Starting phenix.real_space_refine on Thu Mar 5 04:12:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7quq_14151/03_2026/7quq_14151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7quq_14151/03_2026/7quq_14151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7quq_14151/03_2026/7quq_14151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7quq_14151/03_2026/7quq_14151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7quq_14151/03_2026/7quq_14151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7quq_14151/03_2026/7quq_14151.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.115 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3276 2.21 5 O 3615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19095 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "B" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "E" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "F" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.27 Number of scatterers: 19095 At special positions: 0 Unit cell: (71.74, 67.52, 270.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 18 15.00 O 3615 8.00 N 3276 7.00 C 12102 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 865.5 milliseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 51.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.614A pdb=" N SER A 51 " --> pdb=" O ASN A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 74 through 86 removed outlier: 4.497A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.932A pdb=" N GLY A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 130 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 145 through 163 Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.837A pdb=" N THR A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.000A pdb=" N ARG A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 246 removed outlier: 4.361A pdb=" N SER A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.585A pdb=" N GLU A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.811A pdb=" N GLU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 396 removed outlier: 4.071A pdb=" N ARG A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 409 through 428 Processing helix chain 'B' and resid 10 through 28 removed outlier: 4.327A pdb=" N ARG B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 removed outlier: 4.261A pdb=" N VAL B 50 " --> pdb=" O ASN B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.758A pdb=" N LYS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.671A pdb=" N GLY B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.241A pdb=" N ARG B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.576A pdb=" N LEU B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.626A pdb=" N MET B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 31 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.703A pdb=" N SER C 51 " --> pdb=" O ASN C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 74 through 86 removed outlier: 4.433A pdb=" N ILE C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.986A pdb=" N GLY C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 130 Proline residue: C 118 - end of helix Processing helix chain 'C' and resid 145 through 163 Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.910A pdb=" N THR C 195 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 4.009A pdb=" N ARG C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 246 removed outlier: 4.226A pdb=" N SER C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 310 through 314 removed outlier: 3.853A pdb=" N GLU C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 343 removed outlier: 3.535A pdb=" N GLU C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 394 removed outlier: 3.879A pdb=" N ARG C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.652A pdb=" N GLY C 407 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 428 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.970A pdb=" N ARG D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 removed outlier: 4.208A pdb=" N VAL D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 50' Processing helix chain 'D' and resid 72 through 78 removed outlier: 4.057A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.776A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 3.669A pdb=" N GLY D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 removed outlier: 4.156A pdb=" N ARG D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.649A pdb=" N SER D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 336 Processing helix chain 'D' and resid 374 through 389 Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 425 removed outlier: 3.662A pdb=" N MET D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 31 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.686A pdb=" N SER E 51 " --> pdb=" O ASN E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 74 through 86 removed outlier: 4.529A pdb=" N ILE E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.942A pdb=" N GLY E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 Proline residue: E 118 - end of helix Processing helix chain 'E' and resid 145 through 163 Processing helix chain 'E' and resid 184 through 199 removed outlier: 3.735A pdb=" N THR E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 217 removed outlier: 3.628A pdb=" N LEU E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.257A pdb=" N SER E 243 " --> pdb=" O GLY E 239 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.569A pdb=" N PHE E 300 