Starting phenix.real_space_refine (version: dev) on Mon Apr 11 01:44:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw5_10958/04_2022/6yw5_10958_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw5_10958/04_2022/6yw5_10958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw5_10958/04_2022/6yw5_10958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw5_10958/04_2022/6yw5_10958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw5_10958/04_2022/6yw5_10958_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw5_10958/04_2022/6yw5_10958_trim_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.102 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 "DD PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "FF PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "55 PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "77 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 167548 Number of models: 1 Model: "" Number of chains: 47 Chain: "AA" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5790 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 35, 'TRANS': 336} Chain breaks: 5 Chain: "BB" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4570 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 17, 'TRANS': 272} Chain: "CC" Number of atoms: 7539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 7539 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 427} Chain breaks: 2 Chain: "DD" Number of atoms: 4716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4716 Classifications: {'peptide': 290} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 24, 'TRANS': 264, 'PCIS': 1} Chain breaks: 1 Chain: "EE" Number of atoms: 5799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5799 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Chain: "FF" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1902 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "GG" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3524 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 202, 'PCIS': 1} Chain: "HH" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2522 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 148} Chain: "II" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 3995 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "JJ" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3105 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 178, 'PCIS': 1} Chain: "KK" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2020 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "LL" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "MM" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1925 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "NN" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1876 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "OO" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4429 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 256} Chain breaks: 1 Chain: "PP" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1612 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "QQ" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2561 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "RR" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2169 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "SS" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1325 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "TT" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1519 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "UU" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3686 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 17, 'TRANS': 206} Chain: "VV" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4193 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 242} Chain breaks: 2 Chain: "WW" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5745 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "XX" Number of atoms: 6447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6447 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain breaks: 1 Chain: "YY" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1609 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "ZZ" Number of atoms: 5114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 5114 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "11" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1358 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 8, 'TRANS': 79} Chain: "22" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 661 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "33" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3161 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 179, 'PCIS': 1} Chain: "44" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4045 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain: "55" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3651 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain breaks: 1 Chain: "66" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4629 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 264} Chain: "77" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2796 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 13, 'TRANS': 165} Chain: "88" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7327 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain: "00" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 823 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "99" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 639 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "aa" Number of atoms: 45984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1435, 45984 Inner-chain residues flagged as termini: ['pdbres=" Caa 125 "', 'pdbres=" Uaa 326 "', 'pdbres=" Gaa 562 "', 'pdbres=" Uaa1194 "'] Classifications: {'RNA': 1435} Modifications used: {'rna3p_pyr': 547, 'rna2p_pur': 136, 'rna3p_pur': 661, 'rna2p_pyr': 91, '3*END': 5} Link IDs: {'rna3p': 1207, 'rna2p': 227} Chain breaks: 4 Chain: "V" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 641 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "KK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "QQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "XX" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "YY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "77" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "88" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "00" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "aa" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Unusual residues: {' K': 20, ' MG': 91} Classifications: {'undetermined': 111} Link IDs: {None: 110} Time building chain proxies: 50.13, per 1000 atoms: 0.30 Number of scatterers: 167548 At special positions: 0 Unit cell: (238.5, 256.52, 209.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 22 19.00 S 202 16.00 P 1438 15.00 Mg 97 11.99 O 20823 8.00 N 16474 7.00 C 51836 6.00 H 76656 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS11 27 " - pdb=" SG CYS11 58 " distance=2.03 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: 92.35 Conformation dependent library (CDL) restraints added in 7.7 seconds 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14108 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: 295 helices and 38 sheets defined 52.9% alpha, 7.7% beta 376 base pairs and 837 stacking pairs defined. Time for finding SS restraints: 78.79 Creating SS restraints... Processing helix chain 'AA' and resid 8 through 17 removed outlier: 3.793A pdb=" N THRAA 16 " --> pdb=" O ALAAA 12 " (cutoff:3.500A) Processing helix chain 'AA' and resid 56 through 63 removed outlier: 3.534A pdb=" N SERAA 61 " --> pdb=" O GLUAA 57 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARGAA 62 " --> pdb=" O SERAA 58 " (cutoff:3.500A) Processing helix chain 'AA' and resid 72 through 77 removed outlier: 3.545A pdb=" N THRAA 76 " --> pdb=" O PROAA 72 " (cutoff:3.500A) Processing helix chain 'AA' and resid 101 through 115 removed outlier: 4.026A pdb=" N THRAA 107 " --> pdb=" O GLNAA 103 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSAA 109 " --> pdb=" O GLYAA 105 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEUAA 114 " --> pdb=" O LYSAA 110 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASNAA 115 " --> pdb=" O PHEAA 111 " (cutoff:3.500A) Processing helix chain 'AA' and resid 153 through 158 removed outlier: 3.803A pdb=" N ALAAA 157 " --> pdb=" O GLNAA 153 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLUAA 158 " --> pdb=" O ILEAA 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 153 through 158' Processing helix chain 'AA' and resid 167 through 172 removed outlier: 5.879A pdb=" N THRAA 172 " --> pdb=" O LEUAA 168 " (cutoff:3.500A) Processing helix chain 'AA' and resid 173 through 188 removed outlier: 4.146A pdb=" N VALAA 184 " --> pdb=" O LEUAA 180 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARGAA 185 " --> pdb=" O ALAAA 181 " (cutoff:3.500A) Proline residue: AA 186 - end of helix Processing helix chain 'AA' and resid 189 through 213 removed outlier: 3.567A pdb=" N ALAAA 201 " --> pdb=" O LYSAA 197 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALAAA 206 " --> pdb=" O GLNAA 202 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLUAA 210 " --> pdb=" O ALAAA 206 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEUAA 211 " --> pdb=" O ALAAA 207 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLNAA 212 " --> pdb=" O ASNAA 208 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLUAA 213 " --> pdb=" O ARGAA 209 " (cutoff:3.500A) Processing helix chain 'AA' and resid 235 through 250 removed outlier: 5.514A pdb=" N VALAA 239 " --> pdb=" O THRAA 235 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THRAA 240 " --> pdb=" O ASPAA 236 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARGAA 244 " --> pdb=" O THRAA 240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARGAA 247 " --> pdb=" O LEUAA 243 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASNAA 248 " --> pdb=" O ARGAA 244 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASPAA 249 " --> pdb=" O ARGAA 245 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASNAA 250 " --> pdb=" O LEUAA 246 " (cutoff:3.500A) Processing helix chain 'AA' and resid 251 through 262 Processing helix chain 'AA' and resid 406 through 418 removed outlier: 3.862A pdb=" N VALAA 410 " --> pdb=" O LYSAA 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUAA 416 " --> pdb=" O ILEAA 412 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILEAA 417 " --> pdb=" O ALAAA 413 " (cutoff:3.500A) Processing helix chain 'BB' and resid 108 through 115 removed outlier: 3.711A pdb=" N LYSBB 112 " --> pdb=" O GLUBB 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEUBB 113 " --> pdb=" O GLUBB 109 " (cutoff:3.500A) Processing helix chain 'BB' and resid 117 through 131 Proline residue: BB 121 - end of helix Processing helix chain 'BB' and resid 148 through 153 Processing helix chain 'BB' and resid 159 through 167 Processing helix chain 'BB' and resid 178 through 186 removed outlier: 4.252A pdb=" N ALABB 182 " --> pdb=" O ASNBB 178 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARGBB 183 " --> pdb=" O PROBB 179 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYRBB 184 " --> pdb=" O ALABB 180 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILEBB 185 " --> pdb=" O ASNBB 181 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYRBB 186 " --> pdb=" O ALABB 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 178 through 186' Processing helix chain 'BB' and resid 196 through 218 Processing helix chain 'BB' and resid 230 through 242 Processing helix chain 'BB' and resid 257 through 262 Processing helix chain 'BB' and resid 280 through 287 removed outlier: 3.531A pdb=" N ASPBB 286 " --> pdb=" O ASPBB 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGBB 287 " --> pdb=" O HISBB 283 " (cutoff:3.500A) Processing helix chain 'BB' and resid 299 through 304 removed outlier: 3.725A pdb=" N ASNBB 303 " --> pdb=" O ASNBB 299 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N METBB 304 " --> pdb=" O PROBB 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 299 through 304' Processing helix