Starting phenix.real_space_refine on Tue Aug 26 18:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mpd_3534/08_2025/5mpd_3534.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mpd_3534/08_2025/5mpd_3534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5mpd_3534/08_2025/5mpd_3534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mpd_3534/08_2025/5mpd_3534.map" model { file = "/net/cci-nas-00/data/ceres_data/5mpd_3534/08_2025/5mpd_3534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mpd_3534/08_2025/5mpd_3534.cif" } resolution = 4.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 151 5.16 5 C 26021 2.51 5 N 6810 2.21 5 O 7992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 225 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40974 Number of models: 1 Model: "" Number of chains: 13 Chain: "W" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1534 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 187} Chain: "V" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2274 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 282} Chain: "T" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Y" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 435 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain breaks: 1 Chain: "Z" Number of atoms: 7005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7005 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 30, 'TRANS': 875} Chain breaks: 1 Chain: "N" Number of atoms: 6882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6882 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 23, 'TRANS': 866} Chain breaks: 1 Chain: "S" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3894 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 11, 'TRANS': 463} Chain: "P" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 9, 'TRANS': 430} Chain: "Q" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3499 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 426} Chain: "R" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3060 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 7, 'TRANS': 373} Chain breaks: 1 Chain: "U" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2373 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 288} Chain: "O" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3186 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 378} Time building chain proxies: 9.06, per 1000 atoms: 0.22 Number of scatterers: 40974 At special positions: 0 Unit cell: (238.74, 211.14, 227.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 151 16.00 O 7992 8.00 N 6810 7.00 C 26021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9824 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 16 sheets defined 71.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'W' and resid 24 through 44 removed outlier: 3.573A pdb=" N ASP W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE W 37 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 78 removed outlier: 4.042A pdb=" N ILE W 72 " --> pdb=" O GLU W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 99 removed outlier: 3.895A pdb=" N ALA W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 132 removed outlier: 3.776A pdb=" N LEU W 125 " --> pdb=" O SER W 121 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS W 130 " --> pdb=" O ILE W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 154 through 162 Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'V' and resid 31 through 44 removed outlier: 3.626A pdb=" N ALA V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY V 44 " --> pdb=" O HIS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 98 removed outlier: 3.821A pdb=" N GLN V 97 " --> pdb=" O ASP V 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR V 98 " --> pdb=" O MET V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 133 Processing helix chain 'V' and resid 160 through 166 Processing helix chain 'V' and resid 168 through 173 Processing helix chain 'V' and resid 184 through 196 Processing helix chain 'V' and resid 206 through 215 removed outlier: 3.563A pdb=" N LYS V 211 " --> pdb=" O ALA V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 224 removed outlier: 3.504A pdb=" N GLY V 224 " --> pdb=" O GLN V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 255 removed outlier: 3.641A pdb=" N LEU V 238 " --> pdb=" O GLU V 234 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS V 246 " --> pdb=" O LYS V 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN V 250 " --> pdb=" O LYS V 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE V 255 " --> pdb=" O TYR V 251 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 270 Processing helix chain 'V' and resid 275 through 306 Processing helix chain 'T' and resid 8 through 18 removed outlier: 3.521A pdb=" N ALA T 14 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE T 15 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU T 16 " --> pdb=" O SER T 12 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 41 Proline residue: T 28 - end of helix removed outlier: 3.869A pdb=" N ILE T 32 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU T 33 " --> pdb=" O PRO T 29 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE T 35 " --> pdb=" O LYS T 31 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE T 41 " --> pdb=" O ASN T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.527A pdb=" N ASN T 53 " --> pdb=" O ASP T 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE T 57 " --> pdb=" O ASN T 53 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE T 70 " --> pdb=" O ALA T 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 91 removed outlier: 3.638A pdb=" N PHE T 78 " --> pdb=" O ASN T 74 " (cutoff:3.500A) Proline residue: T 87 - end of helix removed outlier: 3.616A pdb=" N SER T 91 " --> pdb=" O PRO T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 116 removed outlier: 3.914A pdb=" N SER T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 130 removed outlier: 3.607A pdb=" N PHE T 122 " --> pdb=" O ASN T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 142 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.560A pdb=" N LEU T 163 " --> pdb=" O LYS T 159 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU T 164 " --> pdb=" O ALA T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 171 removed outlier: 3.866A pdb=" N ILE T 171 " --> pdb=" O SER T 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 168 through 171' Processing helix chain 'T' and resid 174 through 197 removed outlier: 4.662A pdb=" N ILE T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER T 183 " --> pdb=" O ASP T 179 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA T 184 " --> pdb=" O ILE T 180 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU T 195 " --> pdb=" O LYS T 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 209 Processing helix chain 'T' and resid 213 through 224 removed outlier: 3.608A pdb=" N THR T 217 " --> pdb=" O ASN T 213 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU T 218 " --> pdb=" O GLU T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 247 removed outlier: 3.608A pdb=" N LYS T 240 " --> pdb=" O ASN T 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 271 removed outlier: 3.847A pdb=" N ILE T 270 " --> pdb=" O TYR T 266 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU T 271 " --> pdb=" O ALA T 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 131 removed outlier: 3.635A pdb=" N ILE X 126 " --> pdb=" O TYR X 122 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN X 131 " --> pdb=" O GLY X 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 31 removed outlier: 3.507A pdb=" N GLU Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER Y 28 " --> pdb=" O ILE Y 24 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU Y 29 " --> pdb=" O ASN Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 42 Processing helix chain 'Y' and resid 71 through 88 removed outlier: 3.890A pdb=" N LYS Y 85 " --> pdb=" O LEU Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 removed outlier: 3.541A pdb=" N GLU Z 14 " --> pdb=" O GLN Z 10 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 33 Processing helix chain 'Z' and resid 37 through 55 removed outlier: 3.863A pdb=" N ALA Z 43 " --> pdb=" O SER Z 39 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS Z 46 " --> pdb=" O ASP Z 42 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 68 through 78 removed outlier: 3.651A pdb=" N GLU Z 73 " --> pdb=" O ASN Z 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS Z 76 " --> pdb=" O LYS Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 91 removed outlier: 3.548A pdb=" N LEU Z 89 " --> pdb=" O VAL Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 104 removed outlier: 4.270A pdb=" N THR Z 95 " --> pdb=" O PHE Z 91 " (cutoff:3.500A) Proline residue: Z 97 - end of helix removed outlier: 3.865A pdb=" N ILE Z 102 " --> pdb=" O ASP Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 126 removed outlier: 3.640A pdb=" N ALA Z 116 " --> pdb=" O LYS Z 112 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP Z 117 " --> pdb=" O SER Z 113 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL Z 118 " --> pdb=" O SER Z 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 141 removed outlier: 3.769A pdb=" N LEU Z 139 " --> pdb=" O LEU Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 170 removed outlier: 5.610A pdb=" N ILE Z 154 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG Z 155 " --> pdb=" O HIS Z 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS Z 156 " --> pdb=" O GLU Z 152 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU Z 160 " --> pdb=" O HIS Z 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN Z 168 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL Z 169 " --> pdb=" O TYR Z 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 204 removed outlier: 3.560A pdb=" N ASP Z 199 " --> pdb=" O PHE Z 195 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG Z 202 " --> pdb=" O GLU Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 216 removed outlier: 3.950A pdb=" N LEU Z 212 " --> pdb=" O VAL Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 232 removed outlier: 3.962A pdb=" N VAL Z 221 " --> pdb=" O GLU Z 217 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU Z 226 " --> pdb=" O ASP Z 222 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE Z 227 " --> pdb=" O LEU Z 223 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE Z 230 " --> pdb=" O GLU Z 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 252 removed outlier: 3.608A pdb=" N THR Z 241 " --> pdb=" O VAL Z 237 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS Z 246 " --> pdb=" O PHE Z 242 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS Z 252 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 256 removed outlier: 3.588A pdb=" N LEU Z 256 " --> pdb=" O VAL Z 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 253 through 256' Processing helix chain 'Z' and resid 257 through 275 removed outlier: 3.516A pdb=" N ALA Z 263 " --> pdb=" O PRO Z 259 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR Z 267 " --> pdb=" O ALA Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 278 through 289 removed outlier: 3.816A pdb=" N ALA Z 283 " --> pdb=" O THR Z 279 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Z 284 " --> pdb=" O ASP Z 280 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG Z 287 " --> pdb=" O ALA Z 283 " (cutoff:3.500A) Processing helix chain 'Z' and resid 290 through 303 removed outlier: 3.685A pdb=" N ILE Z 294 " --> pdb=" O GLU Z 290 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER Z 296 " --> pdb=" O ASP Z 292 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL Z 297 " --> pdb=" O MET Z 293 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR Z 301 " --> pdb=" O VAL Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 310 through 321 Processing helix chain 'Z' and resid 325 through 332 removed outlier: 3.560A pdb=" N ILE Z 329 " --> pdb=" O GLY Z 325 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE Z 330 " --> pdb=" O VAL Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 339 Processing helix chain 'Z' and resid 342 through 350 removed outlier: 3.740A pdb=" N ASN Z 347 " --> pdb=" O ALA Z 343 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 366 removed outlier: 3.508A pdb=" N GLU Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP Z 356 " --> pdb=" O LYS Z 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Z 359 " --> pdb=" O GLU Z 355 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER Z 360 " --> pdb=" O ASP Z 356 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN Z 364 " --> pdb=" O SER Z 360 " (cutoff:3.500A) Processing helix chain 'Z' and resid 376 through 391 removed outlier: 3.944A pdb=" N LEU Z 381 " --> pdb=" O ALA Z 377 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE Z 385 " --> pdb=" O LEU Z 381 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY Z 388 " --> pdb=" O SER Z 384 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN Z 391 " --> pdb=" O ASN Z 387 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 403 removed outlier: 3.732A pdb=" N VAL Z 401 " --> pdb=" O ASP Z 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 403 through 409 removed outlier: 4.247A pdb=" N VAL Z 407 " --> pdb=" O ASN Z 403 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS Z 409 " --> pdb=" O ASN Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 424 removed outlier: 4.011A pdb=" N THR Z 416 " --> pdb=" O GLY Z 412 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER Z 424 " --> pdb=" O ALA Z 420 " (cutoff:3.500A) Processing helix chain 'Z' and resid 432 through 441 removed outlier: 4.118A pdb=" N LEU Z 436 " --> pdb=" O GLY Z 432 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS Z 438 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR Z 439 " --> pdb=" O GLN Z 435 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR Z 441 " --> pdb=" O ASP Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 444 through 459 removed outlier: 4.150A pdb=" N LYS Z 448 " --> pdb=" O GLU Z 444 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Z 452 " --> pdb=" O LYS Z 448 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU Z 453 " --> pdb=" O ALA Z 449 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 462 No H-bonds generated for 'chain 'Z' and resid 460 through 462' Processing helix chain 'Z' and resid 469 through 480 removed outlier: 3.852A pdb=" N LEU Z 473 " --> pdb=" O PRO Z 469 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR Z 477 " --> pdb=" O LEU Z 473 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 498 Processing helix chain 'Z' and resid 502 through 509 Processing helix chain 'Z' and resid 520 through 522 No H-bonds generated for 'chain 'Z' and resid 520 through 522' Processing helix chain 'Z' and resid 523 through 535 removed outlier: 4.313A pdb=" N SER Z 527 " --> pdb=" O ALA Z 523 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU Z 530 " --> pdb=" O ALA Z 526 " (cutoff:3.500A) Processing helix chain 'Z' and resid 542 through 556 removed outlier: 3.648A pdb=" N ILE Z 546 " --> pdb=" O ILE Z 542 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE Z 550 " --> pdb=" O ILE Z 