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.771A pdb=" N GLU E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 343 removed outlier: 3.590A pdb=" N GLU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 396 removed outlier: 3.909A pdb=" N ARG E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 407 removed outlier: 3.818A pdb=" N GLY E 407 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 428 Processing helix chain 'F' and resid 10 through 28 removed outlier: 3.815A pdb=" N ARG F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 50 removed outlier: 4.331A pdb=" N VAL F 50 " --> pdb=" O ASN F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 110 through 127 removed outlier: 4.584A pdb=" N ASP F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 3.670A pdb=" N GLY F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.830A pdb=" N ASN F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.622A pdb=" N THR F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.695A pdb=" N PHE F 294 " --> pdb=" O ALA F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 330 through 336 Processing helix chain 'F' and resid 374 through 386 Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 425 removed outlier: 3.658A pdb=" N MET F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 removed outlier: 7.975A pdb=" N ILE A 95 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET A 70 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASN A 5 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 136 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 142 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 169 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A 137 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N CYS A 171 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 139 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 173 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N HIS A 141 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 168 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 204 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER A 170 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE A 206 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 172 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS A 203 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N CYS A 274 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 205 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N PHE A 276 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 13.628A pdb=" N ASP A 207 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE A 271 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN A 376 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 369 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR A 323 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 371 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 321 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 373 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR A 319 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 375 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYS A 355 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 319 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY A 357 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 321 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 359 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR A 323 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.557A pdb=" N LEU B 5 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR B 137 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE B 7 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N SER B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE B 134 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE B 168 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 136 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 170 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N HIS B 138 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 200 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA B 268 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU B 202 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N PHE B 270 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 13.248A pdb=" N ASP B 204 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 265 " --> pdb=" O HIS B 371 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA B 315 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 368 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 313 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 94 through 96 removed outlier: 8.333A pdb=" N ILE C 95 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 70 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 5 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 138 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 7 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 9 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 169 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE C 137 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS C 171 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 139 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 173 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HIS C 141 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL C 168 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 204 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER C 