chain 'BB' and resid 305 through 314 Processing helix chain 'BB' and resid 340 through 369 removed outlier: 3.595A pdb=" N ARGBB 361 " --> pdb=" O ARGBB 357 " (cutoff:3.500A) Processing helix chain 'BB' and resid 376 through 396 removed outlier: 3.657A pdb=" N TYRBB 382 " --> pdb=" O ASPBB 378 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARGBB 395 " --> pdb=" O ALABB 391 " (cutoff:3.500A) Processing helix chain 'CC' and resid 19 through 29 removed outlier: 4.070A pdb=" N TYRCC 25 " --> pdb=" O ILECC 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILECC 26 " --> pdb=" O PHECC 22 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASNCC 27 " --> pdb=" O SERCC 23 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASNCC 28 " --> pdb=" O LYSCC 24 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASNCC 29 " --> pdb=" O TYRCC 25 " (cutoff:3.500A) Processing helix chain 'CC' and resid 51 through 57 removed outlier: 4.522A pdb=" N GLUCC 55 " --> pdb=" O PROCC 51 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRPCC 56 " --> pdb=" O ILECC 52 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYSCC 57 " --> pdb=" O SERCC 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 51 through 57' Processing helix chain 'CC' and resid 64 through 88 removed outlier: 4.765A pdb=" N LEUCC 68 " --> pdb=" O ASNCC 64 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASNCC 70 " --> pdb=" O ASNCC 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEUCC 71 " --> pdb=" O ASNCC 67 " (cutoff:3.500A) Proline residue: CC 72 - end of helix removed outlier: 3.816A pdb=" N ILECC 76 " --> pdb=" O PROCC 72 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNCC 87 " --> pdb=" O LYSCC 83 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEUCC 88 " --> pdb=" O ASPCC 84 " (cutoff:3.500A) Processing helix chain 'CC' and resid 91 through 96 Processing helix chain 'CC' and resid 134 through 147 removed outlier: 4.180A pdb=" N ILECC 138 " --> pdb=" O ASNCC 134 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SERCC 139 " --> pdb=" O ARGCC 135 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYSCC 142 " --> pdb=" O ILECC 138 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEUCC 147 " --> pdb=" O LYSCC 143 " (cutoff:3.500A) Processing helix chain 'CC' and resid 148 through 166 removed outlier: 4.454A pdb=" N TYRCC 152 " --> pdb=" O LYSCC 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYSCC 157 " --> pdb=" O PHECC 153 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALCC 165 " --> pdb=" O PHECC 161 " (cutoff:3.500A) Processing helix chain 'CC' and resid 198 through 214 removed outlier: 4.034A pdb=" N ILECC 204 " --> pdb=" O SERCC 200 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILECC 209 " --> pdb=" O TRPCC 205 " (cutoff:3.500A) Processing helix chain 'CC' and resid 215 through 233 removed outlier: 3.935A pdb=" N LEUCC 219 " --> pdb=" O LYSCC 215 " (cutoff:3.500A) Processing helix chain 'CC' and resid 237 through 247 removed outlier: 5.368A pdb=" N ARGCC 241 " --> pdb=" O LYSCC 237 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEUCC 242 " --> pdb=" O LEUCC 238 " (cutoff:3.500A) Processing helix chain 'CC' and resid 263 through 268 removed outlier: 4.753A pdb=" N ASNCC 267 " --> pdb=" O SERCC 263 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SERCC 268 " --> pdb=" O PHECC 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 263 through 268' Processing helix chain 'CC' and resid 269 through 281 removed outlier: 4.450A pdb=" N ASNCC 281 " --> pdb=" O LEUCC 277 " (cutoff:3.500A) Processing helix chain 'CC' and resid 285 through 298 removed outlier: 5.227A pdb=" N ASNCC 298 " --> pdb=" O LEUCC 294 " (cutoff:3.500A) Processing helix chain 'CC' and resid 303 through 309 Processing helix chain 'CC' and resid 319 through 325 removed outlier: 3.591A pdb=" N PHECC 324 " --> pdb=" O LEUCC 320 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYSCC 325 " --> pdb=" O GLUCC 321 " (cutoff:3.500A) Processing helix chain 'CC' and resid 328 through 334 removed outlier: 4.386A pdb=" N ASNCC 334 " --> pdb=" O SERCC 330 " (cutoff:3.500A) Processing helix chain 'CC' and resid 343 through 352 removed outlier: 3.536A pdb=" N LYSCC 350 " --> pdb=" O GLUCC 346 " (cutoff:3.500A) Processing helix chain 'CC' and resid 410 through 428 removed outlier: 6.116A pdb=" N LYSCC 415 " --> pdb=" O ALACC 411 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYRCC 416 " --> pdb=" O LYSCC 412 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALACC 417 " --> pdb=" O ALACC 413 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N LYSCC 418 " --> pdb=" O LYSCC 414 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILECC 419 " --> pdb=" O LYSCC 415 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYRCC 420 " --> pdb=" O TYRCC 416 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLNCC 421 " --> pdb=" O ALACC 417 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILECC 427 " --> pdb=" O ILECC 423 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASNCC 428 " --> pdb=" O PHECC 424 " (cutoff:3.500A) Processing helix chain 'CC' and resid 465 through 471 Processing helix chain 'DD' and resid 3 through 8 removed outlier: 4.026A pdb=" N PHEDD 7 " --> pdb=" O ILEDD 3 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYSDD 8 " --> pdb=" O ARGDD 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'DD' and resid 3 through 8' Processing helix chain 'DD' and resid 22 through 32 Processing helix chain 'DD' and resid 42 through 58 removed outlier: 4.012A pdb=" N TYRDD 57 " --> pdb=" O LEUDD 53 " (cutoff:3.500A) Processing helix chain 'DD' and resid 63 through 71 removed outlier: 3.532A pdb=" N ARGDD 69 " --> pdb=" O ARGDD 65 " (cutoff:3.500A) Processing helix chain 'DD' and resid 82 through 89 Processing helix chain 'DD' and resid 91 through 97 removed outlier: 4.059A pdb=" N ALADD 95 " --> pdb=" O GLYDD 91 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALADD 96 " --> pdb=" O SERDD 92 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLYDD 97 " --> pdb=" O GLUDD 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'DD' and resid 91 through 97' Processing helix chain 'DD' and resid 106 through 114 removed outlier: 4.105A pdb=" N THRDD 111 " --> pdb=" O ALADD 107 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALADD 112 " --> pdb=" O TYRDD 108 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLUDD 114 " --> pdb=" O LYSDD 110 " (cutoff:3.500A) Processing helix chain 'DD' and resid 131 through 143 removed outlier: 4.132A pdb=" N METDD 135 " --> pdb=" O PRODD 131 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THRDD 136 " --> pdb=" O TYRDD 132 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHEDD 137 " --> pdb=" O GLUDD 133 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALADD 138 " --> pdb=" O GLNDD 134 " (cutoff:3.500A) Proline residue: DD 139 - end of helix removed outlier: 3.964A pdb=" N ARGDD 142 " --> pdb=" O ALADD 138 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARGDD 143 " --> pdb=" O PRODD 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'DD' and resid 131 through 143' Processing helix chain 'DD' and resid 144 through 152 removed outlier: 3.663A pdb=" N LEUDD 152 " --> pdb=" O ILEDD 148 " (cutoff:3.500A) Processing helix chain 'DD' and resid 156 through 167 removed outlier: 3.558A pdb=" N GLYDD 167 " --> pdb=" O METDD 163 " (cutoff:3.500A) Processing helix chain 'DD' and resid 192 through 201 Processing helix chain 'DD' and resid 205 through 213 removed outlier: 3.530A pdb=" N ALADD 211 " --> pdb=" O LYSDD 207 " (cutoff:3.500A) Processing helix chain 'DD' and resid 398 through 403 removed outlier: 4.277A pdb=" N PHEDD 402 " --> pdb=" O TYRDD 398 " (cutoff:3.500A) Processing helix chain 'DD' and resid 438 through 452 removed outlier: 4.422A pdb=" N ARGDD 451 " --> pdb=" O ASNDD 447 " (cutoff:3.500A) Processing helix chain 'EE' and resid 61 through 68 removed outlier: 3.526A pdb=" N GLUEE 66 " --> pdb=" O VALEE 62 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N METEE 67 " --> pdb=" O ARGEE 63 " (cutoff:3.500A) Processing helix chain 'EE' and resid 71 through 83 removed outlier: 3.597A pdb=" N SEREE 77 " --> pdb=" O ALAEE 73 " (cutoff:3.500A) Processing helix chain 'EE' and resid 87 through 99 Proline residue: EE 99 - end of helix Processing helix chain 'EE' and resid 100 through 114 removed outlier: 5.198A pdb=" N ASPEE 114 " --> pdb=" O GLUEE 110 " (cutoff:3.500A) Processing helix chain 'EE' and resid 115 through 121 Processing helix chain 'EE' and resid 162 through 180 Processing helix chain 'EE' and resid 239 through 249 Processing helix chain 'EE' and resid 296 through 304 removed outlier: 3.516A pdb=" N LYSEE 301 " --> pdb=" O GLNEE 297 " (cutoff:3.500A) Processing helix chain 'EE' and resid 306 through 313 removed outlier: 3.581A pdb=" N GLNEE 312 " --> pdb=" O ARGEE 308 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEUEE 313 " --> pdb=" O GLNEE 309 " (cutoff:3.500A) Processing helix chain 'EE' and resid 357 through 373 removed outlier: 3.639A pdb=" N METEE 373 " --> pdb=" O ALAEE 369 " (cutoff:3.500A) Processing helix chain 'EE' and resid 411 through 422 Processing helix chain 'EE' and resid 435 through 450 removed outlier: 3.559A pdb=" N VALEE 440 " --> pdb=" O PROEE 436 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLNEE 450 " --> pdb=" O ALAEE 446 " (cutoff:3.500A) Processing helix chain 'EE' and resid 452 through 461 Processing helix chain 'EE' and resid 466 through 473 removed outlier: 3.627A pdb=" N TYREE 472 " --> pdb=" O ARGEE 468 " (cutoff:3.500A) Processing helix chain 'FF' and resid 13 through 32 removed outlier: 3.952A pdb=" N VALFF 17 " --> pdb=" O ASNFF 13 " (cutoff:3.500A) Processing helix chain 'FF' and resid 70 through 85 Proline residue: FF 85 - end of helix Processing helix chain 'FF' and resid 99 through 106 removed outlier: 4.033A pdb=" N ARGFF 105 " --> pdb=" O GLUFF 101 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHEFF 106 " --> pdb=" O THRFF 102 " (cutoff:3.500A) Processing helix chain 'GG' and resid 93 through 99 Processing helix chain 'GG' and resid 101 through 106 Processing helix chain 'GG' and resid 137 through 149 removed outlier: 3.526A pdb=" N LYSGG 145 " --> pdb=" O ASNGG 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEUGG 146 " --> pdb=" O HISGG 142 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYSGG 149 " --> pdb=" O LYSGG 145 " (cutoff:3.500A) Processing helix chain 'GG' and resid 152 through 171 Proline residue: GG 171 - end of helix Processing helix chain 'GG' and resid 187 through 195 removed outlier: 3.823A pdb=" N LEUGG 191 " --> pdb=" O PROGG 187 " (cutoff:3.500A) Proline residue: GG 192 - end of helix Proline residue: GG 195 - end of helix No H-bonds generated for 'chain 'GG' and resid 187 through 195' Processing helix chain 'GG' and resid 196 through 207 Processing helix chain 'GG' and resid 232 through 252 removed outlier: 3.653A pdb=" N LYSGG 250 " --> pdb=" O ASPGG 246 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYSGG 251 " --> pdb=" O VALGG 247 " (cutoff:3.500A) Proline residue: GG 252 - end of helix Processing helix chain 'GG' and resid 259 through 275 removed outlier: 3.589A pdb=" N GLUGG 268 " --> pdb=" O ARGGG 264 " (cutoff:3.500A) Processing helix chain 'GG' and resid 277 through 294 removed outlier: 4.868A pdb=" N ASPGG 281 " --> pdb=" O SERGG 277 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYSGG 282 " --> pdb=" O SERGG 278 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUGG 289 " --> pdb=" O LEUGG 285 " (cutoff:3.500A) Processing helix chain 'GG' and resid 299 through 305 removed outlier: 3.860A pdb=" N LYSGG 305 " --> pdb=" O ALAGG 301 " (cutoff:3.500A) Processing helix chain 'HH' and resid 2 through 20 removed outlier: 3.827A pdb=" N ILEHH 6 " --> pdb=" O GLYHH 2 " (cutoff:3.500A) Processing helix chain 'HH' and resid 29 through 43 Processing helix chain 'HH' and resid 108 through 118 removed outlier: 3.882A pdb=" N ARGHH 117 " --> pdb=" O ASNHH 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLYHH 118 " --> pdb=" O ARGHH 114 " (cutoff:3.500A) Processing helix chain 'HH' and resid 143 through 151 Processing helix chain 'II' and resid 88 through 106 Processing helix chain 'II' and resid 112 through 117 