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 559 through 574 removed outlier: 3.608A pdb=" N VAL Z 563 " --> pdb=" O LYS Z 559 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Z 568 " --> pdb=" O ARG Z 564 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY Z 571 " --> pdb=" O ALA Z 567 " (cutoff:3.500A) Processing helix chain 'Z' and resid 580 through 591 removed outlier: 3.770A pdb=" N VAL Z 584 " --> pdb=" O GLN Z 580 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Z 587 " --> pdb=" O ASP Z 583 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE Z 591 " --> pdb=" O THR Z 587 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 609 removed outlier: 3.691A pdb=" N ALA Z 598 " --> pdb=" O PRO Z 594 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE Z 599 " --> pdb=" O MET Z 595 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL Z 601 " --> pdb=" O SER Z 597 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU Z 602 " --> pdb=" O ALA Z 598 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER Z 605 " --> pdb=" O VAL Z 601 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS Z 606 " --> pdb=" O LEU Z 602 " (cutoff:3.500A) Processing helix chain 'Z' and resid 613 through 635 removed outlier: 4.153A pdb=" N ILE Z 617 " --> pdb=" O ASP Z 613 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU Z 620 " --> pdb=" O LEU Z 616 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG Z 623 " --> pdb=" O ASP Z 619 " (cutoff:3.500A) Proline residue: Z 626 - end of helix removed outlier: 3.914A pdb=" N LYS Z 630 " --> pdb=" O PRO Z 626 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU Z 633 " --> pdb=" O VAL Z 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA Z 635 " --> pdb=" O GLY Z 631 " (cutoff:3.500A) Processing helix chain 'Z' and resid 701 through 727 removed outlier: 3.689A pdb=" N ASP Z 712 " --> pdb=" O GLY Z 708 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS Z 713 " --> pdb=" O LYS Z 709 " (cutoff:3.500A) Processing helix chain 'Z' and resid 730 through 750 removed outlier: 4.158A pdb=" N ASP Z 734 " --> pdb=" O ALA Z 730 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Z 736 " --> pdb=" O ILE Z 732 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA Z 737 " --> pdb=" O VAL Z 733 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU Z 748 " --> pdb=" O ALA Z 744 " (cutoff:3.500A) Processing helix chain 'Z' and resid 750 through 769 removed outlier: 3.718A pdb=" N LYS Z 754 " --> pdb=" O GLU Z 750 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU Z 755 " --> pdb=" O ASP Z 751 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET Z 756 " --> pdb=" O ILE Z 752 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG Z 759 " --> pdb=" O GLU Z 755 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY Z 762 " --> pdb=" O LEU Z 758 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS Z 763 " --> pdb=" O ARG Z 759 " (cutoff:3.500A) Processing helix chain 'Z' and resid 774 through 787 removed outlier: 4.249A pdb=" N LEU Z 778 " --> pdb=" O ARG Z 774 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE Z 782 " --> pdb=" O LEU Z 778 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL Z 783 " --> pdb=" O ALA Z 779 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER Z 786 " --> pdb=" O ILE Z 782 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP Z 787 " --> pdb=" O VAL Z 783 " (cutoff:3.500A) Processing helix chain 'Z' and resid 790 through 801 removed outlier: 4.363A pdb=" N ASP Z 794 " --> pdb=" O MET Z 790 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR Z 795 " --> pdb=" O LYS Z 791 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG Z 798 " --> pdb=" O ASP Z 794 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE Z 799 " --> pdb=" O THR Z 795 " (cutoff:3.500A) Processing helix chain 'Z' and resid 807 through 822 removed outlier: 3.527A pdb=" N SER Z 811 " --> pdb=" O VAL Z 807 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE Z 813 " --> pdb=" O MET Z 809 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS Z 818 " --> pdb=" O ALA Z 814 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY Z 819 " --> pdb=" O MET Z 815 " (cutoff:3.500A) Processing helix chain 'Z' and resid 825 through 839 removed outlier: 3.969A pdb=" N LEU Z 831 " --> pdb=" O LEU Z 827 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG Z 832 " --> pdb=" O ALA Z 828 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR Z 837 " --> pdb=" O GLN Z 833 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER Z 839 " --> pdb=" O ALA Z 835 " (cutoff:3.500A) Processing helix chain 'Z' and resid 863 through 869 removed outlier: 3.691A pdb=" N ASP Z 869 " --> pdb=" O ASP Z 865 " (cutoff:3.500A) Processing helix chain 'Z' and resid 875 through 882 removed outlier: 3.766A pdb=" N SER Z 880 " --> pdb=" O VAL Z 876 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Z 881 " --> pdb=" O THR Z 877 " (cutoff:3.500A) Processing helix chain 'Z' and resid 947 through 950 Processing helix chain 'N' and resid 6 through 13 removed outlier: 3.560A pdb=" N LEU N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 29 removed outlier: 3.516A pdb=" N GLU N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 36 Processing helix chain 'N' and resid 37 through 52 removed outlier: 4.089A pdb=" N ASN N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU N 42 " --> pdb=" O GLU N 38 " (cutoff:3.500A) Proline residue: N 44 - end of helix Processing helix chain 'N' and resid 57 through 73 Processing helix chain 'N' and resid 74 through 86 removed outlier: 3.629A pdb=" N ALA N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 94 removed outlier: 4.069A pdb=" N ASP N 92 " --> pdb=" O ARG N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 118 removed outlier: 3.666A pdb=" N GLN N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 112 " --> pdb=" O MET N 108 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR N 118 " --> pdb=" O SER N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 147 removed outlier: 3.577A pdb=" N GLU N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE N 141 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS N 144 " --> pdb=" O MET N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 160 removed outlier: 4.041A pdb=" N ALA N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU N 159 " --> pdb=" O GLY N 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 173 removed outlier: 3.764A pdb=" N ILE N 166 " --> pdb=" O ARG N 162 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS N 173 " --> pdb=" O ALA N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 196 removed outlier: 3.548A pdb=" N LYS N 184 " --> pdb=" O SER N 180 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU N 189 " --> pdb=" O ILE N 185 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR N 196 " --> pdb=" O LEU N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 removed outlier: 3.689A pdb=" N LEU N 214 " --> pdb=" O SER N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 233 removed outlier: 3.693A pdb=" N LYS N 227 " --> pdb=" O LEU N 223 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 245 removed outlier: 3.954A pdb=" N ALA N 238 " --> pdb=" O ASP N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 265 removed outlier: 3.794A pdb=" N SER N 263 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER N 264 " --> pdb=" O ASP N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 281 removed outlier: 3.910A pdb=" N THR N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA N 279 " --> pdb=" O THR N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 291 removed outlier: 3.982A pdb=" N LEU N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 306 Processing helix chain 'N' and resid 311 through 321 Processing helix chain 'N' and resid 325 through 340 removed outlier: 3.814A pdb=" N VAL N 332 " --> pdb=" O PHE N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 352 Processing helix chain 'N' and resid 352 through 358 removed outlier: 3.633A pdb=" N LEU N 356 " --> pdb=" O ASN N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 370 removed outlier: 3.504A pdb=" N LYS N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE N 365 " --> pdb=" O ASN N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 375 Processing helix chain 'N' and resid 381 through 387 removed outlier: 4.053A pdb=" N MET N 386 " --> pdb=" O GLY N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 390 No H-bonds generated for 'chain 'N' and resid 388 through 390' Processing helix chain 'N' and resid 397 through 412 removed outlier: 3.784A pdb=" N LYS N 401 " --> pdb=" O SER N 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU N 405 " --> pdb=" O LYS N 401 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR N 406 " --> pdb=" O GLY N 402 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 431 removed outlier: 3.661A pdb=" N ASP N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 422 " --> pdb=" O ASP N 418 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN N 425 " --> pdb=" O ASP N 421 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE N 426 " --> pdb=" O TYR N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 454 removed outlier: 3.709A pdb=" N ASP N 440 " --> pdb=" O ASP N 436 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 473 removed outlier: 3.515A pdb=" N VAL N 469 " --> pdb=" O ALA N 465 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 470 " --> pdb=" O LEU N 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 490 removed outlier: 4.002A pdb=" N GLU N 479 " --> pdb=" O ALA N 475 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA N 480 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 483 " --> pdb=" O GLU N 479 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY N 486 " --> pdb=" O ALA N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 508 removed outlier: 3.514A pdb=" N HIS N 499 " --> pdb=" O PRO N 495 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN N 506 " --> pdb=" O PHE N 502 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU N 507 " --> pdb=" O THR N 503 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 525 removed outlier: 3.650A pdb=" N VAL N 519 " --> pdb=" O ARG N 515 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA N 522 " --> pdb=" O ALA N 518 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN N 525 " --> pdb=" O LEU N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 531 Processing helix chain 'N' and resid 532 through 542 removed outlier: 3.612A pdb=" N THR N 537 " --> pdb=" O ASP N 533 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS N 538 " --> pdb=" O ASP N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 544 through 559 removed outlier: 4.009A pdb=" N PHE N 553 " --> pdb=" O TYR N 549 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE N 555 " --> pdb=" O GLY N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 578 removed outlier: 3.616A pdb=" N VAL N 568 " --> pdb=" O ASN N 564 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU N 571 " --> pdb=" O ALA N 567 " (cutoff:3.500A) Processing helix chain 'N' and resid 580 through 595 removed outlier: 3.779A pdb=" N VAL N 588 " --> pdb=" O ARG N 584 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU N 591 " --> pdb=" O ALA N 587 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY N 592 " --> pdb=" O VAL N 588 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE N 593 " --> pdb=" O ILE N 589 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL N 594 " --> pdb=" O ALA N 590 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU N 595 " --> pdb=" O LEU N 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 601 through 610 removed outlier: 3.566A pdb=" N GLN N 607 " --> pdb=" O PRO N 603 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU N 608 " --> pdb=" O ARG N 604 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU N 609 " --> pdb=" O ILE N 605 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 629 removed outlier: 3.773A pdb=" N ALA N 622 " --> pdb=" O ARG N 618 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE N 623 " --> pdb=" O CYS N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 646 removed outlier: 3.672A pdb=" N ILE N 638 " --> pdb=" O LEU N 634 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP N 639 " --> pdb=" O GLN N 635 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL N 640 " --> pdb=" O SER N 636 " (cutoff:3.500A) Proline residue: N 643 - end of helix removed outlier: 4.091A pdb=" N LYS N 646 " --> pdb=" O ASP N 642 " (cutoff:3.500A) Processing helix chain 'N' and resid 649 through 665 removed outlier: 3.569A pdb=" N MET N 662 " --> pdb=" O ILE N 658 " (cutoff:3.500A) Processing helix chain 'N' and resid 672 through 688 removed outlier: 4.111A pdb=" N ALA N 676 " --> pdb=" O ASN N 672 " (cutoff:3.500A) Processing helix chain 'N' and resid 692 through 707 removed outlier: 3.734A pdb=" N GLY N 704 " --> pdb=" O CYS N 700 " (cutoff:3.500A) Processing helix chain 'N' and resid 726 through 737 removed outlier: 3.872A pdb=" N MET N 735 " --> pdb=" O VAL N 731 " (cutoff:3.500A) Processing helix chain 'N' and resid 742 through 751 removed outlier: 3.830A pdb=" N LEU N 745 " --> pdb=" O TRP N 742 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA N 746 " --> pdb=" O PHE N 743 " (cutoff:3.500A) Processing helix chain 'N' and resid 789 through 819 removed outlier: 3.625A pdb=" N GLY N 793 " --> pdb=" O GLU N 789 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU N 797 " --> pdb=" O GLY N 793 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU N 804 " --> pdb=" O ALA N 800 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER N 805 " --> pdb=" O THR N 801 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS N 811 " --> pdb=" O THR N 807 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG N 813 " --> pdb=" O ARG N 809 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA N 814 " --> pdb=" O ALA N 810 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS N 818 " --> pdb=" O ALA N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 820 through 822 No H-bonds generated for 'chain 'N' and resid 820 through 822' Processing helix chain 'N' and resid 875 through 880 removed outlier: 3.968A pdb=" N ARG N 880 " --> pdb=" O PRO N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 925 Processing helix chain 'S' and resid 19 through 42 removed outlier: 3.825A pdb=" N SER S 42 " --> pdb=" O LEU S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 65 Processing helix chain 'S' and resid 71 through 79 Processing helix chain 'S' and resid 84 through 96 Processing helix chain 'S' and resid 119 through 126 removed outlier: 3.590A pdb=" N GLU S 124 " --> pdb=" O SER S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 150 removed outlier: 4.496A pdb=" N ILE S 134 " --> pdb=" O VAL S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 170 removed outlier: 3.509A pdb=" N VAL S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) Proline residue: S 165 - end of helix removed outlier: 3.633A pdb=" N TYR S 170 " --> pdb=" O ASN S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 198 removed outlier: 3.528A pdb=" N ILE S 179 " --> pdb=" O SER S 175 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA S 181 " --> pdb=" O ASN S 177 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS S 182 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU S 183 " --> pdb=" O ILE S 179 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR S 186 " --> pdb=" O LYS S 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS S 191 " --> pdb=" O ILE S 187 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 225 removed outlier: 3.960A pdb=" N ASP S 204 " --> pdb=" O GLU S 200 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN S 205 " --> pdb=" O ILE S 201 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE S 208 " --> pdb=" O ASP S 204 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 209 " --> pdb=" O ASN S 205 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET S 214 " --> pdb=" O LEU S 210 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE S 220 " --> pdb=" O LYS S 216 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU S 223 " --> pdb=" O LYS S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 244 removed outlier: 3.595A pdb=" N ASN S 244 " --> pdb=" O ASP S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 246 through 255 removed outlier: 3.550A pdb=" N ASP S 252 " --> pdb=" O ASP S 248 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 255 " --> pdb=" O SER S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 283 removed outlier: 3.694A pdb=" N GLU S 269 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN S 283 " --> pdb=" O ILE S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 300 removed outlier: 4.144A pdb=" N GLU S 291 " --> pdb=" O SER S 287 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR S 292 " --> pdb=" O THR S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 325 removed outlier: 3.786A pdb=" N GLN S 312 " --> pdb=" O GLY S 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS S 319 " --> pdb=" O LYS S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 329 through 335 removed outlier: 4.178A pdb=" N PHE S 333 " --> pdb=" O GLU S 329 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN S 335 " --> pdb=" O SER S 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 355 removed outlier: 3.511A pdb=" N LEU S 348 " --> pdb=" O PRO S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 367 removed outlier: 3.669A pdb=" N PHE S 360 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR S 361 " --> pdb=" O LEU S 357 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER S 362 " --> pdb=" O LYS S 358 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 374 removed outlier: 3.915A pdb=" N ASP S 374 " --> pdb=" O LEU S 370 " (cutoff:3.500A) Processing helix chain 'S' and resid 376 through 399 removed outlier: 3.748A pdb=" N ARG S 382 " --> pdb=" O GLN S 378 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU S 383 " --> pdb=" O LEU S 379 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG S 384 " --> pdb=" O CYS S 380 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER S 385 " --> pdb=" O VAL S 381 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN S 386 " --> pdb=" O ARG S 382 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE S 388 " --> pdb=" O ARG S 384 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE S 395 " --> pdb=" O GLY S 391 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 Processing helix chain 'S' and resid 415 through 427 removed outlier: 3.668A pdb=" N VAL S 423 " --> pdb=" O VAL S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 489 removed outlier: 4.168A pdb=" N GLN S 459 " --> pdb=" O GLU S 455 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU S 463 " --> pdb=" O GLN S 459 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG S 464 " --> pdb=" O VAL S 460 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP S 473 " --> pdb=" O ASN S 469 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG S 480 " --> pdb=" O LEU S 476 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 481 " --> pdb=" O VAL S 477 " (cutoff:3.500A) Proline residue: S 482 - end of helix removed outlier: 3.707A pdb=" N LYS S 485 " --> pdb=" O TYR S 481 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS S 486 " --> pdb=" O PRO S 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 20 through 31 removed outlier: 3.951A pdb=" N GLN P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 43 removed outlier: 3.701A pdb=" N ALA P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 68 removed outlier: 3.528A pdb=" N ALA P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 86 removed outlier: 3.987A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN P 76 " --> pdb=" O TRP P 72 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 108 removed outlier: 3.983A pdb=" N TYR P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN P 98 " --> pdb=" O GLN P 94 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU P 104 " --> pdb=" O VAL P 100 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 105 " --> pdb=" O MET P 101 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER P 106 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS P 108 " --> pdb=" O LEU P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 Processing helix chain 'P' and resid 131 through 150 removed outlier: 3.781A pdb=" N GLU P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU P 150 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.891A pdb=" N GLN P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.530A pdb=" N SER P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 201 removed outlier: 3.617A pdb=" N ALA P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL P 198 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG P 201 " --> pdb=" O THR P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 209 removed outlier: 3.827A pdb=" N PHE P 208 " --> pdb=" O LEU P 204 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 204 through 209' Processing helix chain 'P' and resid 210 through 212 No H-bonds generated for 'chain 'P' and resid 210 through 212' Processing helix chain 'P' and resid 213 through 231 removed outlier: 3.652A pdb=" N LEU P 218 " --> pdb=" O GLU P 214 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS P 231 " --> pdb=" O ILE P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 246 removed outlier: 3.612A pdb=" N GLU P 243 " --> pdb=" O GLN P 239 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 253 removed outlier: 3.533A pdb=" N ASP P 253 " --> pdb=" O ALA P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 271 Proline residue: P 259 - end of helix removed outlier: 3.633A pdb=" N SER P 262 " --> pdb=" O LYS P 258 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU P 270 " --> pdb=" O TYR P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 287 removed outlier: 3.558A pdb=" N ASP P 279 " --> pdb=" O ASN P 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS P 283 " --> pdb=" O ASP P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 293 removed outlier: 3.856A pdb=" N LYS P 291 " --> pdb=" O ASP P 287 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 292 " --> pdb=" O ASN P 288 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU P 293 " --> pdb=" O ASN P 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 287 through 293' Processing helix chain 'P' and resid 294 through 305 removed outlier: 3.799A pdb=" N LEU P 299 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE P 303 " --> pdb=" O LEU P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 323 removed outlier: 3.672A pdb=" N VAL P 314 " --> pdb=" O ARG P 310 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS P 316 " --> pdb=" O PRO P 312 " (cutoff:3.500A) Proline residue: P 320 - end of helix Processing helix chain 'P' and resid 334 through 339 removed outlier: 3.515A pdb=" N GLU P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 356 removed outlier: 3.569A pdb=" N ARG P 351 " --> pdb=" O GLU P 347 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU P 355 " --> pdb=" O ARG P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 370 Processing helix chain 'P' and resid 372 through 387 removed outlier: 3.509A pdb=" N SER P 381 " --> pdb=" O GLU P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 407 through 440 removed outlier: 3.715A pdb=" N LEU P 411 " --> pdb=" O ASN P 407 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP P 415 " --> pdb=" O LEU P 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP P 420 " --> pdb=" O SER P 416 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU P 427 " --> pdb=" O LEU P 423 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR P 434 " --> pdb=" O GLY P 430 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS P 435 " --> pdb=" O HIS P 431 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU P 436 " --> pdb=" O LEU P 432 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU P 437 " --> pdb=" O ILE P 433 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE P 438 " --> pdb=" O THR P 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 16 Processing helix chain 'Q' and resid 19 through 39 removed outlier: 3.885A pdb=" N ALA Q 23 " --> pdb=" O GLN Q 19 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN Q 25 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER Q 29 " --> pdb=" O GLN Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 65 removed outlier: 3.856A pdb=" N TYR Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 89 removed outlier: 3.652A pdb=" N GLU Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Proline residue: Q 79 - end of helix removed outlier: 3.556A pdb=" N THR Q 82 " --> pdb=" O ILE Q 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU Q 83 " --> pdb=" O PRO Q 79 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA Q 89 " --> pdb=" O MET Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 107 Processing helix chain 'Q' and resid 109 through 127 removed outlier: 4.166A pdb=" N ASP Q 113 " --> pdb=" O ASP Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 149 removed outlier: 3.647A pdb=" N SER Q 136 " --> pdb=" O PHE Q 132 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS Q 149 " --> pdb=" O HIS Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 165 removed outlier: 3.611A pdb=" N ASP Q 160 " --> pdb=" O ALA Q 156 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU Q 162 " --> pdb=" O ILE Q 158 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU Q 164 " --> pdb=" O ASP Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 173 No H-bonds generated for 'chain 'Q' and resid 171 through 173' Processing helix chain 'Q' and resid 174 through 188 removed outlier: 3.721A pdb=" N LYS Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 204 Processing helix chain 'Q' and resid 211 through 229 removed outlier: 3.582A pdb=" N LEU Q 225 " --> pdb=" O MET Q 221 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU Q 228 " --> pdb=" O ILE Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 249 removed outlier: 3.862A pdb=" N ALA Q 235 " --> pdb=" O ASP Q 231 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE Q 236 " --> pdb=" O TYR Q 232 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER Q 237 " --> pdb=" O LYS Q 233 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Q 248 " --> pdb=" O GLU Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 273 removed outlier: 3.615A pdb=" N SER Q 268 " --> pdb=" O TYR Q 264 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS Q 269 " --> pdb=" O MET Q 265 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE Q 270 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 282 removed outlier: 3.716A pdb=" N LYS Q 279 " --> pdb=" O ILE Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 309 removed outlier: 3.524A pdb=" N ASP Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA Q 301 " --> pdb=" O ASP Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 321 removed outlier: 3.757A pdb=" N PHE Q 314 " --> pdb=" O SER Q 310 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN Q 320 " --> pdb=" O THR Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 328 removed outlier: 3.558A pdb=" N ASP Q 328 " --> pdb=" O GLU Q 324 " (cutoff:3.500A) Processing helix chain 'Q' and resid 328 through 352 removed outlier: 3.562A pdb=" N HIS Q 334 " --> pdb=" O LEU Q 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU Q 344 " --> pdb=" O ASP Q 340 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER Q 345 " --> pdb=" O THR Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 367 removed outlier: 3.680A pdb=" N ILE Q 365 " --> pdb=" O HIS Q 361 " (cutoff:3.500A) Processing helix chain 'Q' and resid 369 through 384 removed outlier: 3.755A pdb=" N LEU Q 382 " --> pdb=" O SER Q 378 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 430 removed outlier: 3.535A pdb=" N ASP Q 410 " --> pdb=" O ASP Q 406 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU Q 414 " --> pdb=" O ASP Q 410 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS Q 421 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 431 through 433 No H-bonds generated for 'chain 'Q' and resid 431 through 433' Processing helix chain 'R' and resid 21 through 35 removed outlier: 5.193A pdb=" N SER R 27 " --> pdb=" O ASN R 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 58 removed outlier: 3.786A pdb=" N GLU R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 70 removed outlier: 3.515A pdb=" N LYS R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR R 65 " --> pdb=" O PRO R 61 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU R 68 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 123 Processing helix chain 'R' and resid 128 through 145 removed outlier: 3.664A pdb=" N ILE R 144 " --> pdb=" O TYR R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.971A pdb=" N ALA R 150 " --> pdb=" O ASP R 146 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS R 152 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 182 removed outlier: 4.035A pdb=" N THR R 173 " --> pdb=" O ASP R 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE R 174 " --> pdb=" O VAL R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 202 removed outlier: 3.921A pdb=" N LYS R 190 " --> pdb=" O TYR R 186 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU R 199 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 221 removed outlier: 3.527A pdb=" N ARG R 207 " --> pdb=" O ASP R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 237 removed outlier: 3.855A pdb=" N LYS R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP R 233 " --> pdb=" O LYS R 229 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA R 236 " --> pdb=" O VAL R 232 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR R 237 " --> pdb=" O ASP R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.710A pdb=" N PHE R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 270 Processing helix chain 'R' and resid 273 through 280 removed outlier: 3.645A pdb=" N LEU R 277 " --> pdb=" O SER R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 Processing helix chain 'R' and resid 303 through 315 removed outlier: 3.701A pdb=" N TYR R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 324 removed outlier: 4.071A pdb=" N ARG R 324 " --> pdb=" O TYR R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 345 removed outlier: 3.560A pdb=" N TYR R 