Starting phenix.real_space_refine on Fri Feb 6 12:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efv_47981/02_2026/9efv_47981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efv_47981/02_2026/9efv_47981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9efv_47981/02_2026/9efv_47981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efv_47981/02_2026/9efv_47981_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9efv_47981/02_2026/9efv_47981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efv_47981/02_2026/9efv_47981.map" } resolution = 3.03 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= 0.008 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 S 142 5.16 5 C 15875 2.51 5 N 4259 2.21 5 O 4665 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24947 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3243 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 8, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3342 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3222 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain: "D" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3105 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "E" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2215 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 3 Chain: "F" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2201 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3225 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 10, 'TRANS': 389} Chain breaks: 1 Chain: "K" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 693 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain breaks: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' ZN': 1, '6LT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24419 SG CYS K 42 51.442 94.271 74.904 1.00 31.43 S ATOM 24438 SG CYS K 45 50.849 97.359 77.123 1.00 34.81 S ATOM 24695 SG CYS K 83 53.559 94.827 78.123 1.00 21.86 S ATOM 24624 SG CYS K 75 52.395 83.477 68.569 1.00 17.99 S ATOM 24791 SG CYS K 94 50.917 84.206 71.751 1.00 16.61 S ATOM 24505 SG CYS K 53 56.528 98.347 79.375 1.00 47.72 S ATOM 24528 SG CYS K 56 59.894 100.160 79.254 1.00 51.27 S ATOM 24574 SG CYS K 68 58.096 98.993 75.904 1.00 40.03 S Time building chain proxies: 4.00, per 1000 atoms: 0.16 Number of scatterers: 24947 At special positions: 0 Unit cell: (124.05, 167.054, 205.923, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 142 16.00 F 2 9.00 O 4665 8.00 N 4259 7.00 C 15875 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 140 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 138 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 80 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 45 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 83 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 42 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 94 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 75 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 77 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 56 " Number of angles added : 6 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5950 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 10 sheets defined 66.2% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.675A pdb=" N ALA A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.787A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.690A pdb=" N LEU A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.651A pdb=" N PHE A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 87 " --> pdb=" O ARG A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 87' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.673A pdb=" N HIS A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 removed outlier: 4.027A pdb=" N THR A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 4.181A pdb=" N LYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 145' Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.045A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 removed outlier: 3.671A pdb=" N ASP A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.540A pdb=" N LYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS A 184 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.662A pdb=" N CYS A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.510A pdb=" N SER A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.162A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.771A pdb=" N LEU A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.600A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.986A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.334A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 379 Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 430 through 462 removed outlier: 3.766A pdb=" N ALA A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.529A pdb=" N TYR B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.788A pdb=" N SER B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.805A pdb=" N LYS B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.569A pdb=" N MET B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 4.142A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.550A pdb=" N ILE B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.907A pdb=" N LYS B 123 " --> pdb=" O SER B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 143 removed outlier: 4.127A pdb=" N GLU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 167 through 177 removed outlier: 4.029A pdb=" N ILE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 Processing helix chain 'B' and resid 211 through 223 removed outlier: 3.700A pdb=" N LYS B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.516A pdb=" N GLY B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.736A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.796A pdb=" N SER