removed outlier: 3.644A pdb=" N VALII 116 " --> pdb=" O PROII 112 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLUII 117 " --> pdb=" O ALAII 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'II' and resid 112 through 117' Processing helix chain 'II' and resid 123 through 132 Processing helix chain 'II' and resid 136 through 153 removed outlier: 3.595A pdb=" N LEUII 146 " --> pdb=" O ARGII 142 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALII 147 " --> pdb=" O CYSII 143 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILEII 153 " --> pdb=" O ARGII 149 " (cutoff:3.500A) Processing helix chain 'II' and resid 159 through 170 removed outlier: 3.594A pdb=" N SERII 168 " --> pdb=" O ASPII 164 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHEII 169 " --> pdb=" O VALII 165 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARGII 170 " --> pdb=" O LEUII 166 " (cutoff:3.500A) Processing helix chain 'II' and resid 219 through 224 Processing helix chain 'II' and resid 226 through 235 Processing helix chain 'II' and resid 236 through 241 Processing helix chain 'II' and resid 242 through 247 removed outlier: 3.852A pdb=" N TYRII 246 " --> pdb=" O ARGII 242 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASNII 247 " --> pdb=" O ILEII 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'II' and resid 242 through 247' Processing helix chain 'II' and resid 256 through 277 removed outlier: 3.558A pdb=" N LEUII 266 " --> pdb=" O GLUII 262 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HISII 275 " --> pdb=" O ALAII 271 " (cutoff:3.500A) Proline residue: II 277 - end of helix Processing helix chain 'II' and resid 279 through 287 removed outlier: 3.569A pdb=" N ARGII 285 " --> pdb=" O PROII 281 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 90 through 99 removed outlier: 3.826A pdb=" N LEUJJ 96 " --> pdb=" O SERJJ 92 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYRJJ 97 " --> pdb=" O LEUJJ 93 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUJJ 98 " --> pdb=" O GLUJJ 94 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLNJJ 99 " --> pdb=" O ALAJJ 95 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 120 through 139 removed outlier: 4.213A pdb=" N LEUJJ 124 " --> pdb=" O SERJJ 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYRJJ 137 " --> pdb=" O ARGJJ 133 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 186 through 201 Processing helix chain 'JJ' and resid 220 through 235 removed outlier: 4.029A pdb=" N LYSJJ 227 " --> pdb=" O METJJ 223 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SERJJ 228 " --> pdb=" O ASPJJ 224 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLUJJ 229 " --> pdb=" O GLUJJ 225 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 237 through 242 removed outlier: 4.753A pdb=" N LEUJJ 241 " --> pdb=" O ARGJJ 237 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SERJJ 242 " --> pdb=" O TRPJJ 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'JJ' and resid 237 through 242' Processing helix chain 'JJ' and resid 252 through 266 removed outlier: 3.549A pdb=" N LEUJJ 262 " --> pdb=" O ALAJJ 258 " (cutoff:3.500A) Processing helix chain 'KK' and resid 283 through 288 removed outlier: 4.050A pdb=" N LEUKK 287 " --> pdb=" O SERKK 283 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLYKK 288 " --> pdb=" O CYSKK 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'KK' and resid 283 through 288' Processing helix chain 'KK' and resid 296 through 315 Processing helix chain 'KK' and resid 331 through 343 removed outlier: 4.420A pdb=" N GLUKK 335 " --> pdb=" O GLYKK 331 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILEKK 338 " --> pdb=" O ARGKK 334 " (cutoff:3.500A) Processing helix chain 'KK' and resid 347 through 353 removed outlier: 4.490A pdb=" N SERKK 351 " --> pdb=" O ARGKK 347 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SERKK 352 " --> pdb=" O METKK 348 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILEKK 353 " --> pdb=" O LEUKK 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'KK' and resid 347 through 353' Processing helix chain 'LL' and resid 46 through 53 removed outlier: 3.503A pdb=" N GLYLL 53 " --> pdb=" O GLNLL 49 " (cutoff:3.500A) Processing helix chain 'LL' and resid 65 through 72 removed outlier: 4.703A pdb=" N ILELL 71 " --> pdb=" O ALALL 67 " (cutoff:3.500A) Processing helix chain 'LL' and resid 159 through 164 removed outlier: 3.699A pdb=" N TYRLL 163 " --> pdb=" O SERLL 159 " (cutoff:3.500A) Processing helix chain 'MM' and resid 14 through 22 removed outlier: 4.062A pdb=" N PHEMM 22 " --> pdb=" O ALAMM 18 " (cutoff:3.500A) Processing helix chain 'MM' and resid 26 through 38 removed outlier: 3.618A pdb=" N TYRMM 37 " --> pdb=" O ILEMM 33 " (cutoff:3.500A) Processing helix chain 'MM' and resid 49 through 64 removed outlier: 3.505A pdb=" N THRMM 54 " --> pdb=" O PROMM 50 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THRMM 62 " --> pdb=" O ALAMM 58 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METMM 63 " --> pdb=" O GLUMM 59 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THRMM 64 " --> pdb=" O LEUMM 60 " (cutoff:3.500A) Processing helix chain 'MM' and resid 66 through 83 Processing helix chain 'MM' and resid 85 through 94 Processing helix chain 'MM' and resid 106 through 112 Processing helix chain 'NN' and resid 16 through 33 Processing helix chain 'NN' and resid 34 through 46 removed outlier: 3.574A pdb=" N ARGNN 44 " --> pdb=" O ARGNN 40 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THRNN 46 " --> pdb=" O VALNN 42 " (cutoff:3.500A) Processing helix chain 'NN' and resid 49 through 63 removed outlier: 3.694A pdb=" N THRNN 61 " --> pdb=" O GLNNN 57 " (cutoff:3.500A) Processing helix chain 'NN' and resid 64 through 69 removed outlier: 4.071A pdb=" N ARGNN 68 " --> pdb=" O HISNN 64 " (cutoff:3.500A) Proline residue: NN 69 - end of helix No H-bonds generated for 'chain 'NN' and resid 64 through 69' Processing helix chain 'NN' and resid 92 through 103 Processing helix chain 'OO' and resid 39 through 51 removed outlier: 3.721A pdb=" N ASPOO 50 " --> pdb=" O LYSOO 46 " (cutoff:3.500A) Proline residue: OO 51 - end of helix Processing helix chain 'OO' and resid 52 through 80 removed outlier: 3.543A pdb=" N ALAOO 78 " --> pdb=" O GLNOO 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLYOO 80 " --> pdb=" O ASPOO 76 " (cutoff:3.500A) Processing helix chain 'OO' and resid 88 through 97 removed outlier: 3.741A pdb=" N PHEOO 94 " --> pdb=" O PHEOO 90 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASPOO 95 " --> pdb=" O VALOO 91 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SEROO 96 " --> pdb=" O GLUOO 92 " (cutoff:3.500A) Processing helix chain 'OO' and resid 132 through 148 Processing helix chain 'OO' and resid 159 through 191 removed outlier: 3.845A pdb=" N GLUOO 165 " --> pdb=" O GLUOO 161 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLUOO 166 " --> pdb=" O LYSOO 162 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYSOO 186 " --> pdb=" O GLUOO 182 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEUOO 187 " --> pdb=" O ARGOO 183 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLUOO 188 " --> pdb=" O ILEOO 184 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HISOO 189 " --> pdb=" O ALAOO 185 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLYOO 190 " --> pdb=" O LYSOO 186 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLYOO 191 " --> pdb=" O LEUOO 187 " (cutoff:3.500A) Processing helix chain 'OO' and resid 192 through 207 removed outlier: 3.526A pdb=" N ARGOO 201 " --> pdb=" O HISOO 197 " (cutoff:3.500A) Processing helix chain 'OO' and resid 208 through 216 removed outlier: 5.543A pdb=" N GLNOO 214 " --> pdb=" O HISOO 210 " (cutoff:3.500A) Processing helix chain 'OO' and resid 242 through 264 removed outlier: 5.247A pdb=" N HISOO 264 " --> pdb=" O ALAOO 260 " (cutoff:3.500A) Processing helix chain 'OO' and resid 265 through 270 removed outlier: 4.053A pdb=" N ASPOO 269 " --> pdb=" O GLYOO 265 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYSOO 270 " --> pdb=" O GLYOO 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'OO' and resid 265 through 270' Processing helix chain 'OO' and resid 271 through 295 removed outlier: 3.967A pdb=" N SEROO 275 " --> pdb=" O ASNOO 271 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARGOO 292 " --> pdb=" O ARGOO 288 " (cutoff:3.500A) Processing helix chain 'OO' and resid 297 through 308 removed outlier: 3.715A pdb=" N METOO 303 " --> pdb=" O ARGOO 299 " (cutoff:3.500A) Processing helix chain 'OO' and resid 310 through 315 removed outlier: 4.291A pdb=" N TRPOO 314 " --> pdb=" O THROO 310 " (cutoff:3.500A) Processing helix chain 'PP' and resid 62 through 73 removed outlier: 3.545A pdb=" N TYRPP 68 " --> pdb=" O THRPP 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRPPP 69 " --> pdb=" O ARGPP 65 " (cutoff:3.500A) Processing helix chain 'PP' and resid 77 through 88 Processing helix chain 'QQ' and resid 97 through 102 removed outlier: 4.082A pdb=" N ARGQQ 101 " --> pdb=" O PROQQ 97 " (cutoff:3.500A) Proline residue: QQ 102 - end of helix No H-bonds generated for 'chain 'QQ' and resid 97 through 102' Processing helix chain 'QQ' and resid 106 through 160 removed outlier: 3.734A pdb=" N GLUQQ 139 " --> pdb=" O GLUQQ 135 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARGQQ 150 " --> pdb=" O ARGQQ 146 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYSQQ 157 " --> pdb=" O ALAQQ 153 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILEQQ 158 " --> pdb=" O METQQ 154 " (cutoff:3.500A) Processing helix chain 'RR' and resid 108 through 126 removed outlier: 3.838A pdb=" N LEURR 112 " --> pdb=" O VALRR 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLNRR 113 " --> pdb=" O GLNRR 109 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SERRR 114 " --> pdb=" O GLURR 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N METRR 124 " --> pdb=" O ASNRR 120 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARGRR 126 " --> pdb=" O METRR 122 " (cutoff:3.500A) Processing helix chain 'RR' and resid 136 through 141 removed outlier: 4.082A pdb=" N LEURR 140 " --> pdb=" O ALARR 136 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SERRR 141 " --> pdb=" O PRORR 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'RR' and resid 136 through 141' Processing helix chain 'RR' and resid 157 through 163 Processing helix chain 'RR' and resid 165 through 170 Processing helix chain 'RR' and resid 172 through 181 removed outlier: 3.625A pdb=" N TYRRR 179 " --> pdb=" O LEURR 175 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THRRR 181 " --> pdb=" O SERRR 177 " (cutoff:3.500A) Processing helix chain 'RR' and resid 188 through 193 Processing helix chain 'RR' and resid 195 through 213 Processing helix chain 'RR' and resid 221 through 229 removed outlier: 3.957A pdb=" N ASNRR 227 " --> pdb=" O GLURR 223 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASNRR 229 " --> pdb=" O LEURR 225 " (cutoff:3.500A) Processing helix chain 'SS' and resid 74 through 80 removed outlier: 4.408A pdb=" N PHESS 78 " --> pdb=" O LYSSS 74 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SERSS 79 " --> pdb=" O LEUSS 75 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALASS 80 " --> pdb=" O GLYSS 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 74 through 80' Processing helix chain 'TT' and resid 157 through 163 removed outlier: 3.824A pdb=" N GLYTT 161 " --> pdb=" O ARGTT 157 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARGTT 162 " --> pdb=" O PROTT 158 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THRTT 163 " --> pdb=" O SERTT 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'TT' and resid 157 through 163' Processing helix chain 'TT' and resid 171 through 187 Processing helix chain 'TT' and resid 188 through 198 removed outlier: 3.612A pdb=" N ARGTT 196 " --> pdb=" O VALTT 192 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHETT 197 " --> pdb=" O ARGTT 193 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N HISTT 198 " --> pdb=" O LEUTT 194 " (cutoff:3.500A) Processing helix chain 'TT' and resid 200 through 235 removed outlier: 3.502A pdb=" N PHETT 229 " --> pdb=" O VALTT 225 " (cutoff:3.500A) Processing helix chain 'UU' and