 0.101: 1229 0.101 - 0.151: 392 0.151 - 0.201: 5 0.201 - 0.252: 1 Chirality restraints: 23826 Sorted by residual: chirality pdb=" C4D NAD 24301 " pdb=" C3D NAD 24301 " pdb=" C5D NAD 24301 " pdb=" O4D NAD 24301 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1B NAD 24301 " pdb=" C2B NAD 24301 " pdb=" N9A NAD 24301 " pdb=" O4B NAD 24301 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" C1' G A 932 " pdb=" O4' G A 932 " pdb=" C2' G A 932 " pdb=" N9 G A 932 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 23823 not shown) Planarity restraints: 24071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE e 64 " -0.006 2.00e-02 2.50e+03 1.15e-02 4.00e+00 pdb=" CG PHE e 64 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE e 64 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE e 64 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE e 64 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE e 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE e 64 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE e 64 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE e 64 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE e 64 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE e 64 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE e 64 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 63 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C LYS e 63 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS e 63 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE e 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 373 " 0.011 2.00e-02 2.50e+03 9.18e-03 2.53e+00 pdb=" CG PHE R 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 373 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE R 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE R 373 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 373 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 373 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE R 373 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE R 373 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE R 373 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE R 373 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE R 373 " -0.001 2.00e-02 2.50e+03 ... (remaining 24068 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.19: 9710 2.19 - 2.93: 504001 2.93 - 3.66: 804440 3.66 - 4.40: 1300182 4.40 - 5.14: 1885821 Nonbonded interactions: 4504154 Sorted by model distance: nonbonded pdb=" HG1 THR P 159 " pdb=" OD1 ASP P 161 " model vdw 1.452 1.850 nonbonded pdb="HO2' A A 57 " pdb=" O ALA W 81 " model vdw 1.456 1.850 nonbonded pdb=" O LEU h 25 " pdb=" HG SER h 28 " model vdw 1.469 1.850 nonbonded pdb=" O MET f 85 " pdb=" HG1 THR f 89 " model vdw 1.471 1.850 nonbonded pdb=" O LYS O 241 " pdb=" HG1 THR O 245 " model vdw 1.487 1.850 ... (remaining 4504149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 12 8.98 5 Zn 2 6.06 5 P 2822 5.49 5 Mg 163 5.21 5 S 254 5.16 5 C 68398 2.51 5 N 23064 2.21 5 O 31164 1.98 5 H 97470 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 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: 2.020 Extract box with map and model: 29.440 Check model and map are aligned: 2.460 Convert atoms to be neutral: 1.410 Process input model: 816.250 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 868.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.002 0.052 134314 Z= 0.125 Angle : 0.385 11.950 195116 Z= 0.209 Chirality : 0.030 0.252 23826 Planarity : 0.002 0.035 14493 Dihedral : 12.659 175.437 59903 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -2.78 (0.08), residues: 8088 helix: -2.62 (0.07), residues: 2821 sheet: -1.48 (0.14), residues: 1035 loop : -1.27 (0.09), residues: 4232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1588 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1574 time to evaluate : 10.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 1585 average time/residue: 4.0170 time to fit residues: 8559.7418 Evaluate side-chains 1149 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1147 time to evaluate : 9.353 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 10.0822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 912 optimal weight: 5.9990 chunk 819 optimal weight: 3.9990 chunk 454 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 552 optimal weight: 5.9990 chunk 437 optimal weight: 9.9990 chunk 847 optimal weight: 5.9990 chunk 327 optimal weight: 6.9990 chunk 515 optimal weight: 4.9990 chunk 630 optimal weight: 5.9990 chunk 981 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN C 277 GLN D 250 ASN F 80 GLN F 92 GLN F 151 HIS F 215 ASN G 59 GLN H 95 HIS I 3 GLN I 79 GLN I 130 GLN K 180 GLN L 17 HIS M 221 GLN N 90 GLN N 208 GLN O 259 GLN O 293 ASN P 23 GLN P 137 GLN P 185 ASN P 189 ASN Q 187 HIS Q 350 ASN U 83 GLN 4 30 HIS 4 111 GLN 5 115 ASN 5 292 HIS 5 363 GLN ** 6 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 94 ASN a 187 HIS d 96 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 134314 Z= 0.428 Angle : 0.609 8.092 195116 Z= 0.314 Chirality : 0.042 0.210 23826 Planarity : 0.005 0.115 14493 Dihedral : 11.560 174.345 42900 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.18 (0.09), residues: 8088 helix: -0.54 (0.09), residues: 2884 sheet: -0.96 (0.15), residues: 1014 loop : -0.81 (0.09), residues: 4190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1216 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1128 time to evaluate : 10.