338 " --> pdb=" O ARG R 334 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER R 344 " --> pdb=" O GLN R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 358 Processing helix chain 'R' and resid 360 through 372 removed outlier: 3.505A pdb=" N ASN R 366 " --> pdb=" O ALA R 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP R 367 " --> pdb=" O PHE R 363 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS R 370 " --> pdb=" O ASN R 366 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 424 removed outlier: 3.832A pdb=" N GLN R 399 " --> pdb=" O ASN R 395 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU R 402 " --> pdb=" O ALA R 398 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY R 409 " --> pdb=" O LYS R 405 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 410 " --> pdb=" O GLN R 406 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS R 416 " --> pdb=" O THR R 412 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 421 " --> pdb=" O TYR R 417 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 25 removed outlier: 3.697A pdb=" N LEU U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 19 " --> pdb=" O LEU U 15 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 84 removed outlier: 4.007A pdb=" N ILE U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU U 74 " --> pdb=" O HIS U 70 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET U 79 " --> pdb=" O ASN U 75 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS U 80 " --> pdb=" O MET U 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS U 82 " --> pdb=" O GLU U 78 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE U 83 " --> pdb=" O MET U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 112 removed outlier: 4.272A pdb=" N ILE U 106 " --> pdb=" O SER U 102 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU U 109 " --> pdb=" O LYS U 105 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 Processing helix chain 'U' and resid 185 through 215 removed outlier: 3.504A pdb=" N VAL U 207 " --> pdb=" O LYS U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 235 removed outlier: 3.904A pdb=" N LEU U 226 " --> pdb=" O ASN U 222 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS U 228 " --> pdb=" O THR U 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE U 233 " --> pdb=" O LEU U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 242 through 298 removed outlier: 3.588A pdb=" N ASP U 253 " --> pdb=" O VAL U 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE U 285 " --> pdb=" O LEU U 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU U 291 " --> pdb=" O ALA U 287 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE U 292 " --> pdb=" O PHE U 288 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE U 296 " --> pdb=" O ILE U 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 18 removed outlier: 3.586A pdb=" N THR O 13 " --> pdb=" O THR O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.734A pdb=" N PHE O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 52 removed outlier: 3.516A pdb=" N LEU O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU O 45 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP O 51 " --> pdb=" O LYS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 74 through 89 removed outlier: 3.616A pdb=" N TYR O 81 " --> pdb=" O SER O 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU O 82 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA O 84 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER O 85 " --> pdb=" O TYR O 81 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 118 removed outlier: 3.913A pdb=" N SER O 111 " --> pdb=" O GLN O 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG O 115 " --> pdb=" O SER O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 140 removed outlier: 4.176A pdb=" N ILE O 126 " --> pdb=" O HIS O 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 160 removed outlier: 3.520A pdb=" N ALA O 146 " --> pdb=" O ASP O 142 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP O 148 " --> pdb=" O VAL O 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU O 149 " --> pdb=" O LYS O 145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS O 160 " --> pdb=" O THR O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 183 removed outlier: 3.944A pdb=" N THR O 168 " --> pdb=" O PRO O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 198 removed outlier: 3.563A pdb=" N PHE O 188 " --> pdb=" O ASP O 184 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR O 190 " --> pdb=" O ASN O 186 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU O 194 " --> pdb=" O TYR O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 224 removed outlier: 3.564A pdb=" N LEU O 223 " --> pdb=" O ILE O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 235 Processing helix chain 'O' and resid 236 through 241 Processing helix chain 'O' and resid 245 through 248 Processing helix chain 'O' and resid 249 through 261 removed outlier: 3.635A pdb=" N VAL O 260 " --> pdb=" O ASN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 277 removed outlier: 3.645A pdb=" N PHE O 266 " --> pdb=" O ASP O 262 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS O 276 " --> pdb=" O VAL O 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 283 removed outlier: 3.786A pdb=" N ALA O 281 " --> pdb=" O ILE O 277 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN O 282 " --> pdb=" O PRO O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 303 removed outlier: 3.661A pdb=" N ILE O 291 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS O 292 " --> pdb=" O ARG O 288 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS O 303 " --> pdb=" O THR O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 318 Processing helix chain 'O' and resid 320 through 334 removed outlier: 3.560A pdb=" N VAL O 324 " --> pdb=" O PRO O 320 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU O 325 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS O 326 " --> pdb=" O ASP O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 387 removed outlier: 3.815A pdb=" N THR O 364 " --> pdb=" O GLY O 360 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU O 372 " --> pdb=" O ASP O 368 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL O 377 " --> pdb=" O TRP O 373 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 386 " --> pdb=" O LYS O 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 61 through 66 removed outlier: 6.711A pdb=" N VAL W 61 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER W 53 " --> pdb=" O VAL W 61 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE W 65 " --> pdb=" O VAL W 49 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL W 49 " --> pdb=" O PHE W 65 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU W 4 " --> pdb=" O THR W 48 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY W 50 " --> pdb=" O GLU W 4 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR W 6 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE W 52 " --> pdb=" O THR W 6 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU W 8 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA W 5 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL W 111 " --> pdb=" O ALA W 5 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL W 7 " --> pdb=" O VAL W 111 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE W 113 " --> pdb=" O VAL W 7 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL W 9 " --> pdb=" O PHE W 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN W 108 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASP W 140 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE W 110 " --> pdb=" O ASP W 140 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE W 142 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA W 112 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL W 139 " --> pdb=" O HIS W 170 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU W 172 " --> pdb=" O VAL W 139 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE W 141 " --> pdb=" O LEU W 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 153 through 156 removed outlier: 3.533A pdb=" N ASP V 154 " --> pdb=" O VAL V 140 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL V 137 " --> pdb=" O MET V 103 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL V 105 " --> pdb=" O VAL V 137 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL V 139 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TRP V 107 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL V 141 " --> pdb=" O TRP V 107 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS V 109 " --> pdb=" O VAL V 141 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL V 104 " --> pdb=" O GLY V 55 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY V 55 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY V 106 " --> pdb=" O MET V 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY V 51 " --> pdb=" O TYR V 108 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET V 50 " --> pdb=" O ALA V 70 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA V 70 " --> pdb=" O MET V 50 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU V 52 " --> pdb=" O VAL V 68 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL V 68 " --> pdb=" O LEU V 52 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU V 54 " --> pdb=" O VAL V 66 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP V 67 " --> pdb=" O SER V 30 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS V 204 " --> pdb=" O ILE V 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 8 through 10 removed outlier: 3.642A pdb=" N LEU X 66 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 13 through 15 removed outlier: 4.618A pdb=" N PHE X 98 " --> pdb=" O CYS X 15 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR X 97 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 76 " --> pdb=" O ALA X 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 927 through 929 removed outlier: 3.557A pdb=" N ALA Z 906 " --> pdb=" O VAL Z 929 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN Z 905 " --> pdb=" O THR Z 946 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR Z 946 " --> pdb=" O ASN Z 905 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 952 through 956 removed outlier: 7.018A pdb=" N GLU Z 966 " --> pdb=" O VAL Z 955 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 713 through 715 Processing sheet with id=AA8, first strand: chain 'N' and resid 758 through 762 removed outlier: 3.517A pdb=" N ILE N 759 " --> pdb=" O GLY N 901 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 768 through 769 Processing sheet with id=AB1, first strand: chain 'N' and resid 866 through 869 removed outlier: 3.583A pdb=" N TYR N 866 " --> pdb=" O CYS N 775 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 401 through 403 removed outlier: 3.505A pdb=" N ILE S 402 " --> pdb=" O ILE S 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 399 through 401 removed outlier: 6.841A pdb=" N LYS O 338 " --> pdb=" O SER O 351 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 357 through 358 Processing sheet with id=AB5, first strand: chain 'R' and resid 347 through 349 Processing sheet with id=AB6, first strand: chain 'U' and resid 7 through 10 removed outlier: 5.060A pdb=" N VAL U 48 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP U 40 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY U 91 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY U 39 " --> pdb=" O LEU U 89 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU U 89 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA U 136 " --> pdb=" O LEU U 157 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL U 138 " --> pdb=" O LEU U 155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU U 155 " --> pdb=" O VAL U 138 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS U 144 " --> pdb=" O SER U 149 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER U 149 " --> pdb=" O LYS U 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 56 through 58 removed outlier: 3.505A pdb=" N GLU U 57 " --> pdb=" O PHE U 67 " (cutoff:3.500A) 2220 hydrogen bonds defined for protein. 6594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.38 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.23: 3355 1.23 - 1.47: 19219 1.47 - 1.70: 18829 1.70 - 1.94: 258 1.94 - 2.17: 1 Bond restraints: 41662 Sorted by residual: bond pdb=" CA PRO N 8 " pdb=" CB PRO N 8 " ideal model delta sigma weight residual 1.534 2.174 -0.640 1.49e-02 4.50e+03 1.85e+03 bond pdb=" CA THR S 127 " pdb=" CB THR S 127 " ideal model delta sigma weight residual 1.528 1.801 -0.273 1.66e-02 3.63e+03 2.70e+02 bond pdb=" CA GLN N 738 " pdb=" C GLN N 738 " ideal model delta sigma weight residual 1.521 1.369 0.152 1.17e-02 7.31e+03 1.70e+02 bond pdb=" CA TYR V 196 " pdb=" CB TYR V 196 " ideal model delta sigma weight residual 1.530 1.738 -0.207 1.69e-02 3.50e+03 1.50e+02 bond pdb=" C GLN Y 89 " pdb=" OXT GLN Y 89 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 41657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.01: 55933 10.01 - 20.02: 335 20.02 - 30.03: 9 30.03 - 40.04: 1 40.04 - 50.05: 1 Bond angle restraints: 56279 Sorted by residual: angle pdb=" N PRO N 8 " pdb=" CA PRO N 8 " pdb=" CB PRO N 8 " ideal model delta sigma weight residual 103.33 68.21 35.12 1.10e+00 8.26e-01 1.02e+03 angle pdb=" C TYR V 196 " pdb=" CA TYR V 196 " pdb=" CB TYR V 196 " ideal model delta sigma weight residual 110.42 60.37 50.05 1.99e+00 2.53e-01 6.33e+02 angle pdb=" C ASP Y 65 " pdb=" CA ASP Y 65 " pdb=" CB ASP Y 65 " ideal model delta sigma weight residual 110.10 80.67 29.43 1.90e+00 2.77e-01 2.40e+02 angle pdb=" CA SER S 197 " pdb=" C SER S 197 " pdb=" O SER S 197 " ideal model delta sigma weight residual 120.70 105.28 15.42 1.03e+00 9.43e-01 2.24e+02 angle pdb=" N HIS S 20 " pdb=" CA HIS S 20 " pdb=" C HIS S 20 " ideal model delta sigma weight residual 111.07 126.40 -15.33 1.07e+00 8.73e-01 2.05e+02 ... (remaining 56274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.99: 23108 18.99 - 37.99: 1632 37.99 - 56.98: 350 56.98 - 75.97: 267 75.97 - 94.96: 144 Dihedral angle restraints: 25501 sinusoidal: 10350 harmonic: 15151 Sorted by residual: dihedral pdb=" C TYR V 196 " pdb=" N TYR V 196 " pdb=" CA TYR V 196 " pdb=" CB TYR V 196 " ideal model delta harmonic sigma weight residual -122.60 -75.03 -47.57 0 2.50e+00 1.60e-01 3.62e+02 dihedral pdb=" N PRO N 8 " pdb=" C PRO N 8 " pdb=" CA PRO N 8 " pdb=" CB PRO N 8 " ideal model delta harmonic sigma weight residual 115.10 74.32 40.78 0 2.50e+00 1.60e-01 2.66e+02 dihedral pdb=" N LYS S 126 " pdb=" C LYS S 126 " pdb=" CA LYS S 126 " pdb=" CB LYS S 126 " ideal model delta harmonic sigma weight residual 122.80 161.39 -38.59 0 2.50e+00 1.60e-01 2.38e+02 ... (remaining 25498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 5754 0.317 - 0.634: 663 0.634 - 0.950: 25 0.950 - 1.267: 4 1.267 - 1.584: 1 Chirality restraints: 6447 Sorted by residual: chirality pdb=" CA LYS S 126 " pdb=" N LYS S 126 " pdb=" C LYS S 126 " pdb=" CB LYS S 126 " both_signs ideal model delta sigma weight residual False 2.51 0.93 1.58 2.00e-01 2.50e+01 6.27e+01 chirality pdb=" CA ASP Z 142 " pdb=" N ASP Z 142 " pdb=" C ASP Z 142 " pdb=" CB ASP Z 142 