resid 11 through 22 removed outlier: 4.304A pdb=" N THRUU 22 " --> pdb=" O GLUUU 18 " (cutoff:3.500A) Processing helix chain 'UU' and resid 34 through 41 removed outlier: 4.617A pdb=" N LYSUU 38 " --> pdb=" O PROUU 34 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALAUU 39 " --> pdb=" O LEUUU 35 " (cutoff:3.500A) Processing helix chain 'UU' and resid 78 through 92 removed outlier: 4.353A pdb=" N GLUUU 82 " --> pdb=" O TYRUU 78 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEUUU 83 " --> pdb=" O PROUU 79 " (cutoff:3.500A) Proline residue: UU 92 - end of helix Processing helix chain 'UU' and resid 107 through 113 removed outlier: 4.761A pdb=" N PHEUU 111 " --> pdb=" O LYSUU 107 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEUUU 112 " --> pdb=" O ASPUU 108 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASPUU 113 " --> pdb=" O ALAUU 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'UU' and resid 107 through 113' Processing helix chain 'UU' and resid 126 through 140 removed outlier: 3.600A pdb=" N VALUU 130 " --> pdb=" O SERUU 126 " (cutoff:3.500A) Processing helix chain 'UU' and resid 144 through 178 removed outlier: 3.612A pdb=" N LEUUU 159 " --> pdb=" O GLUUU 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEUUU 162 " --> pdb=" O LYSUU 158 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARGUU 167 " --> pdb=" O GLUUU 163 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARGUU 168 " --> pdb=" O GLNUU 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N METUU 176 " --> pdb=" O GLUUU 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VALUU 177 " --> pdb=" O GLUUU 173 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLYUU 178 " --> pdb=" O ALAUU 174 " (cutoff:3.500A) Processing helix chain 'UU' and resid 184 through 219 removed outlier: 3.510A pdb=" N METUU 190 " --> pdb=" O LEUUU 186 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SERUU 199 " --> pdb=" O LYSUU 195 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALAUU 209 " --> pdb=" O THRUU 205 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARGUU 210 " --> pdb=" O THRUU 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLNUU 211 " --> pdb=" O GLUUU 207 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYRUU 219 " --> pdb=" O ARGUU 215 " (cutoff:3.500A) Processing helix chain 'UU' and resid 93 through 98 removed outlier: 3.542A pdb=" N ARGUU 97 " --> pdb=" O GLUUU 94 " (cutoff:3.500A) Proline residue: UU 98 - end of helix Processing helix chain 'VV' and resid 98 through 104 Processing helix chain 'VV' and resid 107 through 113 Processing helix chain 'VV' and resid 118 through 170 removed outlier: 3.570A pdb=" N LYSVV 152 " --> pdb=" O LYSVV 148 " (cutoff:3.500A) Processing helix chain 'VV' and resid 173 through 180 removed outlier: 3.775A pdb=" N THRVV 179 " --> pdb=" O ASPVV 175 " (cutoff:3.500A) Processing helix chain 'VV' and resid 184 through 189 Processing helix chain 'VV' and resid 198 through 236 removed outlier: 3.504A pdb=" N ILEVV 208 " --> pdb=" O GLUVV 204 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALVV 225 " --> pdb=" O ARGVV 221 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SERVV 232 " --> pdb=" O LEUVV 228 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYSVV 233 " --> pdb=" O TYRVV 229 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASNVV 234 " --> pdb=" O VALVV 230 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHEVV 235 " --> pdb=" O ALAVV 231 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILEVV 236 " --> pdb=" O SERVV 232 " (cutoff:3.500A) Processing helix chain 'VV' and resid 238 through 250 removed outlier: 3.535A pdb=" N LYSVV 248 " --> pdb=" O GLUVV 244 " (cutoff:3.500A) Processing helix chain 'VV' and resid 265 through 270 removed outlier: 3.642A pdb=" N SERVV 269 " --> pdb=" O SERVV 265 " (cutoff:3.500A) Processing helix chain 'VV' and resid 275 through 284 removed outlier: 3.568A pdb=" N GLUVV 282 " --> pdb=" O GLUVV 278 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHEVV 283 " --> pdb=" O LEUVV 279 " (cutoff:3.500A) Processing helix chain 'VV' and resid 294 through 313 removed outlier: 4.298A pdb=" N VALVV 298 " --> pdb=" O THRVV 294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VALVV 302 " --> pdb=" O VALVV 298 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALAVV 308 " --> pdb=" O GLNVV 304 " (cutoff:3.500A) Processing helix chain 'WW' and resid 51 through 72 removed outlier: 3.519A pdb=" N ILEWW 66 " --> pdb=" O ARGWW 62 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEUWW 67 " --> pdb=" O GLUWW 63 " (cutoff:3.500A) Proline residue: WW 68 - end of helix removed outlier: 4.000A pdb=" N LEUWW 71 " --> pdb=" O LEUWW 67 " (cutoff:3.500A) Proline residue: WW 72 - end of helix Processing helix chain 'WW' and resid 73 through 82 removed outlier: 3.857A pdb=" N GLNWW 77 " --> pdb=" O PROWW 73 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSWW 78 " --> pdb=" O GLUWW 74 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILEWW 79 " --> pdb=" O LEUWW 75 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHEWW 80 " --> pdb=" O ARGWW 76 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASNWW 81 " --> pdb=" O GLNWW 77 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYSWW 82 " --> pdb=" O LYSWW 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'WW' and resid 73 through 82' Processing helix chain 'WW' and resid 83 through 92 removed outlier: 5.551A pdb=" N GLUWW 87 " --> pdb=" O LYSWW 83 " (cutoff:3.500A) Proline residue: WW 92 - end of helix Processing helix chain 'WW' and resid 115 through 127 Processing helix chain 'WW' and resid 129 through 147 removed outlier: 4.518A pdb=" N ASNWW 135 " --> pdb=" O GLYWW 131 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEUWW 136 " --> pdb=" O ASPWW 132 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SERWW 137 " --> pdb=" O PHEWW 133 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLYWW 138 " --> pdb=" O ALAWW 134 " (cutoff:3.500A) Processing helix chain 'WW' and resid 153 through 166 removed outlier: 3.822A pdb=" N ALAWW 165 " --> pdb=" O LYSWW 161 " (cutoff:3.500A) Processing helix chain 'WW' and resid 167 through 178 removed outlier: 3.620A pdb=" N ILEWW 171 " --> pdb=" O HISWW 167 " (cutoff:3.500A) Processing helix chain 'WW' and resid 187 through 204 removed outlier: 3.519A pdb=" N GLNWW 199 " --> pdb=" O LEUWW 195 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALAWW 202 " --> pdb=" O ILEWW 198 " (cutoff:3.500A) Processing helix chain 'WW' and resid 208 through 228 removed outlier: 3.591A pdb=" N LYSWW 214 " --> pdb=" O PROWW 210 " (cutoff:3.500A) Processing helix chain 'WW' and resid 229 through 234 removed outlier: 4.843A pdb=" N METWW 233 " --> pdb=" O ASPWW 229 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SERWW 234 " --> pdb=" O GLUWW 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'WW' and resid 229 through 234' Processing helix chain 'WW' and resid 235 through 245 removed outlier: 3.598A pdb=" N GLNWW 240 " --> pdb=" O ASPWW 236 " (cutoff:3.500A) Processing helix chain 'WW' and resid 253 through 270 removed outlier: 4.145A pdb=" N ALAWW 257 " --> pdb=" O GLNWW 253 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARGWW 258 " --> pdb=" O PHEWW 254 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARGWW 268 " --> pdb=" O GLUWW 264 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARGWW 269 " --> pdb=" O LEUWW 265 " (cutoff:3.500A) Processing helix chain 'WW' and resid 275 through 300 removed outlier: 3.753A pdb=" N ASNWW 284 " --> pdb=" O LEUWW 280 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYSWW 287 " --> pdb=" O ALAWW 283 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGWW 298 " --> pdb=" O GLUWW 294 " (cutoff:3.500A) Processing helix chain 'WW' and resid 305 through 310 removed outlier: 4.887A pdb=" N TYRWW 310 " --> pdb=" O LEUWW 306 " (cutoff:3.500A) Processing helix chain 'WW' and resid 311 through 317 removed outlier: 4.293A pdb=" N TYRWW 315 " --> pdb=" O THRWW 311 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VALWW 316 " --> pdb=" O ASPWW 312 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALAWW 317 " --> pdb=" O GLUWW 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'WW' and resid 311 through 317' Processing helix chain 'WW' and resid 321 through 326 removed outlier: 5.343A pdb=" N ILEWW 325 " --> pdb=" O LEUWW 321 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYSWW 326 " --> pdb=" O ARGWW 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'WW' and resid 321 through 326' Processing helix chain 'WW' and resid 328 through 352 removed outlier: 3.528A pdb=" N TYRWW 333 " --> pdb=" O VALWW 329 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SERWW 335 " --> pdb=" O LEUWW 331 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHEWW 336 " --> pdb=" O ARGWW 332 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THRWW 337 " --> pdb=" O TYRWW 333 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLYWW 352 " --> pdb=" O VALWW 348 " (cutoff:3.500A) Processing helix chain 'WW' and resid 353 through 378 removed outlier: 3.781A pdb=" N ILEWW 361 " --> pdb=" O ALAWW 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUWW 373 " --> pdb=" O ALAWW 369 " (cutoff:3.500A) Processing helix chain 'WW' and resid 382 through 392 Processing helix chain 'WW' and resid 108 through 113 Processing helix chain 'XX' and resid 79 through 87 Processing helix chain 'XX' and resid 122 through 133 Processing helix chain 'XX' and resid 152 through 169 Processing helix chain 'XX' and resid 183 through 199 Processing helix chain 'XX' and resid 207 through 213 removed outlier: 4.527A pdb=" N LEUXX 211 " --> pdb=" O GLUXX 207 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THRXX 212 " --> pdb=" O ALAXX 208 " (cutoff:3.500A) Processing helix chain 'XX' and resid 229 through 245 removed outlier: 3.679A pdb=" N ARGXX 242 " --> pdb=" O GLNXX 238 " (cutoff:3.500A) Processing helix chain 'XX' and resid 246 through 252 removed outlier: 3.890A pdb=" N ARGXX 250 " --> pdb=" O LYSXX 246 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N METXX 251 " --> pdb=" O VALXX 247 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASNXX 252 " --> pdb=" O LEUXX 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'XX' and resid 246 through 252' Processing helix chain 'XX' and resid 269 through 277 removed outlier: 3.574A pdb=" N LEUXX 273 " --> pdb=" O PROXX 269 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILEXX 274 " --> pdb=" O LEUXX 270 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALAXX 277 " --> pdb=" O LEUXX 273 " (cutoff:3.500A) Processing helix chain 'XX' and resid 279 through 296 removed outlier: 3.684A pdb=" N ALAXX 283 " --> pdb=" O GLUXX 279 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRPXX 284 " --> pdb=" O ALAXX 280 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THRXX 285 " --> pdb=" O ASPXX 281 " (cutoff:3.500A) Processing helix chain 'XX' and resid 311 through 317 removed outlier: 4.289A pdb=" N ILEXX 315 " --> pdb=" O GLYXX 311 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N METXX 316 " --> pdb=" O LEUXX 312 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYSXX 317 " --> pdb=" O ALAXX 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'XX' and resid 311 through 317' Processing helix chain 'XX' and resid 334 through 346 Processing helix chain 'XX' and resid 368 through 384 Processing helix chain 'XX' and resid 399 through 407 Processing helix chain 'XX' and resid 418 through 433 removed outlier: 3.621A pdb=" N GLYXX 433 " --> pdb=" O TRPXX 429 " (cutoff:3.500A) Processing helix chain 'XX' and resid 440 through 452 removed outlier: 3.906A pdb=" N GLYXX 452 " --> pdb=" O TRPXX 448 " (cutoff:3.500A) Processing helix chain 'XX' and resid 455 through 464 removed outlier: 3.676A pdb=" N ARGXX 461 " --> pdb=" O GLYXX 457 " (cutoff:3.500A) Processing helix chain 'YY' and resid 4 through 20 removed outlier: 3.921A pdb=" N GLNYY 10 " --> pdb=" O ALAYY 6 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEUYY 11 " --> pdb=" O ARGYY 7 " (cutoff:3.500A) Processing helix chain 'YY' and resid 31 through 38 removed outlier: 3.817A pdb=" N LEUYY 35 " --> pdb=" O GLYYY 31 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGYY 38 " --> pdb=" O ILEYY 34 " (cutoff:3.500A) Processing helix chain 'YY' and resid 40 through 47 removed outlier: 3.955A pdb=" N THRYY 46 " --> pdb=" O PROYY 42 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYRYY 47 " --> pdb=" O ALAYY 43 " (cutoff:3.500A) Processing helix chain 'YY' and resid 54 through 63 Processing helix chain 'YY' and resid 71 through 88 Processing helix chain 'ZZ' and resid 62 through 73 removed outlier: 4.724A pdb=" N SERZZ 73 " --> pdb=" O GLUZZ 69 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 78 through 95 removed outlier: 3.838A pdb=" N GLUZZ 82 " --> pdb=" O ASPZZ 78 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARGZZ 83 " --> pdb=" O TRPZZ 79 " (cutoff:3.500A) Proline residue: ZZ 95 - end of helix Processing helix chain 'ZZ' and resid 96 through 118 removed outlier: 4.334A pdb=" N ILEZZ 109 " --> pdb=" O METZZ 105 " (cutoff:3.500A) Proline residue: ZZ 115 - end of helix Processing helix chain 'ZZ' and resid 134 through 139 removed outlier: 3.933A pdb=" N ILEZZ 138 " --> pdb=" O ASPZZ 134 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THRZZ 139 " --> pdb=" O THRZZ 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'ZZ' and resid 134 through 139' Processing helix chain 'ZZ' and resid 153 through 184 removed outlier: 3.808A pdb=" N LYSZZ 159 " --> pdb=" O LEUZZ 155 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N METZZ 177 " --> pdb=" O ALAZZ 173 " (cutoff:3.500A) Proline residue: ZZ 178 - end of helix removed outlier: 4.162A pdb=" N SERZZ 181 " --> pdb=" O METZZ 177 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYSZZ 182 " --> pdb=" O PROZZ 178 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYRZZ 183 " --> pdb=" O LEUZZ 179 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALAZZ 184 " --> pdb=" O LEUZZ 180 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 219 through 224 removed outlier: 3.905A pdb=" N LEUZZ 223 " --> pdb=" O CYSZZ 219 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARGZZ 224 " --> pdb=" O PROZZ 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'ZZ' and resid 219 through 224' Processing helix chain 'ZZ' and resid 227 through 239 removed outlier: 3.525A pdb=" N GLYZZ 239 " --> pdb=" O METZZ 235 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 258 through 279 Processing helix chain 'ZZ' and resid 309 through 334 removed outlier: 3.703A pdb=" N LYSZZ 314 " --> pdb=" O GLUZZ 310 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEUZZ 324 " --> pdb=" O ARGZZ 320 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYSZZ 330 " --> pdb=" O LYSZZ 326 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 338 through 350 removed outlier: 4.230A pdb=" N GLYZZ 350 " --> pdb=" O TYRZZ 346 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 208 through 213 removed outlier: 4.050A pdb=" N ARGZZ 212 " --> pdb=" O PROZZ 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSZZ 213 " --> pdb=" O ALAZZ 210 " (cutoff:3.500A) Processing helix chain '11' and resid 25 through 41 removed outlier: 4.470A pdb=" N ALA11 29 " --> pdb=" O ASN11 25 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL11 30 " --> pdb=" O PRO11 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA11 39 " --> pdb=" O LEU11 35 " (cutoff:3.500A) Processing helix chain '11' and resid 45 through 62 removed outlier: 4.792A pdb=" N ALA11 49 " --> pdb=" O SER11 45 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR11 50 " --> pdb=" O ALA11 46 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL11 51 " --> pdb=" O GLY11 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN11 53 " --> pdb=" O ALA11 49 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET11 59 " --> pdb=" O LEU11 55 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP11 60 " --> pdb=" O ARG11 56 " (cutoff:3.500A) Proline residue: 11 62 - end of helix Processing helix chain '11' and resid 71 through 84 removed outlier: 3.503A pdb=" N HIS11 75 " --> pdb=" O THR11 71 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU11 81 " --> pdb=" O SER11 77 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG11 82 " --> pdb=" O ARG11 78 " (cutoff:3.500A) Processing helix chain '22' and resid 313 through 342 removed outlier: 3.902A pdb=" N LYS22 319 " --> pdb=" O ARG22 315 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU22 320 " --> pdb=" O ARG22 316 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN22 336 " --> pdb=" O ARG22 332 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU22 337 " --> pdb=" O ARG22 333 " (cutoff:3.500A) Processing helix chain '33' and resid 55 through 64 removed outlier: 3.538A pdb=" N GLY33 64 " --> pdb=" O LEU33 60 " (cutoff:3.500A) Processing helix chain '33' and resid 67 through 75 removed outlier: 4.020A pdb=" N ALA33 71 " --> pdb=" O LEU33 67 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP33 72 " --> pdb=" O LYS33 68 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LYS33 73 " --> pdb=" O GLN33 69 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE33 74 " --> pdb=" O HIS33 70 " (cutoff:3.500A) Proline residue: 33 75 - end of helix No H-bonds generated for 'chain '33' and resid 67 through 75' Processing helix chain '33' and resid 76 through 83 removed outlier: 3.606A pdb=" N LEU33 80 " --> pdb=" O THR33 76 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE33 81 " --> pdb=" O TRP33 77 " (cutoff:3.500A) Processing helix chain '33' and resid 84 through 92 Processing helix chain '33' and resid 95 through 112 Processing helix chain '33' and resid 154 through 159 removed outlier: 5.520A pdb=" N SER33 159 " --> pdb=" O VAL33 155 " (cutoff:3.500A) Processing helix chain '33' and resid 213 through 233 removed outlier: 3.555A pdb=" N VAL33 217 " --> pdb=" O ARG33 213 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU33 231 " --> pdb=" O LYS33 227 " (cutoff:3.500A) Processing helix chain '44' and resid 63 through 87 removed outlier: 4.398A pdb=" N GLU44 73 " --> pdb=" O MET44 69 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR44 74 " --> pdb=" O ALA44 70 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE44 77 " --> pdb=" O GLU44 73 " (cutoff:3.500A) Processing helix chain '44' and resid 90 through 95 removed outlier: 4.454A pdb=" N LYS44 94 " --> pdb=" O ASP44 90 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP44 95 " --> pdb=" O PHE44 91 " (cutoff:3.500A) No H-bonds generated for 'chain '44' and resid 90 through 95' Processing helix chain '44' and resid 96 through 104 Processing helix chain '44' and resid 106 through 130 removed outlier: 3.634A pdb=" N ALA44 110 " --> pdb=" O ASP44 106 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N HIS44 111 " --> pdb=" O PRO44 107 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL44 112 " --> pdb=" O GLU44 108 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS44 115 " --> pdb=" O HIS44 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS44 128 " --> pdb=" O PHE44 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU44 129 " --> pdb=" O PHE44 125 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER44 130 " --> pdb=" O PHE44 126 " (cutoff:3.500A) Processing helix chain '44' and resid 137 through 148 removed outlier: 3.700A pdb=" N ASN44 145 " --> pdb=" O PHE44 141 " (cutoff:3.500A) Processing helix chain '44' and resid 150 through 165 Processing helix chain '44' and resid 216 through 236 Processing helix chain '44' and resid 258 through 263 removed outlier: 4.031A pdb=" N TRP44 262 " --> pdb=" O TRP44 258 " (cutoff:3.500A) Processing helix chain '44' and resid 275 through 287 removed outlier: 3.778A pdb=" N ASN44 285 " --> pdb=" O GLN44 281 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET44 286 " --> pdb=" O SER44 282 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE44 287 " --> pdb=" O TRP44 283 " (cutoff:3.500A) Processing helix chain '44' and resid 288 through 297 Processing helix chain '55' and resid 63 through 87 removed outlier: 4.566A pdb=" N GLU55 73 " --> pdb=" O MET55 69 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR55 74 " --> pdb=" O ALA55 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR55 76 " --> pdb=" O THR55 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU55 85 " --> pdb=" O LYS55 81 " (cutoff:3.500A) Processing helix chain '55' and resid 95 through 104 removed outlier: 3.721A pdb=" N ALA55 104 " --> pdb=" O VAL55 100 " (cutoff:3.500A) Processing helix chain '55' and resid 109 through 129 removed outlier: 4.037A pdb=" N HIS55 128 " --> pdb=" O PHE55 124 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU55 129 " --> pdb=" O PHE55 125 " (cutoff:3.500A) Processing helix chain '55' and resid 137 through 148 Processing helix chain '55' and resid 150 through 166 removed outlier: 3.846A pdb=" N MET55 165 " --> pdb=" O THR55 161 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE55 166 " --> pdb=" O ALA55 162 " (cutoff:3.500A) Processing helix chain '55' and resid 258 through 263 removed outlier: 3.909A pdb=" N TRP55 262 " --> pdb=" O TRP55 258 " (cutoff:3.500A) Processing helix chain '55' and resid 275 through 287 removed outlier: 3.915A pdb=" N ASN55 285 " --> pdb=" O GLN55 281 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET55 286 " --> pdb=" O SER55 282 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE55 287 " --> pdb=" O TRP55 283 " (cutoff:3.500A) Processing helix chain '55' and resid 288 through 297 removed outlier: 3.580A pdb=" N ARG55 297 " --> pdb=" O GLU55 293 " (cutoff:3.500A) Processing helix chain '66' and resid 68 through 81 Processing helix chain '66' and resid 82 through 88 removed outlier: 3.853A pdb=" N LYS66 86 " --> pdb=" O GLY66 82 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU66 87 " --> pdb=" O SER66 83 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N HIS66 88 " --> pdb=" O ALA66 84 " (cutoff:3.500A) No H-bonds generated for 'chain '66' and resid 82 through 88' Processing helix chain '66' and resid 121 through 133 Processing helix chain '66' and resid 138 through 147 Processing helix chain '66' and resid 149 through 170 Processing helix chain '66' and resid 174 through 186 removed outlier: 3.962A pdb=" N MET66 184 " --> pdb=" O ALA66 180 " (cutoff:3.500A) Proline residue: 66 186 - end of helix Processing helix chain '66' and resid 207 through 212 removed outlier: 4.116A pdb=" N GLN66 212 " --> pdb=" O SER66 208 " (cutoff:3.500A) Processing helix chain '66' and resid 225 through 234 Processing helix chain '66' and resid 239 through 244 removed outlier: 3.667A pdb=" N LYS66 243 " --> pdb=" O PRO66 239 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU66 244 " --> pdb=" O VAL66 240 " (cutoff:3.500A) No H-bonds generated for 'chain '66' and resid 239 through 244' Processing helix chain '66' and resid 247 through 259 removed outlier: 4.159A pdb=" N GLU66 251 " --> pdb=" O PRO66 247 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU66 256 " --> pdb=" O PHE66 252 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU66 259 " --> pdb=" O ASP66 255 " (cutoff:3.500A) Processing helix chain '66' and resid 261 through 296 removed outlier: 3.516A pdb=" N ALA66 278 " --> pdb=" O ALA66 274 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE66 295 " --> pdb=" O VAL66 291 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR66 296 " --> pdb=" O GLU66 292 " (cutoff:3.500A) Processing helix chain '77' and resid 230 through 242 Processing helix chain '77' and resid 253 through 258 Processing helix chain '77' and resid 268 through 285 removed outlier: 3.550A pdb=" N LYS77 272 " --> pdb=" O ALA77 268 " (cutoff:3.500A) Processing helix chain '77' and resid 298 through 307 Processing helix chain '77' and resid 317 through 329 removed outlier: 3.543A pdb=" N VAL77 324 " --> pdb=" O GLU77 320 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP77 329 " --> pdb=" O ARG77 325 " (cutoff:3.500A) Processing helix chain '77' and resid 338 through 349 removed outlier: 3.795A pdb=" N THR77 348 " --> pdb=" O LYS77 344 " (cutoff:3.500A) Processing helix chain '77' and resid 365 through 378 removed outlier: 3.744A pdb=" N THR77 377 " --> pdb=" O TYR77 373 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE77 378 " --> pdb=" O GLN77 374 " (cutoff:3.500A) Processing helix chain '77' and resid 381 through 400 removed outlier: 4.194A pdb=" N