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 45 residues processed: 1177 average time/residue: 3.9963 time to fit residues: 6380.2669 Evaluate side-chains 1113 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1068 time to evaluate : 9.269 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 28 residues processed: 17 average time/residue: 2.0714 time to fit residues: 68.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 545 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 817 optimal weight: 7.9990 chunk 668 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 chunk 983 optimal weight: 0.5980 chunk 1062 optimal weight: 6.9990 chunk 875 optimal weight: 0.7980 chunk 975 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 788 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN D 250 ASN F 92 GLN G 59 GLN f 99 ASN J 235 GLN K 180 GLN O 259 GLN T 60 GLN U 83 GLN 5 115 ASN ** 6 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 147 GLN d 96 GLN j 63 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.082 134314 Z= 0.153 Angle : 0.487 11.944 195116 Z= 0.253 Chirality : 0.034 0.183 23826 Planarity : 0.004 0.081 14493 Dihedral : 11.653 173.095 42900 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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 (0.09), residues: 8088 helix: 0.60 (0.10), residues: 2888 sheet: -0.68 (0.15), residues: 1012 loop : -0.40 (0.09), residues: 4188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1199 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1112 time to evaluate : 9.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 40 residues processed: 1166 average time/residue: 4.0351 time to fit residues: 6439.3439 Evaluate side-chains 1108 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1068 time to evaluate : 9.336 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 31 residues processed: 10 average time/residue: 2.5142 time to fit residues: 49.9604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 971 optimal weight: 6.9990 chunk 739 optimal weight: 2.9990 chunk 510 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 469 optimal weight: 1.9990 chunk 660 optimal weight: 0.8980 chunk 986 optimal weight: 4.9990 chunk 1044 optimal weight: 50.0000 chunk 515 optimal weight: 0.9980 chunk 935 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN F 92 GLN G 59 GLN f 247 ASN J 235 GLN N 90 GLN N 199 HIS N 208 GLN P 135 GLN Q 20 GLN U 83 GLN 5 115 ASN h 72 ASN b 40 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 134314 Z= 0.192 Angle : 0.483 6.336 195116 Z= 0.252 Chirality : 0.035 0.187 23826 Planarity : 0.004 0.080 14493 Dihedral : 11.653 172.038 42900 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.17 (0.09), residues: 8088 helix: 0.99 (0.10), residues: 2895 sheet: -0.58 (0.15), residues: 1016 loop : -0.24 (0.10), residues: 4177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1176 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1088 time to evaluate : 9.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 45 residues processed: 1152 average time/residue: 3.9592 time to fit residues: 6212.1330 Evaluate side-chains 1105 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1060 time to evaluate : 10.403 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 7 average time/residue: 2.2705 time to fit residues: 38.0722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 870 optimal weight: 1.9990 chunk 593 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 778 optimal weight: 3.9990 chunk 431 optimal weight: 2.9990 chunk 891 optimal weight: 2.9990 chunk 722 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 533 optimal weight: 5.9990 chunk 937 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN E 90 HIS F 92 GLN f 247 ASN f 295 GLN g 55 HIS J 235 GLN N 90 GLN N 208 GLN P 135 GLN Q 20 GLN T 188 HIS 5 115 ASN h 72 ASN b 40 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 134314 Z= 0.276 Angle : 0.517 8.682 195116 Z= 0.269 Chirality : 0.037 0.203 23826 Planarity : 0.004 0.077 14493 Dihedral : 11.741 171.890 42900 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.30 (0.09), residues: 8088 helix: 1.12 (0.10), residues: 2900 sheet: -0.53 (0.15), residues: 1029 loop : -0.18 (0.10), residues: 4159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1149 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1054 time to evaluate : 9.