170 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE C 206 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA C 172 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS C 203 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS C 274 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE C 205 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N PHE C 276 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 13.815A pdb=" N ASP C 207 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE C 271 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN C 376 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER C 369 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR C 323 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 371 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 321 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 373 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR C 319 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN C 375 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LYS C 355 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 319 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY C 357 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 321 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 359 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR C 323 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.679A pdb=" N VAL D 65 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLU D 3 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU D 5 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR D 137 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 7 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N SER D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL D 9 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN D 132 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE D 166 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE D 134 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE D 168 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET D 136 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL D 170 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N HIS D 138 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA D 200 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA D 268 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 202 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N PHE D 270 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 13.166A pdb=" N ASP D 204 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE D 265 " --> pdb=" O HIS D 371 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA D 315 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 368 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 313 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 96 removed outlier: 8.180A pdb=" N ILE E 95 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET E 70 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN E 5 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 136 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU E 169 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE E 137 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS E 171 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 139 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL E 173 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N HIS E 141 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL E 168 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU E 204 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER E 170 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE E 206 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 172 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS E 203 " --> pdb=" O LEU E 272 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS E 274 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 205 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N PHE E 276 " --> pdb=" O ILE E 205 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE E 271 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN E 376 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER E 369 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR E 323 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 371 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL E 321 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU E 373 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR E 319 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN E 375 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LYS E 355 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 319 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY E 357 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL E 321 " --> pdb=" O GLY E 357 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL E 359 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR E 323 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'F' and resid 64 through 65 removed outlier: 6.677A pdb=" N LEU F 5 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR F 137 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE F 7 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N SER F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE F 134 " --> pdb=" O PHE F 166 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE F 168 " --> pdb=" O PHE F 134 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET F 136 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL F 170 " --> pdb=" O MET F 136 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS F 138 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE F 165 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL F 201 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR F 167 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU F 203 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER F 169 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA F 200 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA F 268 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU F 202 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N PHE F 270 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 13.322A pdb=" N ASP F 204 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE F 265 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 52 through 54 904 hydrogen bonds defined for protein. 2682 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: 3.39 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6287 1.34 - 1.46: 4434 1.46 - 1.59: 8584 1.59 - 1.71: 18 1.71 - 1.83: 162 Bond restraints: 19485 Sorted by residual: bond pdb=" C6 G2P D 501 " pdb=" O6 G2P D 501 " ideal model delta sigma weight residual 1.223 1.463 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C6 G2P F 501 " pdb=" O6 G2P F 501 " ideal model delta sigma weight residual 1.223 1.459 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C6 G2P B 501 " pdb=" O6 G2P B 501 " ideal model delta sigma weight residual 1.223 1.457 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C2' G2P D 501 " pdb=" C3' G2P D 501 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 25839 2.49 - 4.99: 473 4.99 - 7.48: 97 7.48 - 9.97: 44 9.97 - 12.47: 19 Bond angle restraints: 26472 Sorted by residual: angle pdb=" C ASN D 298 " pdb=" N PHE D 299 " pdb=" CA PHE D 299 " ideal model delta sigma weight residual 120.71 126.27 -5.56 1.42e+00 4.96e-01 1.53e+01 angle pdb=" C ALA B 99 " pdb=" CA ALA B 99 " pdb=" CB ALA B 99 " ideal model delta sigma weight residual 115.79 111.14 4.65 1.19e+00 7.06e-01 1.53e+01 angle pdb=" C5 G2P E 501 " pdb=" C6 G2P E 501 " pdb=" N1 G2P E 501 " ideal model delta sigma weight residual 110.74 122.25 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C3A G2P F 501 " pdb=" PB G2P F 501 " pdb=" O3B G2P F 501 " ideal model delta sigma weight residual 99.71 110.75 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C5 G2P E 501 " pdb=" C6 G2P E 501 " pdb=" O6 G2P E 501 " ideal model delta sigma weight residual 129.13 118.25 10.88 3.00e+00 1.11e-01 1.31e+01 ... (remaining 26467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 10572 17.36 - 34.72: 965 34.72 - 52.07: 133 52.07 - 69.43: 29 69.43 - 86.79: 22 Dihedral angle restraints: 11721 sinusoidal: 4677 harmonic: 7044 Sorted by residual: dihedral pdb=" CA TRP E 349 " pdb=" C TRP E 349 " pdb=" N ILE E 350 " pdb=" CA ILE E 350 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL B 369 " pdb=" C VAL B 369 " pdb=" N ASN B 370 " pdb=" CA ASN B 370 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS D 163 " pdb=" C LYS D 163 " pdb=" N ARG D 164 " pdb=" CA ARG D 164 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2493 0.068 - 0.135: 447 0.135 - 0.203: 46 0.203 - 0.270: 5 0.270 - 0.338: 3 Chirality restraints: 2994 Sorted by residual: chirality pdb=" CB ILE A 350 " pdb=" CA ILE A 350 " pdb=" CG1 ILE A 350 " pdb=" CG2 ILE A 350 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C3' G2P C 501 " pdb=" C2' G2P C 501 " pdb=" C4' G2P C 501 " pdb=" O3' G2P C 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' G2P A 501 " pdb=" C2' G2P A 501 " pdb=" C4' G2P A 501 " pdb=" O3' G2P A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.43 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2991 not shown) Planarity restraints: 3399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 349 " -0.028 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP E 349 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 349 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 349 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 349 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 299 " 0.018 2.00e-02 2.50e+03 2.57e-02 1.16e+01 pdb=" CG PHE D 299 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D 299 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 299 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 182 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO F 183 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 183 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 183 " 0.043 5.00e-02 4.00e+02 ... (remaining 3396 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 579 2.70 - 3.25: 19525 3.25 - 3.80: 34136 3.80 - 4.35: 45141 4.35 - 4.90: 72412 Nonbonded interactions: 171793 Sorted by model distance: nonbonded pdb=" OG SER D 146 " pdb=" OG1 THR D 189 " model vdw 2.144 3.040 nonbonded pdb=" OG SER B 146 " pdb=" OG1 THR B 189 " model vdw 2.158 3.040 nonbonded pdb=" OG SER F 146 " pdb=" OG1 THR F 189 " model vdw 2.184 3.040 nonbonded pdb=" OG SER E 180 " pdb=" O LEU F 349 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASN E 188 " pdb=" OH TYR E 403 " model vdw 2.188 3.040 ... (remaining 171788 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.670 Find NCS groups from input model: 0.390 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 0.009 0.240 19494 Z= 0.447 Angle : 0.938 12.467 26472 Z= 0.441 Chirality : 0.052 0.338 2994 Planarity : 0.006 0.077 3399 Dihedral : 13.757 