LEU77 400 " --> pdb=" O LEU77 396 " (cutoff:3.500A) Processing helix chain '88' and resid 43 through 52 removed outlier: 3.684A pdb=" N LYS88 52 " --> pdb=" O ALA88 48 " (cutoff:3.500A) Processing helix chain '88' and resid 85 through 103 removed outlier: 3.789A pdb=" N LYS88 91 " --> pdb=" O SER88 87 " (cutoff:3.500A) Proline residue: 88 94 - end of helix removed outlier: 3.682A pdb=" N ARG88 101 " --> pdb=" O LEU88 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER88 102 " --> pdb=" O GLU88 98 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP88 103 " --> pdb=" O TRP88 99 " (cutoff:3.500A) Processing helix chain '88' and resid 123 through 134 removed outlier: 3.785A pdb=" N LYS88 129 " --> pdb=" O ALA88 125 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA88 132 " --> pdb=" O ALA88 128 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU88 133 " --> pdb=" O LYS88 129 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY88 134 " --> pdb=" O GLN88 130 " (cutoff:3.500A) Processing helix chain '88' and resid 135 through 158 removed outlier: 3.980A pdb=" N LYS88 140 " --> pdb=" O GLU88 136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER88 141 " --> pdb=" O GLY88 137 " (cutoff:3.500A) Processing helix chain '88' and resid 172 through 182 removed outlier: 3.772A pdb=" N SER88 178 " --> pdb=" O GLY88 174 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS88 180 " --> pdb=" O GLY88 176 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA88 181 " --> pdb=" O LEU88 177 " (cutoff:3.500A) Proline residue: 88 182 - end of helix Processing helix chain '88' and resid 195 through 200 removed outlier: 4.179A pdb=" N ILE88 199 " --> pdb=" O PRO88 195 " (cutoff:3.500A) Processing helix chain '88' and resid 206 through 214 Proline residue: 88 212 - end of helix Processing helix chain '88' and resid 217 through 225 Processing helix chain '88' and resid 231 through 238 removed outlier: 3.978A pdb=" N TYR88 235 " --> pdb=" O GLY88 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY88 238 " --> pdb=" O VAL88 234 " (cutoff:3.500A) Processing helix chain '88' and resid 245 through 260 removed outlier: 3.690A pdb=" N LEU88 249 " --> pdb=" O HIS88 245 " (cutoff:3.500A) Proline residue: 88 250 - end of helix removed outlier: 3.990A pdb=" N GLU88 258 " --> pdb=" O SER88 254 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU88 259 " --> pdb=" O ARG88 255 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR88 260 " --> pdb=" O LEU88 256 " (cutoff:3.500A) Processing helix chain '88' and resid 266 through 282 removed outlier: 3.804A pdb=" N GLU88 280 " --> pdb=" O ASP88 276 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE88 281 " --> pdb=" O THR88 277 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER88 282 " --> pdb=" O ILE88 278 " (cutoff:3.500A) Processing helix chain '88' and resid 295 through 305 Processing helix chain '88' and resid 309 through 322 removed outlier: 3.507A pdb=" N GLU88 319 " --> pdb=" O ALA88 315 " (cutoff:3.500A) Processing helix chain '88' and resid 329 through 344 removed outlier: 4.120A pdb=" N GLN88 342 " --> pdb=" O GLU88 338 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER88 344 " --> pdb=" O LEU88 340 " (cutoff:3.500A) Processing helix chain '88' and resid 345 through 359 removed outlier: 3.675A pdb=" N ARG88 356 " --> pdb=" O LEU88 352 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS88 359 " --> pdb=" O MET88 355 " (cutoff:3.500A) Processing helix chain '88' and resid 362 through 381 removed outlier: 3.501A pdb=" N LYS88 368 " --> pdb=" O ALA88 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS88 379 " --> pdb=" O ALA88 375 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N HIS88 381 " --> pdb=" O PHE88 377 " (cutoff:3.500A) Processing helix chain '88' and resid 382 through 390 Processing helix chain '88' and resid 406 through 411 removed outlier: 4.401A pdb=" N ILE88 410 " --> pdb=" O SER88 406 " (cutoff:3.500A) Proline residue: 88 411 - end of helix No H-bonds generated for 'chain '88' and resid 406 through 411' Processing helix chain '88' and resid 416 through 422 removed outlier: 5.197A pdb=" N TYR88 420 " --> pdb=" O ILE88 416 " (cutoff:3.500A) Processing helix chain '88' and resid 450 through 461 Processing helix chain '88' and resid 464 through 477 removed outlier: 3.674A pdb=" N ILE88 469 " --> pdb=" O ARG88 465 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE88 472 " --> pdb=" O LEU88 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG88 477 " --> pdb=" O VAL88 473 " (cutoff:3.500A) Processing helix chain '88' and resid 481 through 493 Processing helix chain '00' and resid 40 through 86 removed outlier: 5.483A pdb=" N ASN00 49 " --> pdb=" O ARG00 45 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLU00 50 " --> pdb=" O GLU00 46 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP00 51 " --> pdb=" O LYS00 47 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE00 52 " --> pdb=" O ALA00 48 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA00 53 " --> pdb=" O ASN00 49 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS00 82 " --> pdb=" O THR00 78 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP00 84 " --> pdb=" O SER00 80 " (cutoff:3.500A) Processing helix chain '99' and resid 53 through 88 removed outlier: 4.322A pdb=" N ARG99 57 " --> pdb=" O ALA99 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 120 Processing helix chain 'V' and resid 194 through 200 removed outlier: 3.722A pdb=" N TYR V 198 " --> pdb=" O LEU V 194 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR V 200 " --> pdb=" O SER V 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 194 through 200' Processing sheet with id= 1, first strand: chain 'AA' and resid 84 through 87 removed outlier: 6.837A pdb=" N ASPAA 97 " --> pdb=" O LYSAA 87 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'AA' and resid 328 through 332 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'AA' and resid 389 through 392 removed outlier: 3.860A pdb=" N LYSAA 389 " --> pdb=" O THRAA 401 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'BB' and resid 169 through 172 removed outlier: 5.076A pdb=" N HISBB 169 " --> pdb=" O ILEBB 195 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HISBB 193 " --> pdb=" O GLYBB 171 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'BB' and resid 243 through 246 Processing sheet with id= 6, first strand: chain 'CC' and resid 117 through 122 removed outlier: 3.992A pdb=" N LYSCC 125 " --> pdb=" O THRCC 122 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'CC' and resid 453 through 459 removed outlier: 3.591A pdb=" N GLYCC 434 " --> pdb=" O SERCC 506 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLYCC 497 " --> pdb=" O ARGCC 494 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASNCC 484 " --> pdb=" O GLYCC 507 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'DD' and resid 186 through 191 removed outlier: 4.077A pdb=" N ASPDD 187 " --> pdb=" O TYRDD 420 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N CYSDD 416 " --> pdb=" O VALDD 191 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'EE' and resid 314 through 318 removed outlier: 6.431A pdb=" N METEE 338 " --> pdb=" O LEUEE 318 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'EE' and resid 386 through 391 removed outlier: 6.511A pdb=" N GLYEE 386 " --> pdb=" O SEREE 401 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILEEE 396 " --> pdb=" O LEUEE 431 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARGEE 402 " --> pdb=" O ASPEE 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASPEE 425 " --> pdb=" O ARGEE 402 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'EE' and resid 335 through 342 Processing sheet with id= 12, first strand: chain 'FF' and resid 60 through 68 removed outlier: 5.319A pdb=" N LEUFF 2 " --> pdb=" O LEUFF 95 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'GG' and resid 210 through 216 Processing sheet with id= 14, first strand: chain 'HH' and resid 22 through 28 removed outlier: 6.021A pdb=" N GLYHH 22 " --> pdb=" O LEUHH 83 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASNHH 28 " --> pdb=" O ARGHH 77 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARGHH 77 " --> pdb=" O ASNHH 28 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SERHH 47 " --> pdb=" O GLYHH 82 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'HH' and resid 134 through 137 removed outlier: 6.963A pdb=" N PHEHH 134 " --> pdb=" O LEUHH 157 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'II' and resid 190 through 196 Processing sheet with id= 17, first strand: chain 'JJ' and resid 141 through 144 removed outlier: 6.008A pdb=" N SERJJ 111 " --> pdb=" O TRPJJ 212 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'JJ' and resid 145 through 148 removed outlier: 3.566A pdb=" N LEUJJ 148 " --> pdb=" O ARGJJ 177 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARGJJ 177 " --> pdb=" O LEUJJ 148 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'JJ' and resid 150 through 158 Processing sheet with id= 20, first strand: chain 'KK' and resid 279 through 282 removed outlier: 3.955A pdb=" N VALKK 326 " --> pdb=" O PHEKK 258 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LL' and resid 75 through 79 removed outlier: 5.183A pdb=" N LEULL 127 " --> pdb=" O VALLL 144 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LL' and resid 82 through 87 removed outlier: 5.316A pdb=" N LYSLL 97 " --> pdb=" O ILELL 113 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYSLL 107 " --> pdb=" O LEULL 103 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'OO' and resid 101 through 106 removed outlier: 5.487A pdb=" N SEROO 101 " --> pdb=" O LEUOO 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYSOO 118 " --> pdb=" O SEROO 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLUOO 116 " --> pdb=" O PROOO 105 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'PP' and resid 5 through 11 Processing sheet with id= 25, first strand: chain 'QQ' and resid 18 through 22 Processing sheet with id= 26, first strand: chain 'QQ' and resid 31 through 44 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'SS' and resid 34 through 37 removed outlier: 4.528A pdb=" N LEUSS 51 " --> pdb=" O VALSS 66 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'WW' and resid 93 through 96 Processing sheet with id= 29, first strand: chain 'XX' and resid 117 through 121 removed outlier: 4.023A pdb=" N SERXX 117 " --> pdb=" O ILEXX 151 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'XX' and resid 200 through 206 Processing sheet with id= 31, first strand: chain 'XX' and resid 353 through 360 removed outlier: 6.562A pdb=" N GLYXX 178 " --> pdb=" O THRXX 360 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'ZZ' and resid 196 through 200 Processing sheet with id= 33, first strand: chain '33' and resid 141 through 148 removed outlier: 6.486A pdb=" N ARG33 141 " --> pdb=" O ALA33 137 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA33 137 " --> pdb=" O ARG33 141 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL33 189 " --> pdb=" O VAL33 185 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '44' and resid 183 through 191 removed outlier: 6.625A pdb=" N LEU44 173 " --> pdb=" O ILE44 252 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG44 175 " --> pdb=" O ILE44 250 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP44 248 " --> pdb=" O GLN44 177 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '44' and resid 169 through 173 removed outlier: 4.747A pdb=" N GLY44 169 " --> pdb=" O THR44 257 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU44 253 " --> pdb=" O LEU44 173 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '55' and resid 184 through 190 removed outlier: 6.644A pdb=" N LEU55 173 " --> pdb=" O ILE55 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG55 175 " --> pdb=" O ILE55 250 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '55' and resid 169 through 173 removed outlier: 4.904A pdb=" N GLY55 169 " --> pdb=" O THR55 257 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU55 253 " --> pdb=" O LEU55 173 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '88' and resid 61 through 66 removed outlier: 5.115A pdb=" N ASP88 61 " --> pdb=" O ASN88 76 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY88 112 " --> pdb=" O PHE88 165 " (cutoff:3.500A) 2582 hydrogen bonds defined for protein. 