B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.702A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.570A pdb=" N PHE C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 12 " --> pdb=" O PHE C 8 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 31 through 37 Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 96 through 114 removed outlier: 3.776A pdb=" N ARG C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.744A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.603A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.547A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 removed outlier: 3.556A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.565A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 293 through 311 removed outlier: 3.647A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 399 removed outlier: 3.805A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.913A pdb=" N ARG D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 3.874A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.773A pdb=" N THR D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 77 through 93 removed outlier: 4.537A pdb=" N GLU D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 99 through 117 removed outlier: 3.729A pdb=" N VAL D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 140 through 158 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.747A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 171 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.653A pdb=" N GLN D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 236 removed outlier: 3.616A pdb=" N GLU D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 253 through 258 removed outlier: 4.111A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.575A pdb=" N GLN D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 278 " --> pdb=" O GLY D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 278' Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.949A pdb=" N MET D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.608A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 316 removed outlier: 5.062A pdb=" N ILE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 334 through 343 Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.882A pdb=" N GLN D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 399 " --> pdb=" O TRP D 395 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET D 400 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 58 through 71 Processing helix chain 'E' and resid 114 through 122 removed outlier: 4.043A pdb=" N ALA E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 210 through 217 Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 239 through 244 removed outlier: 4.194A pdb=" N ASN E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 281 removed outlier: 3.814A pdb=" N GLU E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 329 Processing helix chain 'F' and resid 44 through 63 removed outlier: 3.949A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 116 removed outlier: 4.168A pdb=" N TYR F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 115 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.716A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 204 Processing helix chain 'F' and resid 215 through 248 removed outlier: 3.838A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 272 through 311 removed outlier: 4.468A pdb=" N GLY F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 removed outlier: 3.811A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 18 " --> pdb=" O GLN G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 60 through 72 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.700A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 221 Processing helix chain 'H' and resid 12 through 26 removed outlier: 3.650A pdb=" N LEU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 17 " --> pdb=" O PHE H 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 47 removed outlier: 3.556A pdb=" N GLY H 38 " --> pdb=" O PRO H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 68 through 83 removed outlier: 4.256A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 96 removed outlier: 3.704A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 138 removed outlier: 3.510A pdb=" N ALA H 135 " --> pdb=" O ASP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 151 removed outlier: 3.691A pdb=" N ILE H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU H 150 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'I' and resid 22 through 34 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'J' and resid 363 through 385 removed outlier: 3.602A pdb=" N VAL J 367 " --> pdb=" O PRO J 363 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN J 368 " --> pdb=" O LYS J 364 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL J 370 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU J 371 " --> pdb=" O VAL J 367 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP J 372 " --> pdb=" O GLN J 368 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL J 373 " --> pdb=" O THR J 369 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS J 374 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS J 375 " --> pdb=" O LEU J 371 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 376 " --> pdb=" O ASP J 372 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR J 377 " --> pdb=" O VAL J 373 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN J 378 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA J 379 " --> pdb=" O LYS J 375 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU J 380 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL J 381 " --> pdb=" O TYR J 377 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET J 382 " --> pdb=" O ASN J 378 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER J 383 " --> pdb=" O ALA J 379 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA J 384 " --> pdb=" O LEU J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 405 removed outlier: 3.676A pdb=" N LEU J 395 " --> pdb=" O PHE J 391 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP J 396 " --> pdb=" O VAL J 392 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS J 397 " --> pdb=" O ALA J 393 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA J 398 " --> pdb=" O ALA J 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS J 399 " --> pdb=" O LEU J 395 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY J 400 " --> pdb=" O ASP J 396 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG J 401 " --> pdb=" O LYS J 397 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN J 405 " --> pdb=" O ARG J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 410 removed outlier: 3.792A pdb=" N THR J 409 " --> pdb=" O ASN J 406 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS J 410 " --> pdb=" O ALA J 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 406 through 410' Processing helix chain 'J' and resid 417 through 419 No H-bonds generated for 'chain 'J' and resid 417 through 419' Processing helix chain 'J' and resid 420 through 431 removed outlier: 3.999A pdb=" N ARG J 424 " --> pdb=" O GLU J 420 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR J 425 " --> pdb=" O LEU J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 454 removed outlier: 3.793A pdb=" N THR J 445 " --> pdb=" O GLU J 441 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN J 448 " --> pdb=" O ASP J 444 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL J 449 " --> pdb=" O THR J 445 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL J 451 " --> pdb=" O ASN J 447 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS J 454 " --> pdb=" O MET J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 458 through 476 removed outlier: 4.087A pdb=" N PHE J 462 " --> pdb=" O ASP J 458 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS J 476 " --> pdb=" O LYS J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 481 through 496 removed outlier: 3.597A pdb=" N GLN J 494 " --> pdb=" O SER J 490 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA J 495 " --> pdb=" O LYS J 491 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS J 496 " --> pdb=" O LEU J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 501 through 527 removed outlier: 3.709A pdb=" N ARG J 506 " --> pdb=" O SER J 502 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE J 511 " --> pdb=" O MET J 507 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY J 512 " --> pdb=" O PHE J 508 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN J 527 " --> pdb=" O LYS J 523 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 573 Processing helix chain 'J' and resid 582 through 585 Processing helix chain 'J' and resid 605 through 613 Processing helix chain 'J' and resid 614 through 616 No H-bonds generated for 'chain 'J' and resid 614 through 616' Processing helix chain 'J' and resid 622 through 630 Processing helix chain 'J' and resid 632 through 646 Processing helix chain 'J' and resid 709 through 722 removed outlier: 3.690A pdb=" N ALA J 713 " --> pdb=" O LEU J 709 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET J 721 " --> pdb=" O ARG J 717 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG J 722 " --> pdb=" O ILE J 718 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 734 removed outlier: 4.667A pdb=" N GLY J 732 " --> pdb=" O GLN J 728 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU J 733 " --> pdb=" O GLN J 729 " (cutoff:3.500A) Processing helix chain 'J' and resid 745 through 759 removed outlier: 3.538A pdb=" N ILE J 749 " --> pdb=" O ARG J 745 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS J 759 " --> pdb=" O ILE J 755 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.306A pdb=" N THR K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 418 removed outlier: 7.107A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 316 through 318 removed outlier: 7.540A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET H 161 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 166 through 168 removed outlier: 7.831A pdb=" N MET E 78 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA E 97 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 83 through 87 removed outlier: 4.446A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 123 through 127 removed outlier: 6.654A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.673A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 12 through 16 Processing sheet with id=AA8, first strand: chain 'J' and resid 534 through 538 removed outlier: 5.865A pdb=" N VAL K 24 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL J 591 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR J 599 " --> pdb=" O THR J 592 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 619 through 621 removed outlier: 3.658A pdb=" N VAL J 650 " --> pdb=" O LYS J 670 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 70 through 71 1303 hydrogen bonds defined for protein. 