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" CA PRO N 8 " pdb=" N PRO N 8 " pdb=" C PRO N 8 " pdb=" CB PRO N 8 " both_signs ideal model delta sigma weight residual False 2.72 3.78 -1.06 2.00e-01 2.50e+01 2.82e+01 ... (remaining 6444 not shown) Planarity restraints: 7202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 62 " -0.332 2.00e-02 2.50e+03 1.86e-01 6.91e+02 pdb=" CG TYR O 62 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR O 62 " 0.151 2.00e-02 2.50e+03 pdb=" CD2 TYR O 62 " 0.218 2.00e-02 2.50e+03 pdb=" CE1 TYR O 62 " 0.115 2.00e-02 2.50e+03 pdb=" CE2 TYR O 62 " 0.081 2.00e-02 2.50e+03 pdb=" CZ TYR O 62 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR O 62 " -0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 471 " 0.257 2.00e-02 2.50e+03 1.47e-01 4.31e+02 pdb=" CG TYR N 471 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR N 471 " -0.166 2.00e-02 2.50e+03 pdb=" CD2 TYR N 471 " -0.089 2.00e-02 2.50e+03 pdb=" CE1 TYR N 471 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR N 471 " -0.120 2.00e-02 2.50e+03 pdb=" CZ TYR N 471 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR N 471 " 0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 306 " 0.283 2.00e-02 2.50e+03 1.46e-01 4.24e+02 pdb=" CG TYR Q 306 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 306 " -0.135 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 306 " -0.127 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 306 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 306 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR Q 306 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR Q 306 " 0.187 2.00e-02 2.50e+03 ... (remaining 7199 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.50: 5 1.50 - 2.35: 35 2.35 - 3.20: 37372 3.20 - 4.05: 100331 4.05 - 4.90: 180131 Warning: very small nonbonded interaction distances. Nonbonded interactions: 317874 Sorted by model distance: nonbonded pdb=" ND2 ASN Y 21 " pdb=" NH1 ARG S 55 " model vdw 0.656 3.200 nonbonded pdb=" O TYR V 196 " pdb=" CD2 TYR V 196 " model vdw 1.324 3.340 nonbonded pdb=" OE2 GLU V 169 " pdb=" ND2 ASN V 193 " model vdw 1.408 3.120 nonbonded pdb=" O MET N 339 " pdb=" CA GLY N 709 " model vdw 1.427 3.440 nonbonded pdb=" CB ALA W 129 " pdb=" CE2 PHE W 157 " model vdw 1.434 3.760 ... (remaining 317869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 36.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3870 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 : 0.035 0.640 41665 Z= 2.257 Angle : 3.400 50.053 56279 Z= 2.343 Chirality : 0.201 1.584 6447 Planarity : 0.027 0.300 7202 Dihedral : 17.759 94.963 15677 Min Nonbonded Distance : 0.656 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 2.09 % Allowed : 5.60 % Favored : 92.31 % Rotamer: Outliers : 2.78 % Allowed : 6.60 % Favored : 90.62 % Cbeta Deviations : 6.72 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.10), residues: 5108 helix: -0.73 (0.08), residues: 3138 sheet: -1.30 (0.32), residues: 188 loop : -2.58 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.012 ARG T 60 TYR 0.332 0.046 TYR O 62 PHE 0.168 0.038 PHE U 52 TRP 0.176 0.039 TRP P 311 HIS 0.075 0.015 HIS P 282 Details of bonding type rmsd covalent geometry : bond 0.03457 (41662) covalent geometry : angle 3.40025 (56279) hydrogen bonds : bond 0.32811 ( 2220) hydrogen bonds : angle 8.00201 ( 6594) Misc. bond : bond 0.23124 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1753 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1626 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 145 GLN cc_start: 0.5247 (mt0) cc_final: 0.4821 (mt0) REVERT: V 173 THR cc_start: 0.5290 (OUTLIER) cc_final: 0.4553 (m) REVERT: V 237 ASN cc_start: 0.7979 (m-40) cc_final: 0.7580 (m110) REVERT: T 49 ASP cc_start: 0.4836 (m-30) cc_final: 0.4547 (m-30) REVERT: T 64 VAL cc_start: 0.1428 (OUTLIER) cc_final: 0.1178 (m) REVERT: Y 68 GLU cc_start: 0.5430 (mm-30) cc_final: 0.5156 (tp30) REVERT: Z 381 LEU cc_start: 0.4140 (mt) cc_final: 0.3843 (tt) REVERT: Z 505 VAL cc_start: 0.4498 (t) cc_final: 0.4220 (t) REVERT: Z 946 THR cc_start: 0.5305 (m) cc_final: 0.4206 (p) REVERT: N 412 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: N 706 MET cc_start: 0.2161 (tpp) cc_final: 0.1814 (tmm) REVERT: N 735 MET cc_start: 0.5495 (mmt) cc_final: 0.5100 (mmt) REVERT: N 739 PHE cc_start: 0.4833 (OUTLIER) cc_final: 0.4608 (p90) REVERT: N 866 TYR cc_start: 0.1496 (p90) cc_final: 0.1037 (p90) REVERT: N 868 VAL cc_start: 0.2903 (m) cc_final: 0.2622 (m) REVERT: S 204 ASP cc_start: 0.7949 (m-30) cc_final: 0.7382 (t0) REVERT: S 392 ILE cc_start: 0.7100 (mt) cc_final: 0.5550 (mt) REVERT: P 220 TYR cc_start: 0.6111 (t80) cc_final: 0.5858 (t80) REVERT: P 352 VAL cc_start: 0.5728 (t) cc_final: 0.4995 (t) REVERT: P 370 ASP cc_start: 0.6285 (m-30) cc_final: 0.5222 (m-30) REVERT: Q 68 MET cc_start: 0.1494 (pmm) cc_final: 0.0913 (pmm) REVERT: Q 176 ASP cc_start: 0.6188 (m-30) cc_final: 0.5949 (m-30) REVERT: Q 359 ILE cc_start: 0.8099 (mt) cc_final: 0.7848 (tp) REVERT: R 20 ARG cc_start: 0.2968 (mmt180) cc_final: 0.2661 (mmp80) REVERT: R 204 TRP cc_start: 0.6809 (OUTLIER) cc_final: 0.6359 (t60) REVERT: R 272 ASP cc_start: 0.6200 (m-30) cc_final: 0.5828 (m-30) REVERT: U 246 GLU cc_start: 0.6096 (tp30) cc_final: 0.5870 (tp30) REVERT: O 66 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6673 (t) REVERT: O 83 LEU cc_start: 0.6768 (mt) cc_final: 0.5924 (mt) REVERT: O 296 LEU cc_start: 0.7618 (tp) cc_final: 0.7373 (tt) REVERT: O 319 LEU cc_start: 0.5296 (mt) cc_final: 0.4928 (mp) REVERT: O 334 LEU cc_start: 0.7550 (mt) cc_final: 0.6984 (mt) outliers start: 127 outliers final: 26 residues processed: 1716 average time/residue: 0.2522 time to fit residues: 697.4472 Evaluate side-chains 892 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 860 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 86 HIS W 108 GLN W 170 HIS V 102 GLN ** V 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 215 ASN ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 HIS Y 75 ASN Y 88 ASN Z 15 GLN Z 129 ASN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 215 ASN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 387 ASN Z 463 HIS Z 539 ASN Z 549 ASN Z 618 GLN Z 622 HIS Z 829 GLN ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 ASN N 71 ASN N 233 ASN N 240 GLN N 300 ASN N 346 ASN N 444 HIS N 472 ASN N 510 HIS N 564 ASN N 654 GLN N 667 GLN ** N 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 747 HIS N 878 GLN S 20 HIS S 65 ASN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 GLN ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 ASN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 437 ASN S 438 HIS S 470 GLN P 29 GLN ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN ** P 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 230 HIS P 289 ASN P 349 ASN P 385 ASN P 386 GLN Q 37 GLN Q 87 GLN Q 260 GLN ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 372 GLN Q 394 ASN ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN R 195 ASN R 325 HIS ** R 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN U 70 HIS ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 252 HIS U 294 ASN ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 273 GLN O 362 GLN O 389 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.208372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.183701 restraints weight = 130419.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.181609 restraints weight = 96960.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.182486 restraints weight = 95083.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.182685 restraints weight = 71434.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.182841 restraints weight = 67203.953| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 41665 Z= 0.266 Angle : 0.888 15.397 56279 Z= 0.478 Chirality : 0.047 0.203 6447 Planarity : 0.006 0.076 7202 Dihedral : 5.911 39.353 5504 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.60 % Favored : 94.95 % Rotamer: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.11), residues: 5108 helix: 0.39 (0.08), residues: 3299 sheet: -1.07 (0.34), residues: 199 loop : -1.93 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG V 157 TYR 0.043 0.003 TYR T 197 PHE 0.039 0.003 PHE P 267 TRP 0.044 0.003 TRP R 204 HIS 0.020 0.002 HIS V 195 Details of bonding type rmsd covalent geometry : bond 0.00554 (41662) covalent geometry : angle 0.88824 (56279) hydrogen bonds : bond 0.07200 ( 2220) hydrogen bonds : angle 5.32642 ( 6594) Misc. bond : bond 0.00714 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1083 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 92 MET cc_start: 0.5782 (mmm) cc_final: 0.5087 (mmt) REVERT: T 47 GLN cc_start: 0.6668 (tp-100) cc_final: 0.6277 (mp10) REVERT: T 119 THR cc_start: 0.8051 (m) cc_final: 0.7587 (t) REVERT: T 153 MET cc_start: 0.7135 (mmp) cc_final: 0.6378 (mmp) REVERT: T 161 TRP cc_start: 0.5972 (t-100) cc_final: 0.5423 (t-100) REVERT: T 210 PHE cc_start: 0.6958 (m-10) cc_final: 0.6420 (m-10) REVERT: T 232 LYS cc_start: 0.5898 (tttt) cc_final: 0.5600 (mmtm) REVERT: T 235 PHE cc_start: 0.7077 (m-10) cc_final: 0.6715 (m-10) REVERT: T 262 LYS cc_start: 0.8605 (mttt) cc_final: 0.8313 (mttm) REVERT: Y 68 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5824 (tp30) REVERT: Z 23 GLN cc_start: 0.3972 (mt0) cc_final: 0.3609 (tt0) REVERT: Z 64 TYR cc_start: 0.2653 (m-10) cc_final: 0.2084 (m-10) REVERT: Z 76 LYS cc_start: 0.6240 (mttm) cc_final: 0.5378 (mmtm) REVERT: Z 163 GLU cc_start: 0.4478 (tp30) cc_final: 0.3760 (mt-10) REVERT: Z 293 MET cc_start: 0.7302 (mmm) cc_final: 0.6487 (mmm) REVERT: Z 312 TYR cc_start: 0.3395 (m-10) cc_final: 0.3158 (m-10) REVERT: Z 381 LEU cc_start: 0.7217 (mt) cc_final: 0.6527 (tt) REVERT: Z 385 PHE cc_start: 0.6503 (m-10) cc_final: 0.5896 (m-80) REVERT: Z 404 ASP cc_start: 0.5982 (p0) cc_final: 0.5751 (p0) REVERT: Z 534 PHE cc_start: 0.7852 (m-10) cc_final: 0.7630 (m-10) REVERT: Z 575 MET cc_start: 0.8462 (mtm) cc_final: 0.7729 (mtm) REVERT: Z 588 ILE cc_start: 0.6856 (mt) cc_final: 0.6640 (pt) REVERT: Z 734 ASP cc_start: 0.6369 (m-30) cc_final: 0.5725 (t0) REVERT: Z 840 ARG cc_start: 0.8047 (ptt180) cc_final: 0.7814 (ptt180) REVERT: Z 897 HIS cc_start: 0.5556 (t70) cc_final: 0.5068 (m170) REVERT: Z 970 TYR cc_start: 0.4205 (m-10) cc_final: 0.3786 (m-80) REVERT: N 42 GLU cc_start: 0.6468 (mm-30) cc_final: 0.5830 (tm-30) REVERT: N 104 LYS cc_start: 0.7951 (tptt) cc_final: 0.7683 (tttt) REVERT: N 117 TYR cc_start: 0.6025 (t80) cc_final: 0.5783 (t80) REVERT: N 212 ASP cc_start: 0.5648 (m-30) cc_final: 0.4969 (t0) REVERT: N 302 PHE cc_start: 0.3256 (t80) cc_final: 0.2949 (t80) REVERT: N 344 THR cc_start: 0.5829 (t) cc_final: 0.5483 (t) REVERT: N 412 TYR cc_start: 0.2394 (m-10) cc_final: 0.2172 (m-80) REVERT: N 627 ILE cc_start: 0.8257 (mt) cc_final: 0.7819 (mm) REVERT: N 706 MET cc_start: 0.3744 (tpp) cc_final: 0.2648 (tmm) REVERT: N 742 TRP cc_start: 0.6151 (t-100) cc_final: 0.4378 (t-100) REVERT: S 137 PHE cc_start: 0.6372 (t80) cc_final: 0.5788 (t80) REVERT: S 138 MET cc_start: 0.7049 (tpp) cc_final: 0.6777 (tpp) REVERT: S 141 LEU cc_start: 0.8021 (mt) cc_final: 0.7773 (tp) REVERT: S 151 GLU cc_start: 0.5291 (mt-10) cc_final: 0.4463 (mt-10) REVERT: S 280 ASN cc_start: 0.8237 (m110) cc_final: 0.7846 (m110) REVERT: S 392 ILE cc_start: 0.8080 (mt) cc_final: 0.7632 (mt) REVERT: S 458 GLN cc_start: 0.8546 (mt0) cc_final: 0.7859 (mt0) REVERT: S 464 ARG cc_start: 0.7603 (mmt90) cc_final: 0.6847 (mmt90) REVERT: S 473 ASP cc_start: 0.8357 (t0) cc_final: 0.8026 (t0) REVERT: P 96 MET cc_start: 0.7638 (mmm) cc_final: 0.6399 (ttt) REVERT: P 197 THR cc_start: 0.8891 (m) cc_final: 0.8640 (p) REVERT: P 236 GLU cc_start: 0.7532 (tp30) cc_final: 0.7252 (tp30) REVERT: P 240 TYR cc_start: 0.7092 (m-10) cc_final: 0.6377 (m-10) REVERT: P 290 LEU cc_start: 0.6546 (tp) cc_final: 0.5792 (tp) REVERT: P 382 ASP cc_start: 0.6956 (m-30) cc_final: 0.6533 (m-30) REVERT: Q 34 ASP cc_start: 0.6710 (m-30) cc_final: 0.6155 (t0) REVERT: Q 155 LEU cc_start: 0.8895 (tp) cc_final: 0.8591 (tp) REVERT: Q 230 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7857 (mmmt) REVERT: Q 398 TYR cc_start: 0.5950 (m-10) cc_final: 0.5712 (m-10) REVERT: R 118 GLN cc_start: 0.7907 (tt0) cc_final: 0.7688 (pp30) REVERT: R 218 CYS cc_start: 0.8191 (m) cc_final: 0.7752 (t) REVERT: R 248 SER cc_start: 0.7828 (m) cc_final: 0.7435 (p) REVERT: R 254 SER cc_start: 0.8963 (p) cc_final: 0.8488 (p) REVERT: R 335 ARG cc_start: 0.6125 (mtp85) cc_final: 0.5791 (mtt180) REVERT: R 404 VAL cc_start: 0.8587 (m) cc_final: 0.8226 (p) REVERT: R 423 LEU cc_start: 0.8165 (mt) cc_final: 0.7632 (tp) REVERT: U 83 ILE cc_start: 0.7177 (mp) cc_final: 0.6925 (mp) REVERT: U 248 ASP cc_start: 0.7605 (t70) cc_final: 0.6786 (t70) REVERT: U 293 GLU cc_start: 0.4781 (tp30) cc_final: 0.4240 (mt-10) REVERT: O 132 GLU cc_start: 0.8684 (tt0) cc_final: 0.8400 (tt0) REVERT: O 190 TYR cc_start: 0.7385 (m-80) cc_final: 0.7042 (m-80) outliers start: 8 outliers final: 2 residues processed: 1089 average time/residue: 0.2404 time to fit residues: 430.1532 Evaluate side-chains 771 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 769 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 418 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 chunk 467 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 102 optimal weight: 0.0980 chunk 310 optimal weight: 0.0870 chunk 444 optimal weight: 3.9990 chunk 337 optimal weight: 0.6980 chunk 407 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 158 optimal weight: 0.0980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 29 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 170 HIS V 102 GLN ** V 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 131 ASN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 898 HIS Z 926 ASN N 29 ASN N 34 GLN N 182 ASN N 346 ASN ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 679 ASN N 900 ASN S 139 HIS S 244 ASN S 472 HIS P 48 GLN P 78 GLN ** P 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 143 GLN R 385 ASN R 401 HIS U 252 HIS ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 262 GLN O 23 HIS O 169 ASN O 235 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.211349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4531 r_free = 0.4531 target = 0.187581 restraints weight = 130230.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.186159 restraints weight = 103852.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.186301 restraints weight = 91561.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.186098 restraints weight = 84464.