7701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 889 hydrogen bonds 1442 hydrogen bond angles 0 basepair planarities 376 basepair parallelities 837 stacking parallelities Total time for adding SS restraints: 70.97 Time building geometry restraints manager: 97.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 76623 1.03 - 1.22: 446 1.22 - 1.42: 41355 1.42 - 1.61: 53565 1.61 - 1.81: 373 Bond restraints: 172362 Sorted by residual: bond pdb=" C1' ATPXX 501 " pdb=" C2' ATPXX 501 " ideal model delta sigma weight residual 1.531 1.278 0.253 1.20e-02 6.94e+03 4.45e+02 bond pdb=" O3A ATPXX 501 " pdb=" PB ATPXX 501 " ideal model delta sigma weight residual 1.592 1.651 -0.059 1.10e-02 8.26e+03 2.88e+01 bond pdb=" C4' ATPXX 501 " pdb=" C5' ATPXX 501 " ideal model delta sigma weight residual 1.508 1.567 -0.059 1.50e-02 4.44e+03 1.57e+01 bond pdb=" C4 ATPXX 501 " pdb=" N9 ATPXX 501 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.53e+01 bond pdb=" C5 ATPXX 501 " pdb=" N7 ATPXX 501 " ideal model delta sigma weight residual 1.387 1.348 0.039 1.00e-02 1.00e+04 1.49e+01 ... (remaining 172357 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.90: 10642 106.90 - 113.79: 195797 113.79 - 120.67: 62949 120.67 - 127.56: 38827 127.56 - 134.45: 3202 Bond angle restraints: 311417 Sorted by residual: angle pdb=" PB ATPXX 501 " pdb=" O3B ATPXX 501 " pdb=" PG ATPXX 501 " ideal model delta sigma weight residual 139.87 132.51 7.36 1.00e+00 1.00e+00 5.42e+01 angle pdb=" N7 ATPXX 501 " pdb=" C8 ATPXX 501 " pdb=" N9 ATPXX 501 " ideal model delta sigma weight residual 114.08 106.87 7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" N3 ATPXX 501 " pdb=" C4 ATPXX 501 " pdb=" N9 ATPXX 501 " ideal model delta sigma weight residual 127.04 134.45 -7.41 1.15e+00 7.59e-01 4.16e+01 angle pdb=" C5 ATPXX 501 " pdb=" C4 ATPXX 501 " pdb=" N3 ATPXX 501 " ideal model delta sigma weight residual 126.80 120.69 6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C4 ATPXX 501 " pdb=" N9 ATPXX 501 " pdb=" C8 ATPXX 501 " ideal model delta sigma weight residual 105.72 111.78 -6.06 1.00e+00 1.00e+00 3.68e+01 ... (remaining 311412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 67787 34.73 - 69.45: 761 69.45 - 104.18: 53 104.18 - 138.90: 3 138.90 - 173.63: 3 Dihedral angle restraints: 68607 sinusoidal: 43399 harmonic: 25208 Sorted by residual: dihedral pdb=" O4' Uaa 516 " pdb=" C1' Uaa 516 " pdb=" N1 Uaa 516 " pdb=" C2 Uaa 516 " ideal model delta sinusoidal sigma weight residual 200.00 54.74 145.26 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' Caa 951 " pdb=" C1' Caa 951 " pdb=" N1 Caa 951 " pdb=" C2 Caa 951 " ideal model delta sinusoidal sigma weight residual 200.00 68.83 131.17 1 1.50e+01 4.44e-03 7.08e+01 dihedral pdb=" O4' Uaa1152 " pdb=" C1' Uaa1152 " pdb=" N1 Uaa1152 " pdb=" C2 Uaa1152 " ideal model delta sinusoidal sigma weight residual 232.00 58.37 173.63 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 68604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 15617 0.083 - 0.166: 537 0.166 - 0.249: 0 0.249 - 0.332: 2 0.332 - 0.415: 1 Chirality restraints: 16157 Sorted by residual: chirality pdb=" C2' ATPXX 501 " pdb=" C1' ATPXX 501 " pdb=" C3' ATPXX 501 " pdb=" O2' ATPXX 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.26 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C1' ATPXX 501 " pdb=" C2' ATPXX 501 " pdb=" N9 ATPXX 501 " pdb=" O4' ATPXX 501 " both_signs ideal model delta sigma weight residual False 2.41 2.09 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C4' ATPXX 501 " pdb=" C3' ATPXX 501 " pdb=" C5' ATPXX 501 " pdb=" O4' ATPXX 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 16154 not shown) Planarity restraints: 20228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' Aaa 799 " 0.017 2.00e-02 2.50e+03 7.48e-03 1.82e+00 pdb=" N9 Aaa 799 " -0.019 2.00e-02 2.50e+03 pdb=" C8 Aaa 799 " -0.002 2.00e-02 2.50e+03 pdb=" N7 Aaa 799 " 0.001 2.00e-02 2.50e+03 pdb=" C5 Aaa 799 " 0.002 2.00e-02 2.50e+03 pdb=" C6 Aaa 799 " 0.006 2.00e-02 2.50e+03 pdb=" N6 Aaa 799 " 0.002 2.00e-02 2.50e+03 pdb=" N1 Aaa 799 " -0.001 2.00e-02 2.50e+03 pdb=" C2 Aaa 799 " -0.001 2.00e-02 2.50e+03 pdb=" N3 Aaa 799 " -0.002 2.00e-02 2.50e+03 pdb=" C4 Aaa 799 " -0.004 2.00e-02 2.50e+03 pdb=" H8 Aaa 799 " 0.000 2.00e-02 2.50e+03 pdb=" H2 Aaa 799 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILEGG 231 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PROGG 232 " 0.046 5.00e-02 4.00e+02 pdb=" CA PROGG 232 " -0.014 5.00e-02 4.00e+02 pdb=" CD PROGG 232 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEZZ 287 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PROZZ 288 " 0.046 5.00e-02 4.00e+02 pdb=" CA PROZZ 288 " -0.013 5.00e-02 4.00e+02 pdb=" CD PROZZ 288 " -0.015 5.00e-02 4.00e+02 ... (remaining 20225 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.28: 25357 2.28 - 3.00: 424958 3.00 - 3.71: 610848 3.71 - 4.43: 955706 4.43 - 5.14: 1422093 Nonbonded interactions: 3438962 Sorted by model distance: nonbonded pdb="HH22 ARGCC 442 " pdb=" O ARGCC 448 " model vdw 1.568 1.850 nonbonded pdb="HO2' Uaa 737 " pdb=" O5' Uaa 738 " model vdw 1.584 1.850 nonbonded pdb=" O TRPZZ 91 " pdb=" HG1 THRZZ 94 " model vdw 1.593 1.850 nonbonded pdb=" O ASP66 321 " pdb="HH22 ARG66 328 " model vdw 1.596 1.850 nonbonded pdb=" H1 Gaa1136 " pdb=" OP2 Aaa1622 " model vdw 1.597 1.850 ... (remaining 3438957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '44' and (resid 43 through 127 or (resid 128 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 129 through 206 or (resid 237 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 o \ r name HB3 or name HD21 or name HD22)) or resid 238 through 302)) selection = (chain '55' and resid 43 through 302) } 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: 8 Type Number sf(0) Gaussians K 22 8.98 5 P 1438 5.49 5 Mg 97 5.21 5 S 202 5.16 5 C 51836 2.51 5 N 16474 2.21 5 O 20823 1.98 5 H 76656 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.410 Extract box with map and model: 21.260 Check model and map are aligned: 1.670 Convert atoms to be neutral: 0.940 Process input model: 436.920 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 475.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 0.253 95706 Z= 0.140 Angle : 0.369 7.406 136269 Z= 0.208 Chirality : 0.031 0.415 16157 Planarity : 0.002 0.027 12174 Dihedral : 10.004 173.627 40907 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -2.99 (0.08), residues: 7422 helix: -2.37 (0.07), residues: 3335 sheet: -1.31 (0.19), residues: 612 loop : -1.56 (0.10), residues: 3475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1606 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1597 time to evaluate : 7.511 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 outliers start: 9 outliers final: 5 residues processed: 1602 average time/residue: 3.4791 time to fit residues: 7269.9608 Evaluate side-chains 1109 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1104 time to evaluate : 7.661 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 4 average time/residue: 1.8556 time to fit residues: 20.3819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 741 optimal weight: 4.9990 chunk 665 optimal weight: 0.0970 chunk 369 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 688 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 418 optimal weight: 5.9990 chunk 512 optimal weight: 5.9990 chunk 797 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 251 GLN BB 116 GLN BB 203 HIS BB 303 ASN CC 89 GLN ** CC 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 298 ASN CC 306 GLN CC 318 ASN CC 431 ASN DD 123 ASN EE 312 GLN EE 320 HIS GG 249 ASN II 160 GLN JJ 181 GLN KK 302 GLN MM 8 ASN MM 10 ASN MM 104 ASN NN 16 ASN NN 57 GLN OO 58 GLN OO 72 GLN QQ 162 GLN VV 140 GLN VV 153 GLN VV 272 ASN VV 281 ASN VV 306 ASN XX 194 HIS XX 229 GLN XX 238 GLN ZZ 333 GLN 22 341 GLN 33 152 ASN 44 52 ASN 55 75 GLN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 55 281 GLN 66 289 GLN 77 292 GLN 77 308 HIS 00 43 GLN 00 82 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 95706 Z= 0.329 Angle : 0.555 7.388 136269 Z= 0.290 Chirality : 0.039 0.207 16157 Planarity : 0.004 0.068 12174 Dihedral : 10.597 173.561 25529 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.92 (0.09), residues: 7422 helix: -0.08 (0.08), residues: 3387 sheet: -0.81 (0.19), residues: 630 loop : -1.02 (0.10), residues: 3405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1192 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1106 time to evaluate : 7.557 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 outliers start: 86 outliers final: 36 residues processed: 1148 average time/residue: 3.5005 time to fit residues: 5368.5556 Evaluate side-chains 1068 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1032 time to evaluate : 8.450 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 16 residues processed: 21 average time/residue: 2.1284 time to fit residues: 80.9639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 443 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 663 optimal weight: 4.9990 chunk 542 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 798 optimal weight: 3.9990 chunk 862 optimal weight: 10.0000 chunk 711 optimal weight: 8.9990 chunk 792 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 640 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN BB 133 GLN BB 303 ASN CC 58 ASN CC 89 GLN ** CC 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DD 447 ASN EE 312 GLN GG 132 HIS II 241 ASN KK 302 GLN MM 104 ASN RR 198 ASN TT 153 ASN UU 69 ASN VV 272 ASN 44 52 ASN 55 75 GLN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 77 292 GLN 00 43 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 95706 Z= 0.370 Angle : 0.545 6.714 136269 Z= 0.285 Chirality : 0.039 0.218 16157 Planarity : 0.005 0.076 12174 Dihedral : 10.866 172.633 25529 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.19 (0.09), residues: 7422 helix: 0.62 (0.09), residues: 3393 sheet: -0.48 (0.19), residues: 630 loop : -0.75 (0.10), residues: 3399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1159 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1063 time to evaluate : 7.575 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 outliers start: 96 outliers final: 47 residues processed: 1103 average time/residue: 3.2755 time to fit residues: 4792.5596 Evaluate side-chains 1085 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1038 time to evaluate : 8.360 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 19 residues processed: 29 average time/residue: 1.6042 time to fit residues: 85.9221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 789 optimal weight: 4.9990 chunk 600 optimal weight: 8.9990 chunk 414 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 536 optimal weight: 3.9990 chunk 801 optimal weight: 3.9990 chunk 848 optimal weight: 6.9990 chunk 418 optimal weight: 0.0870 chunk 759 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN BB 303 ASN CC 318 ASN ** DD 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 312 GLN GG 249 ASN KK 302 GLN MM 104 ASN OO 40 GLN ** SS 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 153 ASN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN WW 108 ASN ZZ 333 GLN 33 152 ASN 44 52 ASN 55 75 GLN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 55 281 GLN 77 292 GLN 77 308 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 95706 Z= 0.316 Angle : 0.531 6.587 136269 Z= 0.277 Chirality : 0.038 0.201 16157 Planarity : 0.005 0.105 12174 Dihedral : 10.972 171.791 25529 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.10), residues: 7422 helix: 0.94 (0.09), residues: 3401 sheet: -0.31 (0.20), residues: 630 loop : -0.60 (0.11), residues: 3391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1154 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1062 time to evaluate : 7.893 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 outliers start: 92 outliers final: 46 residues processed: 1099 average time/residue: 3.4671 time to fit residues: 5145.8755 Evaluate side-chains 