86.788 7179 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.38 (0.16), residues: 2415 helix: -0.45 (0.15), residues: 1119 sheet: -0.36 (0.27), residues: 375 loop : -1.61 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 197 TYR 0.023 0.002 TYR F 422 PHE 0.058 0.002 PHE D 299 TRP 0.080 0.003 TRP E 349 HIS 0.006 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00904 (19485) covalent geometry : angle 0.93760 (26472) hydrogen bonds : bond 0.16562 ( 904) hydrogen bonds : angle 7.41342 ( 2682) Misc. bond : bond 0.00301 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 481 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 MET cc_start: 0.6080 (mmt) cc_final: 0.5615 (mmp) REVERT: A 315 ARG cc_start: 0.5836 (tpp-160) cc_final: 0.4447 (ptt180) REVERT: A 354 PHE cc_start: 0.7904 (m-80) cc_final: 0.7513 (m-80) REVERT: B 88 GLU cc_start: 0.4830 (mp0) cc_final: 0.4558 (mp0) REVERT: B 193 ILE cc_start: 0.8040 (mt) cc_final: 0.7804 (mt) REVERT: C 403 TYR cc_start: 0.5373 (m-80) cc_final: 0.3917 (m-80) REVERT: D 88 GLU cc_start: 0.5457 (mp0) cc_final: 0.5218 (mp0) REVERT: D 299 PHE cc_start: 0.6615 (m-80) cc_final: 0.6201 (m-80) REVERT: E 219 TRP cc_start: 0.6205 (t-100) cc_final: 0.5990 (t-100) REVERT: E 245 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7125 (ttp80) REVERT: F 73 VAL cc_start: 0.6496 (p) cc_final: 0.5766 (t) REVERT: F 388 MET cc_start: 0.5143 (ptm) cc_final: 0.3943 (mmm) outliers start: 2 outliers final: 2 residues processed: 483 average time/residue: 0.5699 time to fit residues: 310.8268 Evaluate side-chains 274 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 304 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 263 ASN B 285 ASN B 338 ASN C 80 ASN ** D 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 401 ASN ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.203460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.179560 restraints weight = 24098.709| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 1.93 r_work: 0.4442 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 19494 Z= 0.185 Angle : 0.729 12.767 26472 Z= 0.367 Chirality : 0.048 0.292 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.962 89.923 2824 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 2.93 % Allowed : 14.04 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.21 (0.16), residues: 2415 helix: -0.28 (0.15), residues: 1134 sheet: -0.40 (0.27), residues: 357 loop : -1.50 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 46 TYR 0.017 0.002 TYR E 163 PHE 0.034 0.002 PHE D 299 TRP 0.029 0.002 TRP E 349 HIS 0.004 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00405 (19485) covalent geometry : angle 0.72861 (26472) hydrogen bonds : bond 0.05530 ( 904) hydrogen bonds : angle 5.82911 ( 2682) Misc. bond : bond 0.00382 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5995 (t80) cc_final: 0.5521 (t80) REVERT: A 244 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7743 (mtm) REVERT: A 312 MET cc_start: 0.6515 (mmt) cc_final: 0.6020 (mmp) REVERT: A 315 ARG cc_start: 0.6325 (tpp-160) cc_final: 0.4660 (ptt180) REVERT: B 70 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5873 (pp20) REVERT: B 88 GLU cc_start: 0.4884 (mp0) cc_final: 0.4672 (mp0) REVERT: D 291 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6130 (ptp-110) REVERT: D 299 PHE cc_start: 0.7095 (m-80) cc_final: 0.6663 (m-80) REVERT: E 341 ARG cc_start: 0.6335 (ttp-110) cc_final: 0.5743 (tmm-80) REVERT: F 129 LYS cc_start: 0.5201 (mppt) cc_final: 0.4981 (mppt) REVERT: F 175 LEU cc_start: 0.7462 (pt) cc_final: 0.7253 (pp) REVERT: F 224 ASP cc_start: 0.7765 (m-30) cc_final: 0.7528 (m-30) REVERT: F 228 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8323 (mp) REVERT: F 388 MET cc_start: 0.5810 (ptm) cc_final: 0.3811 (mmt) outliers start: 59 outliers final: 18 residues processed: 364 average time/residue: 0.5321 time to fit residues: 221.3649 Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 212 optimal weight: 8.9990 chunk 92 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 16 ASN A 48 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN C 80 ASN C 375 ASN D 53 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS E 90 ASN E 220 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.200698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.176790 restraints weight = 24228.725| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 1.92 r_work: 0.4409 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19494 Z= 0.173 Angle : 0.700 13.430 26472 Z= 0.350 Chirality : 0.047 0.254 2994 Planarity : 0.005 0.051 3399 Dihedral : 9.805 89.305 2820 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.82 % Allowed : 17.61 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.11 (0.17), residues: 2415 helix: -0.14 (0.15), residues: 1131 sheet: -0.50 (0.27), residues: 360 loop : -1.45 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 46 TYR 0.018 0.002 TYR B 398 PHE 0.025 0.002 PHE D 299 TRP 0.017 0.002 TRP E 349 HIS 0.004 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00390 (19485) covalent geometry : angle 0.69978 (26472) hydrogen bonds : bond 0.05127 ( 904) hydrogen bonds : angle 5.65447 ( 2682) Misc. bond : bond 0.00460 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 293 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5920 (t80) cc_final: 0.5479 (t80) REVERT: A 244 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: A 312 MET cc_start: 0.6502 (mmt) cc_final: 0.6258 (mmt) REVERT: A 315 ARG cc_start: 0.6456 (tpp-160) cc_final: 0.4867 (ptt180) REVERT: B 70 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5656 (pp20) REVERT: B 88 GLU cc_start: 0.4946 (mp0) cc_final: 0.4724 (mp0) REVERT: B 355 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5373 (pm20) REVERT: D 76 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5810 (mpp-170) REVERT: D 94 LYS cc_start: 0.3361 (OUTLIER) cc_final: 0.3143 (tppt) REVERT: D 291 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6164 (ptp-110) REVERT: E 341 ARG cc_start: 0.6351 (ttp-110) cc_final: 0.5784 (tmm-80) REVERT: F 106 TYR cc_start: 0.6554 (t80) cc_final: 0.6324 (t80) REVERT: F 129 LYS cc_start: 0.5151 (mppt) cc_final: 0.4887 (mppt) REVERT: F 169 SER cc_start: 0.9000 (m) cc_final: 0.8737 (p) REVERT: F 182 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7207 (pp20) REVERT: F 224 ASP cc_start: 0.7716 (m-30) cc_final: 0.7406 (m-30) REVERT: F 228 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8401 (mp) REVERT: F 325 ASP cc_start: 0.7183 (m-30) cc_final: 0.6903 (m-30) REVERT: F 388 MET cc_start: 0.5708 (ptm) cc_final: 0.3882 (mmt) outliers start: 77 outliers final: 29 residues processed: 343 average time/residue: 0.5077 time to fit residues: 200.0136 Evaluate side-chains 283 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 43 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 229 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.200563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.176253 restraints weight = 24391.968| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.07 r_work: 0.4424 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19494 Z= 0.157 Angle : 0.676 12.529 26472 Z= 0.336 Chirality : 0.046 0.234 2994 Planarity : 0.005 0.051 3399 Dihedral : 9.609 85.708 2820 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.07 % Allowed : 20.54 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.99 (0.17), residues: 2415 helix: -0.00 (0.15), residues: 1131 sheet: -0.60 (0.27), residues: 360 loop : -1.38 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 46 TYR 0.019 0.002 TYR B 398 PHE 0.028 0.002 PHE A 191 TRP 0.018 0.002 TRP A 219 HIS 0.004 0.001 HIS D 8 Details of bonding type rmsd covalent geometry : bond 0.00354 (19485) covalent geometry : angle 0.67585 (26472) hydrogen bonds : bond 0.04803 ( 904) hydrogen bonds : angle 5.52327 ( 2682) Misc. bond : bond 0.00383 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5869 (t80) cc_final: 0.5551 (t80) REVERT: A 244 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7830 (mtm) REVERT: A 312 MET cc_start: 0.6460 (mmt) cc_final: 0.6233 (mmt) REVERT: A 315 ARG cc_start: 0.6373 (tpp-160) cc_final: 0.4952 (ptt180) REVERT: B 70 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5670 (pp20) REVERT: B 355 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5357 (pm20) REVERT: C 3 VAL cc_start: 0.7462 (m) cc_final: 0.7195 (p) REVERT: D 76 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5846 (mpp-170) REVERT: D 94 LYS cc_start: 0.3080 (OUTLIER) cc_final: 0.2830 (tmtt) REVERT: D 291 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.6132 (ptp-110) REVERT: D 420 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.4927 (tp-100) REVERT: E 341 ARG cc_start: 0.6370 (ttp-110) cc_final: 0.5839 (tmm-80) REVERT: F 106 TYR cc_start: 0.6618 (t80) cc_final: 0.6390 (t80) REVERT: F 228 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (mp) REVERT: F 325 ASP cc_start: 0.7251 (m-30) cc_final: 0.6936 (m-30) REVERT: F 388 MET cc_start: 0.5840 (ptm) cc_final: 0.4111 (mmt) outliers start: 82 outliers final: 30 residues processed: 341 average time/residue: 0.4777 time to fit residues: 188.5158 Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 57 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 185 ASN F 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.199017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.175579 restraints weight = 24615.361| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 1.98 r_work: 0.4407 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19494 Z= 0.160 Angle : 0.679 12.404 26472 Z= 0.337 Chirality : 0.046 0.191 2994 Planarity : 0.005 0.057 3399 Dihedral : 9.575 84.225 2820 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.56 % Allowed : 21.78 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.17), residues: 2415 helix: 0.15 (0.15), residues: 1116 sheet: -0.73 (0.27), residues: 369 loop : -1.39 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 46 TYR 0.027 0.002 TYR A 403 PHE 0.021 0.002 PHE E 105 TRP 0.020 0.002 TRP D 102 HIS 0.005 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00363 (19485) covalent geometry : angle 0.67902 (26472) hydrogen bonds : bond 0.04764 ( 904) hydrogen bonds : angle 5.45391 ( 2682) Misc. bond : bond 0.00388 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 264 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: A 312 MET cc_start: 0.6553 (mmt) cc_final: 0.6308 (mmt) REVERT: A 315 ARG cc_start: 0.6483 (tpp-160) cc_final: 0.4965 (ptt180) REVERT: B 70 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5471 (pp20) REVERT: B 355 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5299 (pm20) REVERT: B 398 TYR cc_start: 0.5556 (m-80) cc_final: 0.5298 (m-80) REVERT: C 3 VAL cc_start: 0.7445 (m) cc_final: 0.7189 (p) REVERT: C 151 PHE cc_start: 0.6750 (t80) cc_final: 0.6534 (t80) REVERT: D 76 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5846 (mpp-170) REVERT: D 94 LYS cc_start: 0.3248 (OUTLIER) cc_final: 0.2917 (tmtt) REVERT: D 291 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6313 (ptp-110) REVERT: E 341 ARG cc_start: 0.6442 (ttp-110) cc_final: 0.6010 (tmm-80) REVERT: F 106 TYR cc_start: 0.6608 (t80) cc_final: 0.6337 (t80) REVERT: F 184 TYR cc_start: 0.6366 (m-10) cc_final: 0.6166 (m-10) REVERT: F 224 ASP cc_start: 0.7654 (m-30) cc_final: 0.7422 (m-30) REVERT: F 228 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8540 (mp) REVERT: F 325 ASP cc_start: 0.7315 (m-30) cc_final: 0.6981 (m-30) REVERT: F 388 MET cc_start: 0.5714 (ptm) cc_final: 0.4012 (mmm) outliers start: 92 outliers final: 41 residues processed: 334 average time/residue: 0.4630 time to fit residues: 179.4713 Evaluate side-chains 291 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 193 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 234 optimal weight: 0.0570 chunk 88 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 133 optimal weight: 0.0020 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 306 GLN E 270 HIS F 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.202344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.179309 restraints weight = 24435.935| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 1.93 r_work: 0.4446 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19494 Z= 0.137 Angle : 0.661 12.088 26472 Z= 0.328 Chirality : 0.045 0.179 2994 Planarity : 0.005 0.051 3399 Dihedral : 9.297 83.728 2820 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.12 % Allowed : 22.72 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.86 (0.17), residues: 2415 helix: 0.22 (0.15), residues: 1122 sheet: -0.86 (0.27), residues: 363 loop : -1.32 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 46 TYR 0.018 0.002 TYR C 403 PHE 0.022 0.001 PHE A 191 TRP 0.027 0.002 TRP D 102 HIS 0.004 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00307 (19485) covalent geometry : angle 0.66128 (26472) hydrogen bonds : bond 0.04481 ( 904) hydrogen bonds : angle 5.34150 ( 2682) Misc. bond : bond 0.00310 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 266 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5865 (t80) cc_final: 0.5356 (t80) REVERT: A 234 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7546 (p) REVERT: A 312 MET cc_start: 0.6478 (mmt) cc_final: 0.6265 (mmt) REVERT: B 355 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5181 (pm20) REVERT: B 361 PHE cc_start: 0.5967 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: C 3 VAL cc_start: 0.7441 (m) cc_final: 0.7220 (p) REVERT: C 121 MET cc_start: 0.6571 (mmm) cc_final: 0.6169 (mmm) REVERT: C 151 PHE cc_start: 0.6722 (t80) cc_final: 0.6493 (t80) REVERT: D 76 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5810 (mpp-170) REVERT: D 94 LYS cc_start: 0.3031 (OUTLIER) cc_final: 0.2774 (tmtt) REVERT: D 291 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.6098 (ptp-110) REVERT: E 341 ARG cc_start: 0.6459 (ttp-110) cc_final: 0.5956 (tmm-80) REVERT: F 100 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.5893 (m110) REVERT: F 106 TYR cc_start: 0.6519 (t80) cc_final: 0.6302 (t80) REVERT: F 224 ASP cc_start: 0.7498 (m-30) cc_final: 0.7254 (m-30) REVERT: F 228 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8522 (mp) REVERT: F 325 ASP cc_start: 0.7221 (m-30) cc_final: 0.6884 (m-30) REVERT: F 388 MET cc_start: 0.5678 (ptm) cc_final: 0.3922 (mmt) outliers start: 83 outliers final: 27 residues processed: 331 average time/residue: 0.4573 time to fit residues: 176.2250 Evaluate side-chains 265 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 234 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 296 GLN D 298 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 14 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.195388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.171931 restraints weight = 24749.026| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 1.93 r_work: 0.4377 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19494 Z= 0.204 Angle : 0.735 12.640 26472 Z= 0.366 Chirality : 0.048 0.220 2994 Planarity : 0.005 0.050 3399 Dihedral : 9.671 82.514 2820 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 4.02 % Allowed : 23.56 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.05 (0.17), residues: 2415 helix: 0.12 (0.15), residues: 1122 sheet: -1.06 (0.27), residues: 345 loop : -1.44 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 46 TYR 0.033 0.003 TYR C 403 PHE 0.029 0.002 PHE A 191 TRP 0.028 0.002 TRP D 102 HIS 0.012 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00470 (19485) covalent geometry : angle 0.73521 (26472) hydrogen bonds : bond 0.04939 ( 904) hydrogen bonds : angle 5.51916 ( 2682) Misc. bond : bond 0.00489 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 251 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5943 (t80) cc_final: 0.5406 (t80) REVERT: A 244 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7760 (mtm) REVERT: A 312 MET cc_start: 0.6640 (mmt) cc_final: 0.6439 (mmt) REVERT: B 353 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: B 355 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5314 (pm20) REVERT: C 151 PHE cc_start: 0.6990 (t80) cc_final: 0.6746 (t80) REVERT: C 428 GLN cc_start: 0.4496 (OUTLIER) cc_final: 0.4161 (mm-40) REVERT: D 76 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5726 (mpp-170) REVERT: D 94 LYS cc_start: 0.3703 (OUTLIER) cc_final: 0.3245 (tmtt) REVERT: D 291 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6469 (ptp-110) REVERT: E 341 ARG cc_start: 0.6608 (ttp-110) cc_final: 