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.186232 restraints weight = 78745.287| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41665 Z= 0.154 Angle : 0.676 9.455 56279 Z= 0.361 Chirality : 0.040 0.222 6447 Planarity : 0.005 0.068 7202 Dihedral : 5.182 31.907 5504 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.35 % Favored : 95.30 % Rotamer: Outliers : 0.22 % Allowed : 2.58 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.11), residues: 5108 helix: 0.82 (0.09), residues: 3299 sheet: -0.83 (0.35), residues: 196 loop : -1.67 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 157 TYR 0.025 0.002 TYR T 197 PHE 0.046 0.002 PHE T 82 TRP 0.025 0.002 TRP U 92 HIS 0.011 0.001 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00316 (41662) covalent geometry : angle 0.67590 (56279) hydrogen bonds : bond 0.05745 ( 2220) hydrogen bonds : angle 4.68296 ( 6594) Misc. bond : bond 0.00238 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1041 time to evaluate : 1.563 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: V 60 ASP cc_start: 0.5682 (t0) cc_final: 0.5230 (t0) REVERT: V 92 MET cc_start: 0.6059 (mmm) cc_final: 0.5550 (mmt) REVERT: V 249 GLU cc_start: 0.7871 (mp0) cc_final: 0.7557 (mp0) REVERT: T 47 GLN cc_start: 0.6497 (tp-100) cc_final: 0.6097 (mp10) REVERT: T 67 LEU cc_start: 0.6250 (mp) cc_final: 0.5901 (tp) REVERT: T 150 ARG cc_start: 0.6564 (tmm160) cc_final: 0.5910 (ptm-80) REVERT: T 153 MET cc_start: 0.7186 (mmp) cc_final: 0.6477 (mmp) REVERT: T 161 TRP cc_start: 0.5930 (t-100) cc_final: 0.4666 (t-100) REVERT: T 210 PHE cc_start: 0.6729 (m-10) cc_final: 0.5907 (m-10) REVERT: Y 68 GLU cc_start: 0.5725 (mm-30) cc_final: 0.5340 (tp30) REVERT: Z 23 GLN cc_start: 0.4513 (mt0) cc_final: 0.4063 (tt0) REVERT: Z 64 TYR cc_start: 0.2809 (m-10) cc_final: 0.2343 (m-10) REVERT: Z 76 LYS cc_start: 0.6306 (mttm) cc_final: 0.5495 (mmmt) REVERT: Z 163 GLU cc_start: 0.4203 (tp30) cc_final: 0.3669 (mt-10) REVERT: Z 190 THR cc_start: 0.3839 (m) cc_final: 0.3575 (t) REVERT: Z 381 LEU cc_start: 0.7054 (mt) cc_final: 0.6306 (tt) REVERT: Z 385 PHE cc_start: 0.6749 (m-10) cc_final: 0.6303 (m-80) REVERT: Z 407 VAL cc_start: 0.6106 (t) cc_final: 0.5552 (t) REVERT: Z 534 PHE cc_start: 0.7765 (m-10) cc_final: 0.7536 (m-10) REVERT: Z 560 THR cc_start: 0.4954 (p) cc_final: 0.4481 (t) REVERT: Z 575 MET cc_start: 0.8323 (mtm) cc_final: 0.7800 (mtm) REVERT: Z 588 ILE cc_start: 0.6668 (mt) cc_final: 0.6274 (pt) REVERT: Z 734 ASP cc_start: 0.6213 (m-30) cc_final: 0.5526 (t0) REVERT: Z 801 HIS cc_start: 0.1369 (t-90) cc_final: 0.0650 (t-90) REVERT: Z 840 ARG cc_start: 0.7926 (ptt180) cc_final: 0.7567 (ptt180) REVERT: Z 897 HIS cc_start: 0.5509 (t70) cc_final: 0.5088 (m170) REVERT: Z 970 TYR cc_start: 0.4418 (m-10) cc_final: 0.3857 (t80) REVERT: N 42 GLU cc_start: 0.6282 (mm-30) cc_final: 0.5892 (tm-30) REVERT: N 100 THR cc_start: 0.6292 (m) cc_final: 0.4712 (t) REVERT: N 212 ASP cc_start: 0.5682 (m-30) cc_final: 0.5250 (t0) REVERT: N 302 PHE cc_start: 0.3222 (t80) cc_final: 0.2736 (t80) REVERT: N 412 TYR cc_start: 0.2151 (m-10) cc_final: 0.1776 (m-80) REVERT: N 466 LEU cc_start: 0.4988 (tp) cc_final: 0.4738 (pp) REVERT: N 627 ILE cc_start: 0.8257 (mt) cc_final: 0.7789 (mm) REVERT: N 639 ASP cc_start: 0.8270 (t0) cc_final: 0.7802 (m-30) REVERT: N 706 MET cc_start: 0.3943 (tpp) cc_final: 0.2596 (tmm) REVERT: N 742 TRP cc_start: 0.5368 (t-100) cc_final: 0.4900 (t-100) REVERT: S 139 HIS cc_start: 0.6276 (OUTLIER) cc_final: 0.5315 (m-70) REVERT: S 145 PHE cc_start: 0.5911 (t80) cc_final: 0.5666 (t80) REVERT: S 151 GLU cc_start: 0.5099 (mt-10) cc_final: 0.4378 (mt-10) REVERT: S 232 MET cc_start: 0.6381 (tpt) cc_final: 0.5698 (tpt) REVERT: S 280 ASN cc_start: 0.8279 (m110) cc_final: 0.7881 (m110) REVERT: S 392 ILE cc_start: 0.8109 (mt) cc_final: 0.7534 (mt) REVERT: S 476 LEU cc_start: 0.8605 (tp) cc_final: 0.7952 (pp) REVERT: P 240 TYR cc_start: 0.6909 (m-10) cc_final: 0.6404 (m-80) REVERT: P 382 ASP cc_start: 0.6639 (m-30) cc_final: 0.6293 (m-30) REVERT: Q 230 LYS cc_start: 0.8384 (mmpt) cc_final: 0.8010 (mmmt) REVERT: Q 265 MET cc_start: 0.6179 (tpt) cc_final: 0.5878 (tpt) REVERT: Q 271 MET cc_start: 0.8237 (mtp) cc_final: 0.7645 (tpp) REVERT: Q 306 TYR cc_start: 0.8024 (t80) cc_final: 0.7786 (t80) REVERT: Q 420 ASN cc_start: 0.8201 (t0) cc_final: 0.7799 (t0) REVERT: R 218 CYS cc_start: 0.7913 (m) cc_final: 0.7649 (t) REVERT: R 248 SER cc_start: 0.7720 (m) cc_final: 0.7500 (p) REVERT: R 307 TYR cc_start: 0.8246 (m-80) cc_final: 0.7649 (m-10) REVERT: R 334 ARG cc_start: 0.6931 (ttm170) cc_final: 0.6714 (ttp-110) REVERT: R 335 ARG cc_start: 0.5574 (mtp85) cc_final: 0.5180 (mtt-85) REVERT: R 423 LEU cc_start: 0.8240 (mt) cc_final: 0.7788 (tp) REVERT: U 83 ILE cc_start: 0.7143 (mp) cc_final: 0.6792 (mp) REVERT: U 167 GLU cc_start: 0.7636 (pt0) cc_final: 0.7379 (pt0) REVERT: U 293 GLU cc_start: 0.4880 (tp30) cc_final: 0.4326 (mt-10) REVERT: O 132 GLU cc_start: 0.8905 (tt0) cc_final: 0.8528 (tt0) REVERT: O 177 GLN cc_start: 0.8808 (pm20) cc_final: 0.8373 (pm20) REVERT: O 265 LYS cc_start: 0.7311 (mtmt) cc_final: 0.7063 (mtpt) REVERT: O 291 ILE cc_start: 0.7256 (pt) cc_final: 0.6839 (pt) REVERT: O 319 LEU cc_start: 0.6783 (mt) cc_final: 0.6569 (mt) outliers start: 10 outliers final: 1 residues processed: 1044 average time/residue: 0.2278 time to fit residues: 397.3120 Evaluate side-chains 763 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 761 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 80 optimal weight: 9.9990 chunk 105 optimal weight: 40.0000 chunk 200 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 164 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 HIS ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 255 GLN Z 129 ASN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 275 GLN Z 391 ASN ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 852 GLN ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 959 HIS N 34 GLN ** N 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 ASN N 529 GLN N 614 ASN ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 470 GLN ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN P 282 HIS P 337 HIS ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 106 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 ASN Q 320 GLN ** Q 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS R 130 GLN R 136 ASN ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 70 HIS U 173 HIS U 223 HIS U 252 HIS U 262 GLN O 122 HIS ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 235 HIS O 326 HIS O 389 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.202600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.4483 r_free = 0.4483 target = 0.183153 restraints weight = 131868.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.179963 restraints weight = 135516.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.180630 restraints weight = 122046.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.180716 restraints weight = 101080.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.180759 restraints weight = 93193.102| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 41665 Z= 0.233 Angle : 0.802 18.551 56279 Z= 0.424 Chirality : 0.044 0.224 6447 Planarity : 0.005 0.106 7202 Dihedral : 5.500 34.892 5504 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.01 % Favored : 94.68 % Rotamer: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.11), residues: 5108 helix: 0.31 (0.09), residues: 3313 sheet: -0.90 (0.33), residues: 215 loop : -1.83 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 773 TYR 0.026 0.003 TYR P 168 PHE 0.053 0.003 PHE Q 77 TRP 0.027 0.002 TRP V 117 HIS 0.016 0.002 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00490 (41662) covalent geometry : angle 0.80172 (56279) hydrogen bonds : bond 0.05528 ( 2220) hydrogen bonds : angle 5.04763 ( 6594) Misc. bond : bond 0.00539 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 922 time to evaluate : 1.559 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: W 1 MET cc_start: 0.4024 (mtm) cc_final: 0.1832 (mmt) REVERT: W 157 PHE cc_start: 0.4680 (m-10) cc_final: 0.2928 (m-80) REVERT: V 40 HIS cc_start: 0.7678 (t70) cc_final: 0.7468 (t-170) REVERT: V 60 ASP cc_start: 0.6043 (t0) cc_final: 0.5662 (t0) REVERT: V 92 MET cc_start: 0.6310 (mmm) cc_final: 0.5729 (mmt) REVERT: T 89 TYR cc_start: 0.6506 (m-80) cc_final: 0.6250 (m-80) REVERT: T 123 HIS cc_start: 0.7134 (m90) cc_final: 0.6904 (m90) REVERT: T 153 MET cc_start: 0.7623 (mmp) cc_final: 0.6689 (mmp) REVERT: T 208 LEU cc_start: 0.8073 (mt) cc_final: 0.7861 (mt) REVERT: T 210 PHE cc_start: 0.7302 (m-10) cc_final: 0.7011 (m-10) REVERT: Y 68 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5601 (tp30) REVERT: Y 89 GLN cc_start: 0.6205 (mt0) cc_final: 0.5911 (tt0) REVERT: Z 23 GLN cc_start: 0.4476 (mt0) cc_final: 0.3975 (tt0) REVERT: Z 76 LYS cc_start: 0.6811 (mttm) cc_final: 0.5718 (mmtt) REVERT: Z 163 GLU cc_start: 0.5422 (tp30) cc_final: 0.4366 (mt-10) REVERT: Z 244 ARG cc_start: 0.7334 (ttt90) cc_final: 0.6558 (mtm180) REVERT: Z 312 TYR cc_start: 0.3292 (m-10) cc_final: 0.3047 (m-10) REVERT: Z 381 LEU cc_start: 0.6072 (mt) cc_final: 0.4914 (tt) REVERT: Z 385 PHE cc_start: 0.6091 (m-10) cc_final: 0.5707 (m-80) REVERT: Z 389 PHE cc_start: 0.6311 (m-80) cc_final: 0.5737 (m-80) REVERT: Z 404 ASP cc_start: 0.5972 (p0) cc_final: 0.5384 (p0) REVERT: Z 439 TYR cc_start: 0.6895 (m-80) cc_final: 0.6626 (m-80) REVERT: Z 575 MET cc_start: 0.7851 (mtm) cc_final: 0.7495 (mtm) REVERT: Z 734 ASP cc_start: 0.6809 (m-30) cc_final: 0.5730 (t70) REVERT: Z 831 LEU cc_start: 0.8213 (mm) cc_final: 0.7952 (mm) REVERT: N 17 GLN cc_start: 0.7099 (mt0) cc_final: 0.6843 (mp10) REVERT: N 42 GLU cc_start: 0.6322 (mm-30) cc_final: 0.6076 (tm-30) REVERT: N 212 ASP cc_start: 0.5937 (m-30) cc_final: 0.5418 (t0) REVERT: N 362 TRP cc_start: 0.7220 (m100) cc_final: 0.6890 (m100) REVERT: N 539 MET cc_start: 0.5513 (ptm) cc_final: 0.5290 (ptm) REVERT: N 627 ILE cc_start: 0.8325 (mt) cc_final: 0.7837 (mm) REVERT: N 680 LYS cc_start: 0.7228 (ptpt) cc_final: 0.6957 (tptt) REVERT: N 682 PHE cc_start: 0.5526 (m-10) cc_final: 0.5313 (m-10) REVERT: N 706 MET cc_start: 0.4591 (tpp) cc_final: 0.3140 (tmm) REVERT: N 742 TRP cc_start: 0.4940 (t-100) cc_final: 0.4605 (t-100) REVERT: S 86 SER cc_start: 0.5310 (p) cc_final: 0.4972 (t) REVERT: S 139 HIS cc_start: 0.4890 (m-70) cc_final: 0.4509 (m170) REVERT: S 151 GLU cc_start: 0.3932 (mt-10) cc_final: 0.3248 (mt-10) REVERT: S 232 MET cc_start: 0.6634 (tpt) cc_final: 0.6314 (tpt) REVERT: S 280 ASN cc_start: 0.8325 (m110) cc_final: 0.7615 (m110) REVERT: S 392 ILE cc_start: 0.8293 (mt) cc_final: 0.7920 (mt) REVERT: S 473 ASP cc_start: 0.8159 (t0) cc_final: 0.7853 (t0) REVERT: P 130 ILE cc_start: 0.6734 (pt) cc_final: 0.6125 (pt) REVERT: Q 86 MET cc_start: 0.7319 (ptm) cc_final: 0.6734 (ttp) REVERT: Q 420 ASN cc_start: 0.8603 (t0) cc_final: 0.8361 (t0) REVERT: R 191 LEU cc_start: 0.8016 (mt) cc_final: 0.7614 (pp) REVERT: R 320 LYS cc_start: 0.7514 (ptmt) cc_final: 0.7298 (ptmt) REVERT: R 423 LEU cc_start: 0.8244 (mt) cc_final: 0.7662 (tp) REVERT: U 83 ILE cc_start: 0.7498 (mp) cc_final: 0.7241 (mp) REVERT: U 198 LYS cc_start: 0.8539 (pttp) cc_final: 0.8282 (pttp) REVERT: U 293 GLU cc_start: 0.3992 (tp30) cc_final: 0.3658 (mm-30) REVERT: O 177 GLN cc_start: 0.8462 (pm20) cc_final: 0.7979 (pm20) REVERT: O 205 ILE cc_start: 0.3761 (mp) cc_final: 0.3490 (pt) REVERT: O 323 ASN cc_start: 0.6087 (m-40) cc_final: 0.5874 (m-40) REVERT: O 363 ILE cc_start: 0.6325 (mp) cc_final: 0.5405 (mp) REVERT: O 374 ASN cc_start: 0.6589 (t0) cc_final: 0.6342 (t0) outliers start: 3 outliers final: 0 residues processed: 925 average time/residue: 0.2171 time to fit residues: 334.5710 Evaluate side-chains 718 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 262 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 469 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 441 optimal weight: 30.0000 chunk 139 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 439 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 125 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 167 ASN ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN T 116 GLN X 102 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 GLN ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 360 GLN N 375 HIS N 430 ASN N 654 GLN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 244 ASN P 48 GLN P 286 ASN Q 37 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.200528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.183406 restraints weight = 129212.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.180280 restraints weight = 186413.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.178836 restraints weight = 149531.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.178767 restraints weight = 131247.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.179042 restraints weight = 107928.777| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.7868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 41665 Z= 0.236 Angle : 0.791 14.628 56279 Z= 0.414 Chirality : 0.044 0.255 6447 Planarity : 0.005 0.074 7202 Dihedral : 5.582 36.414 5504 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % Rotamer: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.11), residues: 5108 helix: 0.15 (0.09), residues: 3302 sheet: -1.14 (0.36), residues: 185 loop : -1.90 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 139 TYR 0.065 0.002 TYR T 197 PHE 0.032 0.003 PHE Q 77 TRP 0.051 0.003 TRP R 204 HIS 0.020 0.002 HIS Q 178 Details of bonding type rmsd covalent geometry : bond 0.00476 (41662) covalent geometry : angle 0.79079 (56279) hydrogen bonds : bond 0.05314 ( 2220) hydrogen bonds : angle 5.13258 ( 6594) Misc. bond : bond 0.00340 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 899 time to evaluate : 1.620 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: W 1 MET cc_start: 0.3480 (mtm) cc_final: 0.1981 (mmt) REVERT: T 81 TYR cc_start: 0.7796 (m-10) cc_final: 0.7569 (m-10) REVERT: T 123 HIS cc_start: 0.7624 (m90) cc_final: 0.7092 (m90) REVERT: T 147 LYS cc_start: 0.6150 (tttp) cc_final: 0.5869 (tttm) REVERT: T 153 MET cc_start: 0.7513 (mmp) cc_final: 0.6570 (mmp) REVERT: T 161 TRP cc_start: 0.5816 (t-100) cc_final: 0.5352 (t-100) REVERT: Y 68 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5839 (pm20) REVERT: Z 23 GLN cc_start: 0.4862 (mt0) cc_final: 0.4025 (tp40) REVERT: Z 291 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7279 (mt-10) REVERT: Z 312 TYR cc_start: 0.3295 (m-10) cc_final: 0.3019 (m-10) REVERT: Z 381 LEU cc_start: 0.5868 (mt) cc_final: 0.4821 (tt) REVERT: Z 385 PHE cc_start: 0.6862 (m-10) cc_final: 0.6263 (m-10) REVERT: Z 389 PHE cc_start: 0.6564 (m-80) cc_final: 0.5964 (m-80) REVERT: Z 404 ASP cc_start: 0.5754 (p0) cc_final: 0.5270 (p0) REVERT: Z 575 MET cc_start: 0.8033 (mtm) cc_final: 0.7671 (mtm) REVERT: Z 734 ASP cc_start: 0.6476 (m-30) cc_final: 0.5053 (t70) REVERT: Z 831 LEU cc_start: 0.8176 (mm) cc_final: 0.7903 (mm) REVERT: N 42 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5940 (tm-30) REVERT: N 386 MET cc_start: 0.4083 (mmp) cc_final: 0.3878 (mmp) REVERT: N 539 MET cc_start: 0.5608 (ptm) cc_final: 0.5280 (ptm) REVERT: N 627 ILE cc_start: 0.8412 (mt) cc_final: 0.7924 (mm) REVERT: N 653 ARG cc_start: 0.6964 (mtm180) cc_final: 0.6671 (mtm180) REVERT: N 680 LYS cc_start: 0.7042 (ptpt) cc_final: 0.6595 (tptt) REVERT: N 706 MET cc_start: 0.4536 (tpp) cc_final: 0.3147 (tmm) REVERT: N 742 TRP cc_start: 0.4936 (t-100) cc_final: 0.4432 (t-100) REVERT: S 139 HIS cc_start: 0.5242 (m-70) cc_final: 0.4424 (m170) REVERT: S 151 GLU cc_start: 0.4257 (mt-10) cc_final: 0.3455 (mt-10) REVERT: S 324 MET cc_start: 0.6421 (mtm) cc_final: 0.6146 (mtm) REVERT: S 392 ILE cc_start: 0.8345 (mt) cc_final: 0.8041 (mt) REVERT: S 444 GLU cc_start: 0.6068 (tp30) cc_final: 0.5772 (tp30) REVERT: S 473 ASP cc_start: 0.7901 (t0) cc_final: 0.7658 (t0) REVERT: S 474 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8152 (mm-30) REVERT: S 479 MET cc_start: 0.4931 (tpt) cc_final: 0.3040 (tpt) REVERT: P 24 ILE cc_start: 0.6130 (mt) cc_final: 0.5285 (mm) REVERT: P 72 TRP cc_start: 0.5576 (p90) cc_final: 0.5167 (p90) REVERT: P 130 ILE cc_start: 0.6341 (pt) cc_final: 0.5388 (pt) REVERT: Q 183 LYS cc_start: 0.8754 (tppt) cc_final: 0.7816 (mmtm) REVERT: Q 265 MET cc_start: 0.6323 (tpt) cc_final: 0.5954 (tpp) REVERT: Q 306 TYR cc_start: 0.8647 (t80) cc_final: 0.8409 (t80) REVERT: Q 390 LEU cc_start: 0.7554 (tt) cc_final: 0.7319 (tt) REVERT: R 389 GLU cc_start: 0.7017 (pm20) cc_final: 0.6635 (pm20) REVERT: R 423 LEU cc_start: 0.7895 (mt) cc_final: 0.7400 (tp) REVERT: U 83 ILE cc_start: 0.7506 (mp) cc_final: 0.7182 (mp) REVERT: U 192 ASN cc_start: 0.7160 (t0) cc_final: 0.6914 (t0) REVERT: U 293 GLU cc_start: 0.3689 (tp30) cc_final: 0.3463 (mm-30) REVERT: O 177 GLN cc_start: 0.8308 (pm20) cc_final: 0.8072 (pm20) REVERT: O 186 ASN cc_start: 0.8685 (p0) cc_final: 0.8420 (p0) REVERT: O 363 ILE cc_start: 0.6100 (mp) cc_final: 0.5312 (mp) outliers start: 3 outliers final: 0 residues processed: 901 average time/residue: 0.2308 time to fit residues: 347.7781 Evaluate side-chains 694 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 473 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 487 optimal weight: 8.9990 chunk 401 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 470 optimal weight: 9.9990 chunk 441 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 GLN ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 898 HIS N 34 GLN ** N 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 317 HIS S 334 HIS ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN P 285 GLN P 337 HIS P 348 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 320 GLN R 399 GLN ** U 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 262 GLN ** O 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS O 374 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.200504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.183797 restraints weight = 129805.