1066 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1020 time to evaluate : 7.708 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 21 residues processed: 27 average time/residue: 1.8279 time to fit residues: 92.3355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 706 optimal weight: 10.0000 chunk 481 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 631 optimal weight: 9.9990 chunk 350 optimal weight: 3.9990 chunk 724 optimal weight: 7.9990 chunk 586 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 433 optimal weight: 6.9990 chunk 761 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 250 ASN CC 89 GLN ** DD 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 312 GLN FF 55 GLN KK 302 GLN MM 104 ASN OO 40 GLN OO 58 GLN QQ 85 HIS ** SS 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 153 ASN UU 56 GLN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN 55 75 GLN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 77 292 GLN 77 308 HIS 00 82 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 95706 Z= 0.338 Angle : 0.536 6.636 136269 Z= 0.280 Chirality : 0.039 0.211 16157 Planarity : 0.005 0.088 12174 Dihedral : 11.063 171.242 25529 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 0.37 (0.10), residues: 7422 helix: 1.12 (0.09), residues: 3401 sheet: -0.14 (0.20), residues: 617 loop : -0.52 (0.11), residues: 3404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1138 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1047 time to evaluate : 8.471 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 outliers start: 91 outliers final: 50 residues processed: 1087 average time/residue: 3.3313 time to fit residues: 4820.1046 Evaluate side-chains 1063 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1013 time to evaluate : 7.661 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 25 residues processed: 26 average time/residue: 1.6064 time to fit residues: 78.4191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 285 optimal weight: 3.9990 chunk 764 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 498 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 849 optimal weight: 8.9990 chunk 705 optimal weight: 7.9990 chunk 393 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 445 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 250 ASN BB 116 GLN BB 303 ASN CC 89 GLN CC 318 ASN CC 404 GLN ** DD 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 312 GLN FF 55 GLN JJ 170 ASN MM 104 ASN OO 40 GLN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN XX 238 GLN 33 152 ASN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 55 281 GLN 77 292 GLN 77 308 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 95706 Z= 0.244 Angle : 0.507 6.404 136269 Z= 0.264 Chirality : 0.036 0.178 16157 Planarity : 0.004 0.090 12174 Dihedral : 11.069 170.737 25529 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 0.60 (0.10), residues: 7422 helix: 1.32 (0.09), residues: 3406 sheet: -0.05 (0.20), residues: 616 loop : -0.40 (0.11), residues: 3400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1103 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1041 time to evaluate : 7.645 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 outliers start: 62 outliers final: 40 residues processed: 1079 average time/residue: 3.2827 time to fit residues: 4712.7949 Evaluate side-chains 1035 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 995 time to evaluate : 7.653 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 28 residues processed: 14 average time/residue: 2.0858 time to fit residues: 52.9513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 819 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 484 optimal weight: 4.9990 chunk 620 optimal weight: 0.6980 chunk 480 optimal weight: 2.9990 chunk 715 optimal weight: 0.3980 chunk 474 optimal weight: 7.9990 chunk 846 optimal weight: 10.0000 chunk 529 optimal weight: 6.9990 chunk 515 optimal weight: 3.9990 chunk 390 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 202 GLN AA 250 ASN DD 442 ASN EE 312 GLN FF 55 GLN KK 302 GLN MM 104 ASN OO 40 GLN QQ 162 GLN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN WW 108 ASN XX 238 GLN ZZ 333 GLN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 77 292 GLN 77 308 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 95706 Z= 0.232 Angle : 0.500 7.349 136269 Z= 0.260 Chirality : 0.036 0.176 16157 Planarity : 0.004 0.107 12174 Dihedral : 11.060 170.688 25529 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 0.78 (0.10), residues: 7422 helix: 1.47 (0.09), residues: 3408 sheet: 0.01 (0.20), residues: 606 loop : -0.30 (0.11), residues: 3408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1089 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1023 time to evaluate : 7.531 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 outliers start: 66 outliers final: 40 residues processed: 1067 average time/residue: 3.2705 time to fit residues: 4640.7018 Evaluate side-chains 1053 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1013 time to evaluate : 7.532 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 11 average time/residue: 1.9199 time to fit residues: 42.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 523 optimal weight: 0.8980 chunk 337 optimal weight: 0.6980 chunk 505 optimal weight: 4.9990 chunk 254 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 538 optimal weight: 2.9990 chunk 576 optimal weight: 0.9990 chunk 418 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 665 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 250 ASN BB 116 GLN BB 303 ASN CC 89 GLN CC 318 ASN CC 404 GLN EE 312 GLN FF 55 GLN KK 302 GLN MM 104 ASN OO 40 GLN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN XX 238 GLN 22 341 GLN 33 152 ASN ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 55 281 GLN 77 292 GLN 77 308 HIS 00 43 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 95706 Z= 0.132 Angle : 0.477 9.331 136269 Z= 0.247 Chirality : 0.033 0.188 16157 Planarity : 0.004 0.105 12174 Dihedral : 11.008 170.610 25529 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 1.05 (0.10), residues: 7422 helix: 1.71 (0.09), residues: 3411 sheet: 0.06 (0.21), residues: 606 loop : -0.16 (0.11), residues: 3405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1104 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1052 time to evaluate : 7.441 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 outliers start: 52 outliers final: 33 residues processed: 1090 average time/residue: 3.2222 time to fit residues: 4694.4306 Evaluate side-chains 1051 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1018 time to evaluate : 7.576 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 4 average time/residue: 2.2073 time to fit residues: 21.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 769 optimal weight: 10.0000 chunk 810 optimal weight: 3.9990 chunk 739 optimal weight: 7.9990 chunk 788 optimal weight: 3.9990 chunk 474 optimal weight: 6.9990 chunk 343 optimal weight: 0.8980 chunk 619 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 712 optimal weight: 6.9990 chunk 745 optimal weight: 10.0000 chunk 785 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 250 ASN BB 303 ASN EE 312 GLN FF 55 GLN KK 302 GLN MM 104 ASN OO 40 GLN ** SS 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 153 ASN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN XX 238 GLN ZZ 333 GLN 44 52 ASN ** 55 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 77 292 GLN 77 308 HIS 88 131 ASN ** 00 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 95706 Z= 0.315 Angle : 0.522 9.071 136269 Z= 0.271 Chirality : 0.038 0.201 16157 Planarity : 0.004 0.105 12174 Dihedral : 11.033 171.329 25529 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 0.99 (0.10), residues: 7422 helix: 1.64 (0.09), residues: 3417 sheet: 0.10 (0.20), residues: 606 loop : -0.19 (0.11), residues: 3399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1072 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1019 time to evaluate : 8.535 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 outliers start: 53 outliers final: 37 residues processed: 1052 average time/residue: 3.2977 time to fit residues: 4637.1116 Evaluate side-chains 1035 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 998 time to evaluate : 7.595 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 28 residues processed: 9 average time/residue: 1.6119 time to fit residues: 33.1036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 517 optimal weight: 4.9990 chunk 833 optimal weight: 10.0000 chunk 508 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 579 optimal weight: 0.9980 chunk 874 optimal weight: 0.6980 chunk 805 optimal weight: 6.9990 chunk 696 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 538 optimal weight: 2.9990 chunk 427 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 250 ASN CC 318 ASN EE 312 GLN FF 55 GLN II 187 GLN KK 302 GLN MM 104 ASN RR 130 ASN ** SS 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 226 ASN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN XX 238 GLN 33 152 ASN ** 55 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 55 281 GLN 77 292 GLN 77 308 HIS ** 00 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 00 75 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 95706 Z= 0.178 Angle : 0.497 8.594 136269 Z= 0.258 Chirality : 0.035 0.208 16157 Planarity : 0.004 0.121 12174 Dihedral : 11.047 170.952 25529 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 1.08 (0.10), residues: 7422 helix: 1.72 (0.09), residues: 3416 sheet: 0.10 (0.20), residues: 606 loop : -0.14 (0.11), residues: 3400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14844 Ramachandran restraints generated. 7422 Oldfield, 0 Emsley, 7422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 185 is missing expected H atoms. Skipping. Evaluate side-chains 1052 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1012 time to evaluate : 7.483 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 outliers start: 40 outliers final: 31 residues processed: 1044 average time/residue: 3.2815 time to fit residues: 4599.7871 Evaluate side-chains 1031 residues out of total 6410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1000 time to evaluate : 7.542 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 3 average time/residue: 1.2732 time to fit residues: 16.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 553 optimal weight: 3.9990 chunk 741 optimal weight: 4.9990 chunk 213 optimal weight: 0.2980 chunk 642 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 697 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 716 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 ASN AA 250 ASN BB 303 ASN CC 89 GLN EE 312 GLN FF 55 GLN KK 302 GLN MM 104 ASN OO 40 GLN ** SS 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TT 226 ASN UU 69 ASN VV 272 ASN VV 281 ASN VV 306 ASN XX 238 GLN ZZ 333 GLN ** 55 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 55 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 177 GLN ** 55 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 55 237 ASN 77 292 GLN 77 308 HIS ** 00 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 99 73 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.086174 restraints weight = 289697.301| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.28 r_work: 0.2774 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.2706 rms_B_bonded: 1.81 restraints_weight: 0.1250 r_work: 0.2649 rms_B_bonded: 2.55 restraints_weight: 0.0625 r_work: 0.2557 rms_B_bonded: 3.93 restraints_weight: 0.0312 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.155 95706 Z= 0.154 Angle : 0.484 10.475 136269 Z= 0.251 Chirality : 0.034 0.171 16157 Planarity : 0.004 0.176 12174 Dihedral : 11.023 170.959 25529 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: 1.20 (0.10), residues: 7422 helix: 1.82 (0.09), residues: 3418 sheet: 0.11 (0.21), residues: 606 loop : -0.07 (0.11), residues: 3398 =============================================================================== Job complete usr+sys time: 65574.58 seconds wall clock time: 1116 minutes 56.53 seconds (67016.53 seconds total)