3828 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: 3.84 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5746 1.33 - 1.45: 5066 1.45 - 1.58: 14350 1.58 - 1.70: 0 1.70 - 1.82: 227 Bond restraints: 25389 Sorted by residual: bond pdb=" CA ASP F 273 " pdb=" C ASP F 273 " ideal model delta sigma weight residual 1.522 1.490 0.031 1.37e-02 5.33e+03 5.28e+00 bond pdb=" C LEU F 270 " pdb=" O LEU F 270 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.26e-02 6.30e+03 4.58e+00 bond pdb=" CA SER F 271 " pdb=" C SER F 271 " ideal model delta sigma weight residual 1.526 1.509 0.017 1.23e-02 6.61e+03 2.00e+00 bond pdb=" C ASP F 273 " pdb=" N LYS F 274 " ideal model delta sigma weight residual 1.334 1.314 0.020 1.43e-02 4.89e+03 1.99e+00 bond pdb=" C VAL F 269 " pdb=" O VAL F 269 " ideal model delta sigma weight residual 1.239 1.220 0.019 1.34e-02 5.57e+03 1.97e+00 ... (remaining 25384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 33918 2.30 - 4.59: 290 4.59 - 6.89: 46 6.89 - 9.18: 8 9.18 - 11.48: 5 Bond angle restraints: 34267 Sorted by residual: angle pdb=" N LEU E 256 " pdb=" CA LEU E 256 " pdb=" C LEU E 256 " ideal model delta sigma weight residual 114.56 108.35 6.21 1.27e+00 6.20e-01 2.39e+01 angle pdb=" C ARG F 79 " pdb=" N ASN F 80 " pdb=" CA ASN F 80 " ideal model delta sigma weight residual 121.81 132.11 -10.30 2.16e+00 2.14e-01 2.27e+01 angle pdb=" C PHE C 403 " pdb=" N VAL C 404 " pdb=" CA VAL C 404 " ideal model delta sigma weight residual 121.97 129.74 -7.77 1.80e+00 3.09e-01 1.86e+01 angle pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " ideal model delta sigma weight residual 112.70 124.18 -11.48 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C CYS K 53 " pdb=" N ILE K 54 " pdb=" CA ILE K 54 " ideal model delta sigma weight residual 121.97 128.82 -6.85 1.80e+00 3.09e-01 1.45e+01 ... (remaining 34262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12998 17.98 - 35.95: 1870 35.95 - 53.93: 519 53.93 - 71.90: 118 71.90 - 89.88: 46 Dihedral angle restraints: 15551 sinusoidal: 6391 harmonic: 9160 Sorted by residual: dihedral pdb=" CA HIS F 160 " pdb=" C HIS F 160 " pdb=" N THR F 161 " pdb=" CA THR F 161 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ILE D 330 " pdb=" C ILE D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA VAL F 165 " pdb=" C VAL F 165 " pdb=" N SER F 166 " pdb=" CA SER F 166 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 15548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3412 0.058 - 0.115: 429 0.115 - 0.173: 24 0.173 - 0.231: 1 0.231 - 0.288: 1 Chirality restraints: 3867 Sorted by residual: chirality pdb=" CB VAL C 404 " pdb=" CA VAL C 404 " pdb=" CG1 VAL C 404 " pdb=" CG2 VAL C 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA LEU F 270 " pdb=" N LEU F 270 " pdb=" C LEU F 270 " pdb=" CB LEU F 270 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA ILE F 175 " pdb=" N ILE F 175 " pdb=" C ILE F 175 " pdb=" CB ILE F 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 3864 not shown) Planarity restraints: 4369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 132 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO F 133 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 133 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 133 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 184 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C GLY E 184 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY E 184 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA E 185 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 293 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLY F 293 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY F 293 " -0.012 2.00e-02 2.50e+03 pdb=" N THR F 294 " -0.011 2.00e-02 2.50e+03 ... (remaining 4366 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 7 2.40 - 3.03: 14150 3.03 - 3.65: 36887 3.65 - 4.28: 54374 4.28 - 4.90: 90605 Nonbonded interactions: 196023 Sorted by model distance: nonbonded pdb=" N4 6LT E 401 " pdb="ZN ZN E 402 " model vdw 1.780 2.310 nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 402 " model vdw 1.983 2.230 nonbonded pdb=" OD2 ASP K 97 " pdb="ZN ZN K 202 " model vdw 1.983 2.230 nonbonded pdb=" OD1 ASP K 97 " pdb="ZN ZN K 202 " model vdw 2.006 2.230 nonbonded pdb=" CG ASP K 97 " pdb="ZN ZN K 202 " model vdw 2.106 2.460 ... (remaining 196018 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.330 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 0.003 0.099 25403 Z= 0.133 Angle : 0.555 11.479 34273 Z= 0.295 Chirality : 0.038 0.288 3867 Planarity : 0.003 0.048 4369 Dihedral : 18.638 89.880 9601 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.97 % Favored : 94.77 % Rotamer: Outliers : 1.28 % Allowed : 25.60 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.19 (0.15), residues: 3059 helix: 0.68 (0.12), residues: 1804 sheet: -1.48 (0.47), residues: 123 loop : -1.20 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 115 TYR 0.017 0.001 TYR A 172 PHE 0.021 0.001 PHE J 498 TRP 0.018 0.001 TRP E 246 HIS 0.005 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00243 (25389) covalent geometry : angle 0.55400 (34267) hydrogen bonds : bond 0.23442 ( 1303) hydrogen bonds : angle 6.47132 ( 3828) metal coordination : bond 0.00670 ( 13) metal coordination : angle 2.70985 ( 6) Misc. bond : bond 0.09923 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: -0.0013 (ppp) cc_final: -0.1891 (ptp) REVERT: A 214 ASN cc_start: 0.6807 (p0) cc_final: 0.6590 (p0) REVERT: C 21 MET cc_start: 0.5889 (tpp) cc_final: 0.5678 (mmt) REVERT: F 79 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6491 (tpm170) outliers start: 35 outliers final: 29 residues processed: 280 average time/residue: 0.1566 time to fit residues: 68.9672 Evaluate side-chains 273 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 243 ASN Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 643 LEU Chi-restraints excluded: chain J residue 757 ILE Chi-restraints excluded: chain K residue 42 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN C 218 HIS C 327 GLN D 41 GLN I 49 GLN J 505 GLN K 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.111359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.085947 restraints weight = 69750.565| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.23 r_work: 0.3298 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25403 Z= 0.144 Angle : 0.554 8.883 34273 Z= 0.289 Chirality : 0.039 0.281 3867 Planarity : 0.004 0.051 4369 Dihedral : 5.376 75.370 3431 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 2.52 % Allowed : 24.07 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.38 (0.15), residues: 3059 helix: 1.20 (0.12), residues: 