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.181085 restraints weight = 181459.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.179691 restraints weight = 142317.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.179754 restraints weight = 121167.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.179903 restraints weight = 100564.131| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.8268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 41665 Z= 0.193 Angle : 0.734 14.056 56279 Z= 0.386 Chirality : 0.043 0.266 6447 Planarity : 0.005 0.055 7202 Dihedral : 5.516 36.672 5504 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.07 % Rotamer: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.11), residues: 5108 helix: 0.16 (0.09), residues: 3294 sheet: -1.20 (0.36), residues: 188 loop : -1.85 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 331 TYR 0.050 0.002 TYR R 297 PHE 0.039 0.002 PHE T 82 TRP 0.029 0.002 TRP P 257 HIS 0.014 0.002 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00418 (41662) covalent geometry : angle 0.73370 (56279) hydrogen bonds : bond 0.05091 ( 2220) hydrogen bonds : angle 5.09163 ( 6594) Misc. bond : bond 0.00468 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 893 time to evaluate : 1.350 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: W 1 MET cc_start: 0.3742 (mtm) cc_final: 0.2253 (mmt) REVERT: V 60 ASP cc_start: 0.6080 (t0) cc_final: 0.5143 (t0) REVERT: V 126 GLN cc_start: 0.6736 (tt0) cc_final: 0.6389 (tt0) REVERT: V 264 GLU cc_start: 0.4378 (tp30) cc_final: 0.4162 (tp30) REVERT: T 81 TYR cc_start: 0.7738 (m-10) cc_final: 0.7450 (m-10) REVERT: T 150 ARG cc_start: 0.7041 (tmm160) cc_final: 0.6509 (ptm-80) REVERT: T 153 MET cc_start: 0.7305 (mmp) cc_final: 0.6311 (mmp) REVERT: T 161 TRP cc_start: 0.6172 (t-100) cc_final: 0.5440 (t-100) REVERT: T 262 LYS cc_start: 0.8226 (mttt) cc_final: 0.6881 (mttm) REVERT: Y 68 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5677 (tp30) REVERT: Z 23 GLN cc_start: 0.4885 (mt0) cc_final: 0.3989 (tp40) REVERT: Z 249 MET cc_start: 0.3823 (mmt) cc_final: 0.3614 (tpp) REVERT: Z 291 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7338 (mt-10) REVERT: Z 312 TYR cc_start: 0.3007 (m-10) cc_final: 0.2766 (m-10) REVERT: Z 389 PHE cc_start: 0.6444 (m-80) cc_final: 0.5905 (m-80) REVERT: Z 404 ASP cc_start: 0.5315 (p0) cc_final: 0.4908 (p0) REVERT: Z 575 MET cc_start: 0.7457 (mtm) cc_final: 0.7149 (mtm) REVERT: Z 734 ASP cc_start: 0.6942 (m-30) cc_final: 0.5252 (t70) REVERT: Z 831 LEU cc_start: 0.8302 (mm) cc_final: 0.7975 (mm) REVERT: N 42 GLU cc_start: 0.6265 (mm-30) cc_final: 0.6056 (tp30) REVERT: N 539 MET cc_start: 0.5340 (ptm) cc_final: 0.5081 (ptm) REVERT: N 605 ILE cc_start: 0.6878 (pt) cc_final: 0.6628 (pt) REVERT: N 627 ILE cc_start: 0.8392 (mt) cc_final: 0.7911 (mm) REVERT: N 680 LYS cc_start: 0.6960 (ptpt) cc_final: 0.6541 (tptt) REVERT: N 706 MET cc_start: 0.4625 (tpp) cc_final: 0.3185 (tmm) REVERT: S 139 HIS cc_start: 0.5081 (m-70) cc_final: 0.4329 (m170) REVERT: S 151 GLU cc_start: 0.4130 (mt-10) cc_final: 0.2869 (mt-10) REVERT: S 215 MET cc_start: 0.7365 (tpt) cc_final: 0.7060 (mmm) REVERT: S 458 GLN cc_start: 0.8333 (mt0) cc_final: 0.8047 (tm-30) REVERT: S 473 ASP cc_start: 0.7946 (t0) cc_final: 0.7706 (t0) REVERT: S 474 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8144 (mm-30) REVERT: S 479 MET cc_start: 0.4674 (tpt) cc_final: 0.3061 (tpt) REVERT: P 24 ILE cc_start: 0.6189 (mt) cc_final: 0.5322 (mm) REVERT: P 290 LEU cc_start: 0.6978 (tp) cc_final: 0.6228 (tp) REVERT: Q 52 ASN cc_start: 0.6661 (t0) cc_final: 0.6076 (t0) REVERT: Q 183 LYS cc_start: 0.8604 (tppt) cc_final: 0.8151 (mmtm) REVERT: R 267 LYS cc_start: 0.7901 (tptp) cc_final: 0.7306 (tptp) REVERT: R 423 LEU cc_start: 0.8065 (mt) cc_final: 0.7526 (tp) REVERT: U 83 ILE cc_start: 0.7357 (mp) cc_final: 0.7085 (mp) REVERT: U 293 GLU cc_start: 0.3395 (tp30) cc_final: 0.3113 (mm-30) REVERT: O 177 GLN cc_start: 0.8305 (pm20) cc_final: 0.8017 (pm20) REVERT: O 288 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7699 (mmm-85) REVERT: O 332 ILE cc_start: 0.7449 (tp) cc_final: 0.6790 (tp) REVERT: O 336 LEU cc_start: 0.4437 (mt) cc_final: 0.4198 (mt) REVERT: O 363 ILE cc_start: 0.5680 (mp) cc_final: 0.5068 (mp) outliers start: 4 outliers final: 0 residues processed: 896 average time/residue: 0.2337 time to fit residues: 348.1081 Evaluate side-chains 688 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 108 optimal weight: 40.0000 chunk 104 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 271 optimal weight: 30.0000 chunk 412 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 473 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 311 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 150 ASN V 186 GLN ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 539 ASN ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 771 HIS Z 871 HIS ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 360 GLN ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 444 HIS N 738 GLN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 283 GLN S 334 HIS S 335 GLN ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 ASN P 286 ASN P 337 HIS P 417 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 308 ASN Q 334 HIS R 397 ASN ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.197768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.181242 restraints weight = 130697.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.178329 restraints weight = 174185.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.176313 restraints weight = 166469.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.176316 restraints weight = 137681.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.176432 restraints weight = 121014.991| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 41665 Z= 0.225 Angle : 0.805 12.081 56279 Z= 0.424 Chirality : 0.045 0.299 6447 Planarity : 0.005 0.094 7202 Dihedral : 5.818 38.735 5504 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.30 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.11), residues: 5108 helix: -0.13 (0.09), residues: 3281 sheet: -1.13 (0.37), residues: 180 loop : -1.93 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 254 TYR 0.050 0.003 TYR R 297 PHE 0.036 0.003 PHE Z 146 TRP 0.033 0.003 TRP S 184 HIS 0.018 0.002 HIS Q 178 Details of bonding type rmsd covalent geometry : bond 0.00484 (41662) covalent geometry : angle 0.80513 (56279) hydrogen bonds : bond 0.05417 ( 2220) hydrogen bonds : angle 5.36324 ( 6594) Misc. bond : bond 0.00461 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 884 time to evaluate : 1.078 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: W 1 MET cc_start: 0.3790 (mtm) cc_final: 0.2095 (mmt) REVERT: V 40 HIS cc_start: 0.7451 (t70) cc_final: 0.7087 (t-170) REVERT: V 250 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7105 (mm-40) REVERT: T 81 TYR cc_start: 0.7477 (m-10) cc_final: 0.7193 (m-10) REVERT: T 121 LYS cc_start: 0.7404 (mttm) cc_final: 0.7052 (mmmt) REVERT: T 150 ARG cc_start: 0.7378 (tmm160) cc_final: 0.6940 (ptt90) REVERT: T 153 MET cc_start: 0.7123 (mmp) cc_final: 0.6183 (mmp) REVERT: Y 68 GLU cc_start: 0.6047 (mm-30) cc_final: 0.5753 (tp30) REVERT: Z 23 GLN cc_start: 0.5081 (mt0) cc_final: 0.4325 (tp40) REVERT: Z 270 SER cc_start: 0.8212 (m) cc_final: 0.7691 (p) REVERT: Z 291 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7388 (mt-10) REVERT: Z 389 PHE cc_start: 0.6518 (m-80) cc_final: 0.5839 (m-80) REVERT: Z 404 ASP cc_start: 0.5370 (p0) cc_final: 0.4980 (p0) REVERT: Z 734 ASP cc_start: 0.6655 (m-30) cc_final: 0.5068 (t70) REVERT: Z 754 LYS cc_start: 0.5961 (tptm) cc_final: 0.5759 (tptm) REVERT: Z 831 LEU cc_start: 0.8333 (mm) cc_final: 0.8006 (mm) REVERT: N 221 ASP cc_start: 0.6020 (m-30) cc_final: 0.4673 (p0) REVERT: N 324 LYS cc_start: 0.5636 (mmmt) cc_final: 0.5047 (mmmt) REVERT: N 438 ASP cc_start: 0.7077 (m-30) cc_final: 0.6638 (t70) REVERT: N 605 ILE cc_start: 0.6908 (pt) cc_final: 0.6698 (pt) REVERT: N 627 ILE cc_start: 0.8479 (mt) cc_final: 0.8031 (mm) REVERT: N 680 LYS cc_start: 0.7034 (ptpt) cc_final: 0.6778 (ptmt) REVERT: N 706 MET cc_start: 0.4747 (tpp) cc_final: 0.3582 (tmm) REVERT: N 770 LYS cc_start: 0.6654 (tptp) cc_final: 0.6414 (tptp) REVERT: S 151 GLU cc_start: 0.4122 (mt-10) cc_final: 0.3086 (mt-10) REVERT: S 189 LEU cc_start: 0.8162 (tp) cc_final: 0.7550 (tp) REVERT: S 193 THR cc_start: 0.8056 (m) cc_final: 0.7807 (m) REVERT: S 239 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7069 (mmm160) REVERT: S 324 MET cc_start: 0.6473 (mtm) cc_final: 0.6036 (mtm) REVERT: S 377 TYR cc_start: 0.5182 (t80) cc_final: 0.4897 (t80) REVERT: S 444 GLU cc_start: 0.6488 (tp30) cc_final: 0.6168 (tp30) REVERT: S 479 MET cc_start: 0.4905 (tpt) cc_final: 0.3318 (tpt) REVERT: P 24 ILE cc_start: 0.6111 (mt) cc_final: 0.5518 (mm) REVERT: P 56 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7163 (tptp) REVERT: P 130 ILE cc_start: 0.6178 (pt) cc_final: 0.5615 (pt) REVERT: P 290 LEU cc_start: 0.7176 (tp) cc_final: 0.6811 (tp) REVERT: P 386 GLN cc_start: 0.8085 (pm20) cc_final: 0.7798 (pm20) REVERT: P 399 ILE cc_start: 0.7715 (mm) cc_final: 0.7499 (mm) REVERT: Q 52 ASN cc_start: 0.6831 (t0) cc_final: 0.6282 (t0) REVERT: Q 183 LYS cc_start: 0.8560 (tppt) cc_final: 0.8248 (tppt) REVERT: Q 325 LEU cc_start: 0.7374 (tt) cc_final: 0.7151 (tt) REVERT: Q 401 GLU cc_start: 0.7737 (tp30) cc_final: 0.7406 (tp30) REVERT: R 389 GLU cc_start: 0.7132 (pm20) cc_final: 0.6914 (pm20) REVERT: R 423 LEU cc_start: 0.8079 (mt) cc_final: 0.7502 (tp) REVERT: U 83 ILE cc_start: 0.7618 (mp) cc_final: 0.7270 (mp) REVERT: U 252 HIS cc_start: 0.7545 (m-70) cc_final: 0.7052 (m90) REVERT: O 177 GLN cc_start: 0.8299 (pm20) cc_final: 0.8014 (pm20) REVERT: O 307 MET cc_start: 0.7991 (tpt) cc_final: 0.7444 (tpt) REVERT: O 363 ILE cc_start: 0.5503 (mp) cc_final: 0.4957 (mp) outliers start: 0 outliers final: 0 residues processed: 884 average time/residue: 0.2177 time to fit residues: 322.3375 Evaluate side-chains 696 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 169 optimal weight: 8.9990 chunk 455 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 423 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 387 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 71 GLN ** T 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 ASN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 435 GLN Z 760 HIS Z 959 HIS ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 444 HIS ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 690 HIS S 244 ASN S 280 ASN S 335 GLN ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 HIS P 337 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 334 HIS R 415 GLN U 192 ASN ** U 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 260 ASN U 262 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS O 374 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.201668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.185564 restraints weight = 129665.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.184235 restraints weight = 153428.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.181686 restraints weight = 134977.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.183052 restraints weight = 112857.