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 53 residues processed: 1120 average time/residue: 4.0645 time to fit residues: 6211.6257 Evaluate side-chains 1093 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1040 time to evaluate : 9.306 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 44 residues processed: 9 average time/residue: 2.7403 time to fit residues: 47.7377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 351 optimal weight: 7.9990 chunk 940 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 613 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 1045 optimal weight: 50.0000 chunk 868 optimal weight: 1.9990 chunk 484 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 549 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN D 250 ASN F 92 GLN G 59 GLN f 247 ASN J 235 GLN K 180 GLN N 90 GLN N 208 GLN P 135 GLN Q 20 GLN U 83 GLN 5 115 ASN 6 177 GLN h 72 ASN b 40 HIS b 57 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 134314 Z= 0.293 Angle : 0.532 9.608 195116 Z= 0.277 Chirality : 0.038 0.207 23826 Planarity : 0.005 0.118 14493 Dihedral : 11.854 171.659 42900 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.42 (0.09), residues: 8088 helix: 1.22 (0.10), residues: 2905 sheet: -0.43 (0.15), residues: 1018 loop : -0.12 (0.10), residues: 4165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1182 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1072 time to evaluate : 9.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 65 residues processed: 1146 average time/residue: 4.0185 time to fit residues: 6262.0128 Evaluate side-chains 1116 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1051 time to evaluate : 9.390 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 52 residues processed: 13 average time/residue: 1.9277 time to fit residues: 53.4457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 1008 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 595 optimal weight: 3.9990 chunk 763 optimal weight: 2.9990 chunk 591 optimal weight: 5.9990 chunk 880 optimal weight: 1.9990 chunk 584 optimal weight: 9.9990 chunk 1041 optimal weight: 50.0000 chunk 652 optimal weight: 0.9980 chunk 635 optimal weight: 3.9990 chunk 481 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN F 92 GLN f 247 ASN J 235 GLN N 90 GLN N 208 GLN P 135 GLN Q 20 GLN 5 115 ASN 6 177 GLN 7 111 GLN h 72 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 134314 Z= 0.260 Angle : 0.520 9.067 195116 Z= 0.271 Chirality : 0.037 0.204 23826 Planarity : 0.005 0.088 14493 Dihedral : 11.889 171.251 42900 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.52 (0.09), residues: 8088 helix: 1.32 (0.10), residues: 2906 sheet: -0.39 (0.15), residues: 1031 loop : -0.06 (0.10), residues: 4151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1157 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1059 time to evaluate : 9.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 66 residues processed: 1128 average time/residue: 4.0026 time to fit residues: 6114.3365 Evaluate side-chains 1098 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1032 time to evaluate : 9.685 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 55 residues processed: 11 average time/residue: 2.8135 time to fit residues: 56.7855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 644 optimal weight: 5.9990 chunk 416 optimal weight: 5.9990 chunk 622 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 204 optimal weight: 50.0000 chunk 201 optimal weight: 50.0000 chunk 662 optimal weight: 8.9990 chunk 709 optimal weight: 5.9990 chunk 515 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 818 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN G 59 GLN f 247 ASN I 113 GLN J 235 GLN N 90 GLN N 208 GLN O 221 GLN P 135 GLN Q 20 GLN U 83 GLN 6 177 GLN 9 234 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.117 134314 Z= 0.491 Angle : 0.626 17.320 195116 Z= 0.321 Chirality : 0.044 0.230 23826 Planarity : 0.006 0.091 14493 Dihedral : 12.029 171.309 42900 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.27 % Favored : 97.71 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.30 (0.09), residues: 8088 helix: 1.10 (0.10), residues: 2903 sheet: -0.45 (0.15), residues: 1047 loop : -0.17 (0.09), residues: 4138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1138 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1036 time to evaluate : 9.