1867 sheet: -1.50 (0.48), residues: 120 loop : -1.21 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 64 TYR 0.017 0.001 TYR A 172 PHE 0.020 0.001 PHE J 566 TRP 0.017 0.001 TRP E 246 HIS 0.007 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00321 (25389) covalent geometry : angle 0.55294 (34267) hydrogen bonds : bond 0.04588 ( 1303) hydrogen bonds : angle 4.33789 ( 3828) metal coordination : bond 0.00888 ( 13) metal coordination : angle 2.54972 ( 6) Misc. bond : bond 0.00316 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 264 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: -0.0984 (ppp) cc_final: -0.1695 (ptp) REVERT: A 386 MET cc_start: 0.8853 (mtp) cc_final: 0.8607 (mtm) REVERT: B 163 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: B 331 LYS cc_start: 0.8284 (mttp) cc_final: 0.8072 (mmtm) REVERT: C 131 MET cc_start: 0.8392 (ttt) cc_final: 0.8056 (ttt) REVERT: F 79 ARG cc_start: 0.7559 (mtp85) cc_final: 0.6677 (tpm170) REVERT: F 88 GLU cc_start: 0.6419 (tt0) cc_final: 0.6177 (tt0) REVERT: G 203 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7466 (t0) REVERT: H 49 ASP cc_start: 0.8182 (t0) cc_final: 0.7833 (t0) REVERT: H 142 GLU cc_start: 0.7295 (mp0) cc_final: 0.7002 (mp0) REVERT: H 160 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7897 (mmp80) REVERT: K 37 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6804 (mp) outliers start: 69 outliers final: 42 residues processed: 319 average time/residue: 0.1596 time to fit residues: 79.6839 Evaluate side-chains 297 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 483 ASP Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 735 LEU Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 292 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 126 optimal weight: 0.0370 chunk 153 optimal weight: 3.9990 chunk 299 optimal weight: 0.6980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 79 ASN B 223 HIS C 218 HIS C 265 GLN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.111249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086012 restraints weight = 69597.370| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.19 r_work: 0.3300 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25403 Z= 0.114 Angle : 0.496 8.859 34273 Z= 0.259 Chirality : 0.038 0.307 3867 Planarity : 0.003 0.047 4369 Dihedral : 4.561 59.535 3399 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.13 % Favored : 94.61 % Rotamer: Outliers : 2.78 % Allowed : 24.10 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.68 (0.16), residues: 3059 helix: 1.50 (0.12), residues: 1884 sheet: -1.53 (0.48), residues: 122 loop : -1.24 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 64 TYR 0.020 0.001 TYR A 172 PHE 0.018 0.001 PHE J 566 TRP 0.016 0.001 TRP E 246 HIS 0.007 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00252 (25389) covalent geometry : angle 0.49592 (34267) hydrogen bonds : bond 0.04020 ( 1303) hydrogen bonds : angle 3.98733 ( 3828) metal coordination : bond 0.00342 ( 13) metal coordination : angle 1.45226 ( 6) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 260 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: -0.1072 (ppp) cc_final: -0.1776 (ptp) REVERT: A 249 LEU cc_start: 0.7326 (mm) cc_final: 0.7028 (mp) REVERT: B 163 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: B 331 LYS cc_start: 0.8314 (mttp) cc_final: 0.8076 (mmtm) REVERT: C 131 MET cc_start: 0.8457 (ttt) cc_final: 0.8123 (ttt) REVERT: F 79 ARG cc_start: 0.7631 (mtp85) cc_final: 0.6687 (tpm170) REVERT: G 203 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7558 (t0) REVERT: H 49 ASP cc_start: 0.8145 (t0) cc_final: 0.7779 (t0) outliers start: 76 outliers final: 47 residues processed: 322 average time/residue: 0.1595 time to fit residues: 80.9954 Evaluate side-chains 297 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 184 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 169 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 249 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS C 265 GLN C 320 GLN F 303 ASN K 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.109911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084403 restraints weight = 69219.721| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.20 r_work: 0.3259 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25403 Z= 0.160 Angle : 0.532 8.164 34273 Z= 0.276 Chirality : 0.040 0.343 3867 Planarity : 0.004 0.047 4369 Dihedral : 4.532 59.373 3394 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.66 % Favored : 94.08 % Rotamer: Outliers : 3.04 % Allowed : 23.96 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.74 (0.16), residues: 3059 helix: 1.60 (0.12), residues: 1875 sheet: -1.43 (0.47), residues: 128 loop : -1.30 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 115 TYR 0.018 0.001 TYR C 185 PHE 0.022 0.001 PHE J 566 TRP 0.016 0.001 TRP E 246 HIS 0.006 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00379 (25389) covalent geometry : angle 0.53110 (34267) hydrogen bonds : bond 0.03839 ( 1303) hydrogen bonds : angle 3.93036 ( 3828) metal coordination : bond 0.00874 ( 13) metal coordination : angle 1.78876 ( 6) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 258 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: -0.0975 (ppp) cc_final: -0.1662 (ptp) REVERT: A 386 MET cc_start: 0.8804 (mtm) cc_final: 0.8593 (mtt) REVERT: B 100 ARG cc_start: 0.7604 (tpt-90) cc_final: 0.7283 (tpt-90) REVERT: B 163 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: B 331 LYS cc_start: 0.8315 (mttp) cc_final: 0.8033 (mmtm) REVERT: F 79 ARG cc_start: 0.7599 (mtp85) cc_final: 0.6724 (tpm170) REVERT: F 84 MET cc_start: 0.8533 (mtt) cc_final: 0.8310 (mtt) REVERT: F 88 GLU cc_start: 0.5993 (tt0) cc_final: 0.5698 (tt0) REVERT: G 203 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7557 (t0) REVERT: H 49 ASP cc_start: 0.8165 (t0) cc_final: 0.7778 (t0) REVERT: J 515 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7831 (ttpt) REVERT: K 37 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6692 (mp) outliers start: 83 outliers final: 61 residues processed: 327 average time/residue: 0.1589 time to fit residues: 81.0684 Evaluate side-chains 309 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 735 LEU Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 746 VAL Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 3 optimal weight: 0.4980 chunk 216 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 291 optimal weight: 0.0870 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS C 265 GLN K 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.109582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084148 restraints weight = 68757.606| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.16 r_work: 0.3255 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25403 Z= 0.150 Angle : 0.532 8.614 34273 Z= 0.277 Chirality : 0.040 0.354 3867 Planarity : 0.003 0.046 4369 Dihedral : 4.527 58.833 3390 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.21 % Rotamer: Outliers : 3.00 % Allowed : 24.10 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.77 (0.16), residues: 3059 helix: 1.63 (0.12), residues: 1878 sheet: -1.04 (0.48), residues: 133 loop : -1.37 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 115 TYR 0.017 0.001 TYR A 172 PHE 0.042 0.001 PHE K 81 TRP 0.015 0.001 TRP E 246 HIS 0.004 0.001 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00353 (25389) covalent geometry : angle 0.53147 (34267) hydrogen bonds : bond 0.03663 ( 1303) hydrogen bonds : angle 3.85085 ( 3828) metal coordination : bond 0.00647 ( 13) metal coordination : angle 1.74006 ( 6) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 255 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.7380 (mm) cc_final: 0.7126 (mp) REVERT: B 163 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: F 79 ARG cc_start: 0.7613 (mtp85) cc_final: 0.6641 (tpm170) REVERT: F 88 GLU cc_start: 0.5973 (tt0) cc_final: 0.5569 (tt0) REVERT: F 160 HIS cc_start: 0.7216 (p-80) cc_final: 0.6981 (p-80) REVERT: F 186 LEU cc_start: 0.6970 (mt) cc_final: 0.6699 (mm) REVERT: G 203 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7570 (t0) REVERT: H 49 ASP cc_start: 0.8165 (t0) cc_final: 0.7777 (t0) REVERT: J 515 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7860 (ttpt) REVERT: K 37 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6706 (mp) outliers start: 82 outliers final: 59 residues processed: 320 average time/residue: 0.1590 time to fit residues: 79.7541 Evaluate side-chains 310 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 746 VAL Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 191 optimal weight: 0.0020 chunk 75 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 302 optimal weight: 0.1980 chunk 194 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS C 265 GLN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.110639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085401 restraints weight = 69292.063| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.38 r_work: 0.3269 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25403 Z= 0.103 Angle : 0.500 9.317 34273 Z= 0.261 Chirality : 0.038 0.315 3867 Planarity : 0.003 0.046 4369 Dihedral : 4.399 58.826 3390 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 2.71 % Allowed : 24.32 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.92 (0.16), residues: 3059 helix: 1.75 (0.12), residues: 1879 sheet: -0.96 (0.49), residues: 128 loop : -1.32 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 64 TYR 0.014 0.001 TYR A 172 PHE 0.028 0.001 PHE K 81 TRP 0.015 0.001 TRP E 246 HIS 0.006 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00226 (25389) covalent geometry : angle 0.49992 (34267) hydrogen bonds : bond 0.03265 ( 1303) hydrogen bonds : angle 3.72270 ( 3828) metal coordination : bond 0.00341 ( 13) metal coordination : angle 1.17655 ( 6) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 252 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: B 289 SER cc_start: 0.6093 (OUTLIER) cc_final: 0.5805 (p) REVERT: C 271 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8319 (t0) REVERT: F 79 ARG cc_start: 0.7614 (mtp85) cc_final: 0.6619 (tpm170) REVERT: F 88 GLU cc_start: 0.6009 (tt0) cc_final: 0.5597 (tt0) REVERT: F 186 LEU cc_start: 0.6741 (mt) cc_final: 0.6475 (mm) REVERT: G 203 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7710 (t0) REVERT: H 49 ASP cc_start: 0.8189 (t0) cc_final: 0.7810 (t0) REVERT: I 54 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7304 (tptp) REVERT: J 515 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7774 (ttpt) outliers start: 74 outliers final: 50 residues processed: 313 average time/residue: 0.1651 time to fit residues: 82.3307 Evaluate side-chains 302 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 762 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 215 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN C 92 HIS C 218 HIS C 265 GLN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.110182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085071 restraints weight = 69117.298| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.16 r_work: 0.3279 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25403 Z= 0.111 Angle : 0.506 12.027 34273 Z= 0.261 Chirality : 0.038 0.311 3867 Planarity : 0.003 0.045 4369 Dihedral : 4.380 59.164 3390 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.30 % Favored : 94.44 % Rotamer: Outliers : 2.89 % Allowed : 24.03 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.94 (0.16), residues: 3059 helix: 1.77 (0.12), residues: 1879 sheet: -0.92 (0.50), residues: 128 loop : -1.32 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 64 TYR 0.013 0.001 TYR A 172 PHE 0.023 0.001 PHE K 81 TRP 0.015 