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.182711 restraints weight = 83862.065| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.8989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 41665 Z= 0.147 Angle : 0.690 11.592 56279 Z= 0.363 Chirality : 0.042 0.231 6447 Planarity : 0.004 0.058 7202 Dihedral : 5.369 36.861 5504 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.29 % Favored : 94.54 % Rotamer: Outliers : 0.02 % Allowed : 0.87 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.11), residues: 5108 helix: 0.19 (0.09), residues: 3284 sheet: -1.29 (0.37), residues: 183 loop : -1.73 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG S 51 TYR 0.042 0.002 TYR R 297 PHE 0.031 0.002 PHE S 88 TRP 0.039 0.002 TRP S 184 HIS 0.012 0.001 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00316 (41662) covalent geometry : angle 0.69014 (56279) hydrogen bonds : bond 0.04724 ( 2220) hydrogen bonds : angle 5.00768 ( 6594) Misc. bond : bond 0.00457 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 885 time to evaluate : 1.307 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: W 1 MET cc_start: 0.3895 (mtm) cc_final: 0.2256 (mmt) REVERT: W 49 VAL cc_start: 0.4629 (m) cc_final: 0.4217 (p) REVERT: V 209 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6965 (mm-30) REVERT: T 81 TYR cc_start: 0.7433 (m-10) cc_final: 0.7080 (m-10) REVERT: T 121 LYS cc_start: 0.7351 (mttm) cc_final: 0.6974 (mmmt) REVERT: T 150 ARG cc_start: 0.6994 (tmm160) cc_final: 0.6656 (ptm-80) REVERT: T 153 MET cc_start: 0.7135 (mmp) cc_final: 0.6447 (mmp) REVERT: T 161 TRP cc_start: 0.6254 (t-100) cc_final: 0.5635 (t-100) REVERT: T 257 THR cc_start: 0.6235 (t) cc_final: 0.5895 (t) REVERT: Y 29 LEU cc_start: 0.8997 (pp) cc_final: 0.8618 (pp) REVERT: Y 68 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5950 (tp30) REVERT: Z 23 GLN cc_start: 0.4909 (mt0) cc_final: 0.3992 (tp40) REVERT: Z 244 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7239 (mtt180) REVERT: Z 270 SER cc_start: 0.7900 (m) cc_final: 0.7299 (p) REVERT: Z 277 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6480 (mm-30) REVERT: Z 291 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7250 (mt-10) REVERT: Z 381 LEU cc_start: 0.6852 (mt) cc_final: 0.5858 (tt) REVERT: Z 389 PHE cc_start: 0.6216 (m-80) cc_final: 0.5594 (m-80) REVERT: Z 404 ASP cc_start: 0.5458 (p0) cc_final: 0.5129 (p0) REVERT: Z 734 ASP cc_start: 0.6790 (m-30) cc_final: 0.5186 (t70) REVERT: Z 754 LYS cc_start: 0.6043 (tptm) cc_final: 0.5785 (tptm) REVERT: Z 831 LEU cc_start: 0.8075 (mm) cc_final: 0.7783 (mm) REVERT: N 221 ASP cc_start: 0.5792 (m-30) cc_final: 0.4635 (p0) REVERT: N 627 ILE cc_start: 0.8388 (mt) cc_final: 0.7914 (mm) REVERT: N 680 LYS cc_start: 0.7031 (ptpt) cc_final: 0.6510 (mmmt) REVERT: N 696 LYS cc_start: 0.6138 (mppt) cc_final: 0.5920 (mppt) REVERT: N 706 MET cc_start: 0.5171 (tpp) cc_final: 0.4062 (tmm) REVERT: S 51 ARG cc_start: 0.6602 (ttp80) cc_final: 0.6284 (ttp80) REVERT: S 151 GLU cc_start: 0.3733 (mt-10) cc_final: 0.2712 (mt-10) REVERT: S 173 LEU cc_start: 0.7564 (tp) cc_final: 0.7323 (tp) REVERT: S 182 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6417 (mttp) REVERT: S 324 MET cc_start: 0.6020 (mtm) cc_final: 0.5563 (mtm) REVERT: S 377 TYR cc_start: 0.5143 (t80) cc_final: 0.4861 (t80) REVERT: S 479 MET cc_start: 0.4561 (tpt) cc_final: 0.3194 (tpt) REVERT: P 24 ILE cc_start: 0.6149 (mt) cc_final: 0.5665 (mm) REVERT: P 173 MET cc_start: 0.7907 (pmm) cc_final: 0.7406 (pmm) REVERT: Q 325 LEU cc_start: 0.7396 (tt) cc_final: 0.7066 (tt) REVERT: Q 374 GLU cc_start: 0.7678 (pm20) cc_final: 0.7160 (pm20) REVERT: Q 401 GLU cc_start: 0.7336 (tp30) cc_final: 0.6882 (tp30) REVERT: R 423 LEU cc_start: 0.7848 (mt) cc_final: 0.7427 (tp) REVERT: U 24 ARG cc_start: 0.6166 (mmp80) cc_final: 0.5273 (ttm170) REVERT: U 83 ILE cc_start: 0.7548 (mp) cc_final: 0.7190 (mp) REVERT: U 132 LEU cc_start: 0.5269 (mt) cc_final: 0.5048 (mt) REVERT: U 188 ILE cc_start: 0.7862 (mp) cc_final: 0.7317 (mp) REVERT: O 177 GLN cc_start: 0.8267 (pm20) cc_final: 0.8015 (pm20) REVERT: O 307 MET cc_start: 0.7496 (tpt) cc_final: 0.6877 (tpt) REVERT: O 363 ILE cc_start: 0.5180 (mp) cc_final: 0.4706 (mp) outliers start: 1 outliers final: 0 residues processed: 885 average time/residue: 0.2295 time to fit residues: 340.2323 Evaluate side-chains 709 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 301 optimal weight: 7.9990 chunk 412 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 322 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 466 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 488 optimal weight: 20.0000 chunk 311 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 403 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 308 ASN ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 688 ASN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 317 HIS S 334 HIS S 458 GLN ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 286 ASN P 337 HIS P 417 HIS ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 308 ASN ** Q 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN U 223 HIS U 251 ASN ** U 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 260 ASN U 262 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 235 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.199690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.183338 restraints weight = 130626.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.181282 restraints weight = 161876.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.179849 restraints weight = 132151.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.179922 restraints weight = 108512.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.179890 restraints weight = 99602.728| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.9255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41665 Z= 0.171 Angle : 0.726 12.375 56279 Z= 0.382 Chirality : 0.043 0.230 6447 Planarity : 0.005 0.137 7202 Dihedral : 5.420 36.774 5504 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.99 % Favored : 93.79 % Rotamer: Outliers : 0.02 % Allowed : 0.92 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.11), residues: 5108 helix: 0.16 (0.09), residues: 3282 sheet: -1.27 (0.36), residues: 187 loop : -1.73 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 51 TYR 0.047 0.002 TYR R 297 PHE 0.051 0.002 PHE Z 242 TRP 0.048 0.002 TRP S 147 HIS 0.012 0.002 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00370 (41662) covalent geometry : angle 0.72551 (56279) hydrogen bonds : bond 0.04810 ( 2220) hydrogen bonds : angle 5.09064 ( 6594) Misc. bond : bond 0.00502 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 862 time to evaluate : 1.566 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: W 1 MET cc_start: 0.3711 (mtm) cc_final: 0.2052 (mmt) REVERT: V 209 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7093 (mm-30) REVERT: T 153 MET cc_start: 0.7076 (mmp) cc_final: 0.6458 (mmp) REVERT: T 176 SER cc_start: 0.7485 (m) cc_final: 0.7232 (p) REVERT: Y 68 GLU cc_start: 0.6241 (mm-30) cc_final: 0.6010 (tp30) REVERT: Z 23 GLN cc_start: 0.5061 (mt0) cc_final: 0.4255 (tp40) REVERT: Z 244 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7240 (mtt180) REVERT: Z 277 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6517 (mm-30) REVERT: Z 291 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7251 (mt-10) REVERT: Z 381 LEU cc_start: 0.6775 (mt) cc_final: 0.5666 (tt) REVERT: Z 389 PHE cc_start: 0.6463 (m-80) cc_final: 0.5822 (m-80) REVERT: Z 404 ASP cc_start: 0.5366 (p0) cc_final: 0.5136 (p0) REVERT: Z 575 MET cc_start: 0.7328 (mtm) cc_final: 0.6972 (mtm) REVERT: Z 734 ASP cc_start: 0.6723 (m-30) cc_final: 0.5194 (t70) REVERT: Z 754 LYS cc_start: 0.5980 (tptm) cc_final: 0.5738 (tptm) REVERT: Z 831 LEU cc_start: 0.8077 (mm) cc_final: 0.7809 (mm) REVERT: N 221 ASP cc_start: 0.5993 (m-30) cc_final: 0.4636 (p0) REVERT: N 324 LYS cc_start: 0.5395 (mmmt) cc_final: 0.4922 (mmmt) REVERT: N 627 ILE cc_start: 0.8465 (mt) cc_final: 0.8021 (mm) REVERT: N 680 LYS cc_start: 0.7027 (ptpt) cc_final: 0.6405 (mmmt) REVERT: N 706 MET cc_start: 0.5343 (tpp) cc_final: 0.4230 (tmm) REVERT: N 770 LYS cc_start: 0.6526 (tptp) cc_final: 0.6289 (tptp) REVERT: S 151 GLU cc_start: 0.4083 (mt-10) cc_final: 0.2870 (mt-10) REVERT: S 324 MET cc_start: 0.6240 (mtm) cc_final: 0.5794 (mtm) REVERT: S 444 GLU cc_start: 0.6227 (tp30) cc_final: 0.5826 (tp30) REVERT: S 479 MET cc_start: 0.4752 (tpt) cc_final: 0.3324 (tpt) REVERT: P 24 ILE cc_start: 0.5998 (mt) cc_final: 0.5610 (mm) REVERT: P 56 LYS cc_start: 0.7540 (ttpp) cc_final: 0.7126 (tptp) REVERT: Q 113 ASP cc_start: 0.3822 (t70) cc_final: 0.3528 (t70) REVERT: Q 183 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8456 (tppt) REVERT: Q 271 MET cc_start: 0.7902 (ptp) cc_final: 0.7641 (ptp) REVERT: Q 374 GLU cc_start: 0.8015 (pm20) cc_final: 0.7326 (pm20) REVERT: Q 387 TYR cc_start: 0.6099 (p90) cc_final: 0.5810 (p90) REVERT: Q 401 GLU cc_start: 0.7571 (tp30) cc_final: 0.7037 (tp30) REVERT: R 229 LYS cc_start: 0.8311 (pttm) cc_final: 0.8046 (pttm) REVERT: R 423 LEU cc_start: 0.7951 (mt) cc_final: 0.7453 (tp) REVERT: U 83 ILE cc_start: 0.7549 (mp) cc_final: 0.7244 (mp) REVERT: U 132 LEU cc_start: 0.5622 (mt) cc_final: 0.5405 (mt) REVERT: U 252 HIS cc_start: 0.6837 (m-70) cc_final: 0.6628 (m90) REVERT: O 177 GLN cc_start: 0.8310 (pm20) cc_final: 0.8015 (pm20) REVERT: O 307 MET cc_start: 0.7419 (tpt) cc_final: 0.6875 (tpt) REVERT: O 363 ILE cc_start: 0.5215 (mp) cc_final: 0.4862 (mp) REVERT: O 374 ASN cc_start: 0.6755 (t0) cc_final: 0.6215 (t0) outliers start: 1 outliers final: 0 residues processed: 862 average time/residue: 0.2294 time to fit residues: 331.3723 Evaluate side-chains 702 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 257 optimal weight: 30.0000 chunk 278 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 408 optimal weight: 0.4980 chunk 248 optimal weight: 0.0030 chunk 156 optimal weight: 20.0000 chunk 283 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 144 optimal weight: 40.0000 chunk 464 optimal weight: 8.9990 overall best weight: 3.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 GLN ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 688 ASN ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 317 HIS P 337 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 HIS Q 247 HIS Q 308 ASN Q 334 HIS ** R 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 260 ASN U 262 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.200594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.184463 restraints weight = 130952.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.182591 restraints weight = 171079.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.181244 restraints weight = 129045.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.181549 restraints weight = 109072.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.181438 restraints weight = 95462.270| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.9424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41665 Z= 0.162 Angle : 0.724 10.909 56279 Z= 0.380 Chirality : 0.043 0.224 6447 Planarity : 0.005 0.060 7202 Dihedral : 5.365 37.933 5504 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.74 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.11), residues: 5108 helix: 0.13 (0.09), residues: 3270 sheet: -1.36 (0.36), residues: 190 loop : -1.66 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 51 TYR 0.051 0.002 TYR R 297 PHE 0.038 0.002 PHE Z 242 TRP 0.041 0.002 TRP S 184 HIS 0.013 0.001 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00351 (41662) covalent geometry : angle 0.72418 (56279) hydrogen bonds : bond 0.04737 ( 2220) hydrogen bonds : angle 5.06865 ( 6594) Misc. bond : bond 0.00471 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 862 time to evaluate : 1.199 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: W 1 MET cc_start: 0.3720 (mtm) cc_final: 0.2163 (mmt) REVERT: V 103 MET cc_start: 0.7674 (ppp) cc_final: 0.7467 (ppp) REVERT: T 81 TYR cc_start: 0.6942 (m-10) cc_final: 0.6580 (m-10) REVERT: T 153 MET cc_start: 0.7028 (mmp) cc_final: 0.6447 (mmp) REVERT: T 176 SER cc_start: 0.7382 (m) cc_final: 0.7130 (p) REVERT: Y 26 LYS cc_start: 0.7321 (mttp) cc_final: 0.6297 (mmtt) REVERT: Y 68 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5957 (tp30) REVERT: Z 23 GLN cc_start: 0.5059 (mt0) cc_final: 0.4256 (tp40) REVERT: Z 277 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6526 (mm-30) REVERT: Z 381 LEU cc_start: 0.6875 (mt) cc_final: 0.5759 (tt) REVERT: Z 389 PHE cc_start: 0.6353 (m-80) cc_final: 0.5808 (m-80) REVERT: Z 404 ASP cc_start: 0.5060 (p0) cc_final: 0.4685 (p0) REVERT: Z 575 MET cc_start: 0.7064 (mtm) cc_final: 0.6786 (mtm) REVERT: Z 734 ASP cc_start: 0.6462 (m-30) cc_final: 0.4937 (t70) REVERT: Z 754 LYS cc_start: 0.6022 (tptm) cc_final: 0.5769 (tptm) REVERT: Z 831 LEU cc_start: 0.8050 (mm) cc_final: 0.7767 (mm) REVERT: N 221 ASP cc_start: 0.5976 (m-30) cc_final: 0.4652 (p0) REVERT: N 324 LYS cc_start: 0.5475 (mmmt) cc_final: 0.4924 (mmmt) REVERT: N 415 PHE cc_start: 0.5742 (m-80) cc_final: 0.5004 (m-10) REVERT: N 618 ARG cc_start: 0.8270 (mtm180) cc_final: 0.8030 (mtm180) REVERT: N 627 ILE cc_start: 0.8439 (mt) cc_final: 0.8014 (mm) REVERT: N 696 LYS cc_start: 0.6053 (mppt) cc_final: 0.5819 (mppt) REVERT: N 706 MET cc_start: 0.5399 (tpp) cc_final: 0.4296 (tmm) REVERT: N 770 LYS cc_start: 0.6607 (tptp) cc_final: 0.6399 (tptp) REVERT: N 857 TYR cc_start: 0.5678 (m-80) cc_final: 0.5219 (m-10) REVERT: S 189 LEU cc_start: 0.8430 (tp) cc_final: 0.8179 (tp) REVERT: S 215 MET cc_start: 0.6631 (mpp) cc_final: 0.6416 (mpp) REVERT: S 271 ARG cc_start: 0.6279 (mpt90) cc_final: 0.5678 (mmt180) REVERT: S 324 MET cc_start: 0.6227 (mtm) cc_final: 0.5765 (mtt) REVERT: S 444 GLU cc_start: 0.6158 (tp30) cc_final: 0.5807 (tp30) REVERT: S 474 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7888 (pp20) REVERT: S 479 MET cc_start: 0.4208 (tpt) cc_final: 0.2832 (tpt) REVERT: P 56 LYS cc_start: 0.7458 (ttpp) cc_final: 0.6984 (tptp) REVERT: P 160 LEU cc_start: 0.8417 (tp) cc_final: 0.7606 (tp) REVERT: P 186 LEU cc_start: 0.8212 (mp) cc_final: 0.7626 (mt) REVERT: P 427 GLU cc_start: 0.6965 (pp20) cc_final: 0.6655 (tm-30) REVERT: Q 271 MET cc_start: 0.7853 (ptp) cc_final: 0.7471 (ptp) REVERT: Q 371 GLN cc_start: 0.6244 (mm-40) cc_final: 0.5872 (mm-40) REVERT: Q 374 GLU cc_start: 0.8135 (pm20) cc_final: 0.7453 (pm20) REVERT: Q 401 GLU cc_start: 0.7322 (tp30) cc_final: 0.6840 (tp30) REVERT: Q 415 LEU cc_start: 0.8868 (tp) cc_final: 0.8658 (tp) REVERT: R 197 MET cc_start: 0.6262 (ppp) cc_final: 0.5652 (ptt) REVERT: R 423 LEU cc_start: 0.7853 (mt) cc_final: 0.7352 (tp) REVERT: U 84 ASN cc_start: 0.8011 (m-40) cc_final: 0.7808 (m-40) REVERT: O 307 MET cc_start: 0.7424 (tpt) cc_final: 0.6876 (tpt) REVERT: O 363 ILE cc_start: 0.5264 (mp) cc_final: 0.4894 (mp) outliers start: 0 outliers final: 0 residues processed: 862 average time/residue: 0.2285 time to fit residues: 328.3207 Evaluate side-chains 716 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 716 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 229 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 439 optimal weight: 6.9990 chunk 383 optimal weight: 0.9980 chunk 498 optimal weight: 9.9990 chunk 474 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 492 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 688 ASN S 139 HIS ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 317 HIS S 334 HIS S 472 HIS P 78 GLN P 337 HIS P 417 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 HIS Q 308 ASN R 132 GLN ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 260 ASN U 262 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.201384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.180801 restraints weight = 129610.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.179127 restraints weight = 104280.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.179535 restraints weight = 92416.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.179804 restraints weight = 79941.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.179956 restraints weight = 70892.618| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.9510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41665 Z= 0.149 Angle : 0.709 11.764 56279 Z= 0.374 Chirality : 0.042 0.223 6447 Planarity : 0.005 0.084 7202 Dihedral : 5.245 38.233 5504 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.91 % Favored : 93.87 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.12), residues: 5108 helix: 0.19 (0.09), residues: 3276 sheet: -1.17 (0.37), residues: 184 loop : -1.63 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG O 135 TYR 0.020 0.002 TYR Z 358 PHE 0.052 0.002 PHE Z 242 TRP 0.038 0.002 TRP S 184 HIS 0.013 0.001 HIS O 235 Details of bonding type rmsd covalent geometry : bond 0.00322 (41662) covalent geometry : angle 0.70891 (56279) hydrogen bonds : bond 0.04539 ( 2220) hydrogen bonds : angle 5.03298 ( 6594) Misc. bond : bond 0.00459 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9885.54 seconds wall clock time: 170 minutes 38.45 seconds (10238.45 seconds total)