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 76 residues processed: 1115 average time/residue: 4.0994 time to fit residues: 6252.1743 Evaluate side-chains 1096 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1020 time to evaluate : 9.384 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 65 residues processed: 12 average time/residue: 3.1117 time to fit residues: 65.5255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 947 optimal weight: 8.9990 chunk 998 optimal weight: 0.9980 chunk 910 optimal weight: 8.9990 chunk 970 optimal weight: 0.9980 chunk 997 optimal weight: 2.9990 chunk 584 optimal weight: 9.9990 chunk 422 optimal weight: 6.9990 chunk 762 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 chunk 877 optimal weight: 0.8980 chunk 918 optimal weight: 30.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN C 277 GLN D 250 ASN G 59 GLN ** f 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN J 235 GLN K 180 GLN N 208 GLN P 135 GLN Q 20 GLN T 60 GLN U 83 GLN 8 242 ASN h 72 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 134314 Z= 0.153 Angle : 0.501 12.136 195116 Z= 0.262 Chirality : 0.035 0.196 23826 Planarity : 0.004 0.094 14493 Dihedral : 11.968 170.556 42900 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.62 (0.09), residues: 8088 helix: 1.40 (0.10), residues: 2912 sheet: -0.33 (0.15), residues: 1007 loop : -0.02 (0.10), residues: 4169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1131 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1048 time to evaluate : 9.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 68 residues processed: 1118 average time/residue: 3.9786 time to fit residues: 6035.3937 Evaluate side-chains 1101 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1033 time to evaluate : 9.251 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 61 residues processed: 8 average time/residue: 1.9343 time to fit residues: 36.7332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 967 optimal weight: 3.9990 chunk 637 optimal weight: 0.8980 chunk 1026 optimal weight: 6.9990 chunk 626 optimal weight: 5.9990 chunk 487 optimal weight: 4.9990 chunk 713 optimal weight: 5.9990 chunk 1076 optimal weight: 40.0000 chunk 991 optimal weight: 2.9990 chunk 857 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 662 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN D 250 ASN f 247 ASN I 113 GLN J 235 GLN N 90 GLN N 208 GLN P 135 GLN U 83 GLN 5 166 GLN 6 177 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 134314 Z= 0.222 Angle : 0.506 11.756 195116 Z= 0.264 Chirality : 0.036 0.201 23826 Planarity : 0.004 0.106 14493 Dihedral : 11.931 170.535 42900 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.67 (0.09), residues: 8088 helix: 1.43 (0.10), residues: 2924 sheet: -0.31 (0.16), residues: 1012 loop : 0.03 (0.10), residues: 4152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16176 Ramachandran restraints generated. 8088 Oldfield, 0 Emsley, 8088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 97 is missing expected H atoms. Skipping. Evaluate side-chains 1114 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1040 time to evaluate : 9.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 65 residues processed: 1105 average time/residue: 4.0453 time to fit residues: 6087.1676 Evaluate side-chains 1086 residues out of total 6995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1021 time to evaluate : 9.256 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 61 residues processed: 5 average time/residue: 2.2290 time to fit residues: 28.3154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 525 optimal weight: 4.9990 chunk 681 optimal weight: 2.9990 chunk 913 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 790 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 858 optimal weight: 5.9990 chunk 359 optimal weight: 8.9990 chunk 882 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN D 250 ASN G 59 GLN f 247 ASN I 113 GLN J 235 GLN N 90 GLN P 135 GLN Q 20 GLN U 83 GLN 5 166 GLN 6 177 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.097616 restraints weight = 337588.402| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 0.91 r_work: 0.2907 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2849 rms_B_bonded: 1.52 restraints_weight: 0.1250 r_work: 0.2801 rms_B_bonded: 2.16 restraints_weight: 0.0625 r_work: 0.2723 rms_B_bonded: 3.31 restraints_weight: 0.0312 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 134314 Z= 0.326 Angle : 0.550 13.203 195116 Z= 0.285 Chirality : 0.039 0.211 23826 Planarity : 0.005 0.082 14493 Dihedral : 11.982 170.981 42900 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.59 (0.09), residues: 8088 helix: 1.36 (0.10), residues: 2917 sheet: -0.33 (0.15), residues: 1031 loop : -0.02 (0.10), residues: 4140 =============================================================================== Job complete usr+sys time: 89622.99 seconds wall clock time: 1527 minutes 4.61 seconds (91624.61 seconds total)