0.001 TRP E 246 HIS 0.006 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00253 (25389) covalent geometry : angle 0.50564 (34267) hydrogen bonds : bond 0.03253 ( 1303) hydrogen bonds : angle 3.68067 ( 3828) metal coordination : bond 0.00572 ( 13) metal coordination : angle 1.12855 ( 6) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.6267 (m90) REVERT: B 163 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: B 289 SER cc_start: 0.6055 (OUTLIER) cc_final: 0.5785 (p) REVERT: C 271 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8324 (t0) REVERT: F 79 ARG cc_start: 0.7576 (mtp85) cc_final: 0.6600 (tpm170) REVERT: F 88 GLU cc_start: 0.5884 (tt0) cc_final: 0.5511 (tt0) REVERT: F 186 LEU cc_start: 0.6839 (mt) cc_final: 0.6579 (mm) REVERT: G 203 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7985 (t0) REVERT: H 49 ASP cc_start: 0.8170 (t0) cc_final: 0.7798 (t0) REVERT: I 54 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7311 (tptp) REVERT: J 515 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7812 (ttpt) REVERT: K 37 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6603 (mp) outliers start: 79 outliers final: 59 residues processed: 313 average time/residue: 0.1650 time to fit residues: 82.0791 Evaluate side-chains 311 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 735 LEU Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 762 LEU Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 278 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 287 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.109642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084558 restraints weight = 69444.307| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.18 r_work: 0.3259 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25403 Z= 0.132 Angle : 0.531 11.012 34273 Z= 0.274 Chirality : 0.039 0.305 3867 Planarity : 0.003 0.045 4369 Dihedral : 4.444 59.098 3390 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.62 % Favored : 94.12 % Rotamer: Outliers : 2.82 % Allowed : 24.21 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.88 (0.16), residues: 3059 helix: 1.69 (0.12), residues: 1897 sheet: -0.83 (0.50), residues: 126 loop : -1.35 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 64 TYR 0.015 0.001 TYR C 185 PHE 0.020 0.001 PHE K 81 TRP 0.015 0.001 TRP E 246 HIS 0.008 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00311 (25389) covalent geometry : angle 0.53043 (34267) hydrogen bonds : bond 0.03362 ( 1303) hydrogen bonds : angle 3.71581 ( 3828) metal coordination : bond 0.00495 ( 13) metal coordination : angle 1.70941 ( 6) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 250 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 TYR cc_start: 0.8149 (m-80) cc_final: 0.7943 (m-80) REVERT: B 163 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: B 289 SER cc_start: 0.6140 (OUTLIER) cc_final: 0.5861 (p) REVERT: C 271 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8333 (t0) REVERT: C 380 MET cc_start: 0.8550 (mtp) cc_final: 0.8330 (mtp) REVERT: F 79 ARG cc_start: 0.7601 (mtp85) cc_final: 0.6719 (tpm170) REVERT: F 88 GLU cc_start: 0.5966 (tt0) cc_final: 0.5554 (tt0) REVERT: F 154 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8685 (tm) REVERT: F 186 LEU cc_start: 0.6999 (mt) cc_final: 0.6749 (mm) REVERT: G 203 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7977 (t0) REVERT: H 49 ASP cc_start: 0.8165 (t0) cc_final: 0.7802 (t0) REVERT: I 54 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7299 (tptp) REVERT: J 515 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7808 (ttpt) REVERT: K 37 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6554 (mp) outliers start: 77 outliers final: 60 residues processed: 316 average time/residue: 0.1570 time to fit residues: 78.9913 Evaluate side-chains 310 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 242 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 762 LEU Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 263 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 218 optimal weight: 0.4980 chunk 246 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 300 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS C 265 GLN F 80 ASN I 40 GLN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.109863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084886 restraints weight = 69048.641| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.14 r_work: 0.3276 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25403 Z= 0.111 Angle : 0.523 11.948 34273 Z= 0.269 Chirality : 0.038 0.309 3867 Planarity : 0.003 0.046 4369 Dihedral : 4.410 59.154 3390 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.33 % Favored : 94.38 % Rotamer: Outliers : 2.82 % Allowed : 24.21 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.97 (0.16), residues: 3059 helix: 1.78 (0.12), residues: 1877 sheet: -0.89 (0.49), residues: 128 loop : -1.29 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 64 TYR 0.012 0.001 TYR E 228 PHE 0.024 0.001 PHE J 498 TRP 0.014 0.001 TRP E 246 HIS 0.008 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00252 (25389) covalent geometry : angle 0.52284 (34267) hydrogen bonds : bond 0.03189 ( 1303) hydrogen bonds : angle 3.67312 ( 3828) metal coordination : bond 0.00403 ( 13) metal coordination : angle 1.20613 ( 6) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 244 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: -0.1083 (ppp) cc_final: -0.1747 (ptp) REVERT: A 357 TYR cc_start: 0.8164 (m-80) cc_final: 0.7958 (m-80) REVERT: B 163 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: B 167 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8293 (ptpp) REVERT: B 289 SER cc_start: 0.6055 (OUTLIER) cc_final: 0.5791 (p) REVERT: C 271 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8336 (t0) REVERT: D 118 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7374 (tp30) REVERT: F 79 ARG cc_start: 0.7658 (mtp85) cc_final: 0.6469 (tpm170) REVERT: F 88 GLU cc_start: 0.5883 (tt0) cc_final: 0.5485 (tt0) REVERT: F 186 LEU cc_start: 0.6876 (mt) cc_final: 0.6633 (mm) REVERT: G 203 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8007 (t0) REVERT: H 49 ASP cc_start: 0.8145 (t0) cc_final: 0.7802 (t0) REVERT: I 54 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7296 (tptp) REVERT: J 463 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: J 515 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7824 (ttpt) REVERT: K 26 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7767 (mtpp) REVERT: K 37 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6549 (mp) outliers start: 77 outliers final: 61 residues processed: 308 average time/residue: 0.1616 time to fit residues: 79.0139 Evaluate side-chains 310 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 463 GLN Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 762 LEU Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 141 optimal weight: 0.0570 chunk 212 optimal weight: 0.4980 chunk 279 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS C 265 GLN I 39 GLN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.109484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084403 restraints weight = 69300.602| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.19 r_work: 0.3264 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25403 Z= 0.122 Angle : 0.534 12.788 34273 Z= 0.275 Chirality : 0.039 0.307 3867 Planarity : 0.003 0.046 4369 Dihedral : 4.451 59.396 3390 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.62 % Favored : 94.08 % Rotamer: Outliers : 2.56 % Allowed : 24.58 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.94 (0.16), residues: 3059 helix: 1.75 (0.12), residues: 1880 sheet: -0.80 (0.49), residues: 126 loop : -1.31 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.014 0.001 TYR C 185 PHE 0.019 0.001 PHE J 566 TRP 0.014 0.001 TRP E 246 HIS 0.008 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00282 (25389) covalent geometry : angle 0.53377 (34267) hydrogen bonds : bond 0.03265 ( 1303) hydrogen bonds : angle 3.67986 ( 3828) metal coordination : bond 0.00555 ( 13) metal coordination : angle 1.27911 ( 6) Misc. bond : bond 0.00016 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6118 Ramachandran restraints generated. 3059 Oldfield, 0 Emsley, 3059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 243 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: -0.1079 (ppp) cc_final: -0.1738 (ptp) REVERT: B 163 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 167 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8276 (ptpp) REVERT: B 289 SER cc_start: 0.6104 (OUTLIER) cc_final: 0.5834 (p) REVERT: C 271 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8343 (t0) REVERT: D 118 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7324 (tp30) REVERT: F 79 ARG cc_start: 0.7598 (mtp85) cc_final: 0.6377 (tpm170) REVERT: F 88 GLU cc_start: 0.5917 (tt0) cc_final: 0.5500 (tt0) REVERT: F 186 LEU cc_start: 0.6960 (mt) cc_final: 0.6708 (mm) REVERT: G 203 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8008 (t0) REVERT: H 49 ASP cc_start: 0.8150 (t0) cc_final: 0.7733 (t0) REVERT: I 54 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7272 (tptp) REVERT: J 463 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: J 515 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7803 (ttpt) REVERT: K 26 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7762 (mtpp) REVERT: K 37 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6517 (mp) outliers start: 70 outliers final: 58 residues processed: 303 average time/residue: 0.1722 time to fit residues: 82.6588 Evaluate side-chains 308 residues out of total 2735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 241 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain J residue 382 MET Chi-restraints excluded: chain J residue 442 LEU Chi-restraints excluded: chain J residue 463 GLN Chi-restraints excluded: chain J residue 465 PHE Chi-restraints excluded: chain J residue 492 LEU Chi-restraints excluded: chain J residue 515 LYS Chi-restraints excluded: chain J residue 536 SER Chi-restraints excluded: chain J residue 601 LEU Chi-restraints excluded: chain J residue 684 ILE Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain J residue 738 LEU Chi-restraints excluded: chain J residue 762 LEU Chi-restraints excluded: chain J residue 771 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 214 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 258 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 218 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.109184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.084248 restraints weight = 69135.139| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.13 r_work: 0.3261 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25403 Z= 0.138 Angle : 0.543 11.813 34273 Z= 0.279 Chirality : 0.039 0.311 3867 Planarity : 0.003 0.046 4369 Dihedral : 4.491 59.326 3390 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.56 % Favored : 94.15 % Rotamer: Outliers : 2.63 % Allowed : 24.62 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.91 (0.16), residues: 3059 helix: 1.73 (0.12), residues: 1883 sheet: -0.81 (0.49), residues: 126 loop : -1.33 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 160 TYR 0.016 0.001 TYR C 185 PHE 0.026 0.001 PHE J 498 TRP 0.014 0.001 TRP E 246 HIS 0.008 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00326 (25389) covalent geometry : angle 0.54306 (34267) hydrogen bonds : bond 0.03333 ( 1303) hydrogen bonds : angle 3.70323 ( 3828) metal coordination : bond 0.00605 ( 13) metal coordination : angle 1.42293 ( 6) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6791.83 seconds wall clock time: 116 minutes 56.60 seconds (7016.60 seconds total)