0.6130 (tmm-80) REVERT: F 106 TYR cc_start: 0.6405 (t80) cc_final: 0.6192 (t80) REVERT: F 158 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.5374 (pm20) REVERT: F 224 ASP cc_start: 0.7546 (m-30) cc_final: 0.7270 (m-30) REVERT: F 228 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8694 (mp) REVERT: F 325 ASP cc_start: 0.7656 (m-30) cc_final: 0.7305 (m-30) REVERT: F 388 MET cc_start: 0.5971 (ptm) cc_final: 0.4269 (mmt) outliers start: 81 outliers final: 41 residues processed: 313 average time/residue: 0.4646 time to fit residues: 168.0455 Evaluate side-chains 273 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 407 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 7 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 400 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.196062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.172681 restraints weight = 24729.220| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 1.94 r_work: 0.4382 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19494 Z= 0.181 Angle : 0.725 12.373 26472 Z= 0.359 Chirality : 0.048 0.251 2994 Planarity : 0.005 0.054 3399 Dihedral : 9.555 80.733 2820 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.52 % Allowed : 24.55 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.03 (0.17), residues: 2415 helix: 0.11 (0.15), residues: 1122 sheet: -0.93 (0.27), residues: 366 loop : -1.45 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 123 TYR 0.031 0.002 TYR C 403 PHE 0.032 0.002 PHE A 191 TRP 0.031 0.002 TRP D 102 HIS 0.005 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00416 (19485) covalent geometry : angle 0.72542 (26472) hydrogen bonds : bond 0.04790 ( 904) hydrogen bonds : angle 5.50803 ( 2682) Misc. bond : bond 0.00434 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5849 (t80) cc_final: 0.5343 (t80) REVERT: A 234 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7663 (p) REVERT: B 286 PHE cc_start: 0.6383 (t80) cc_final: 0.6123 (t80) REVERT: B 355 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5171 (pm20) REVERT: C 3 VAL cc_start: 0.7388 (m) cc_final: 0.7123 (p) REVERT: C 151 PHE cc_start: 0.7063 (t80) cc_final: 0.6774 (t80) REVERT: D 94 LYS cc_start: 0.3631 (OUTLIER) cc_final: 0.3257 (tmtt) REVERT: D 291 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6499 (ptp-110) REVERT: E 341 ARG cc_start: 0.6624 (ttp-110) cc_final: 0.6121 (tmm-80) REVERT: F 106 TYR cc_start: 0.6415 (t80) cc_final: 0.6199 (t80) REVERT: F 158 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.5396 (pm20) REVERT: F 184 TYR cc_start: 0.6257 (m-10) cc_final: 0.6026 (m-10) REVERT: F 224 ASP cc_start: 0.7549 (m-30) cc_final: 0.7275 (m-30) REVERT: F 228 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (mp) REVERT: F 325 ASP cc_start: 0.7635 (m-30) cc_final: 0.7276 (m-30) REVERT: F 388 MET cc_start: 0.5975 (ptm) cc_final: 0.4325 (mmt) outliers start: 71 outliers final: 39 residues processed: 292 average time/residue: 0.4523 time to fit residues: 153.0707 Evaluate side-chains 267 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 26 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 194 optimal weight: 0.0870 chunk 148 optimal weight: 1.9990 chunk 235 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 247 ASN B 400 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN E 178 GLN E 188 ASN E 401 ASN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.198555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.175666 restraints weight = 24448.163| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 1.90 r_work: 0.4418 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19494 Z= 0.147 Angle : 0.701 12.225 26472 Z= 0.345 Chirality : 0.046 0.187 2994 Planarity : 0.005 0.076 3399 Dihedral : 9.196 79.876 2820 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.63 % Allowed : 25.69 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.17), residues: 2415 helix: 0.16 (0.16), residues: 1122 sheet: -1.00 (0.27), residues: 363 loop : -1.37 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 46 TYR 0.020 0.002 TYR C 403 PHE 0.029 0.001 PHE A 191 TRP 0.037 0.002 TRP D 102 HIS 0.005 0.001 HIS D 8 Details of bonding type rmsd covalent geometry : bond 0.00336 (19485) covalent geometry : angle 0.70065 (26472) hydrogen bonds : bond 0.04501 ( 904) hydrogen bonds : angle 5.40275 ( 2682) Misc. bond : bond 0.00339 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5776 (t80) cc_final: 0.5326 (t80) REVERT: A 234 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7608 (p) REVERT: B 343 MET cc_start: 0.6195 (mmm) cc_final: 0.5828 (mmm) REVERT: B 355 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5135 (pm20) REVERT: B 361 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.4225 (m-80) REVERT: C 3 VAL cc_start: 0.7349 (m) cc_final: 0.7129 (p) REVERT: C 110 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6112 (mm) REVERT: C 151 PHE cc_start: 0.6766 (t80) cc_final: 0.6494 (t80) REVERT: D 94 LYS cc_start: 0.3533 (OUTLIER) cc_final: 0.3210 (tmtt) REVERT: D 291 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6351 (ptp-110) REVERT: E 341 ARG cc_start: 0.6540 (ttp-110) cc_final: 0.6039 (tmm-80) REVERT: F 31 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5328 (t) REVERT: F 106 TYR cc_start: 0.6435 (t80) cc_final: 0.6223 (t80) REVERT: F 158 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5263 (pm20) REVERT: F 160 TYR cc_start: 0.4865 (OUTLIER) cc_final: 0.3270 (m-10) REVERT: F 224 ASP cc_start: 0.7558 (m-30) cc_final: 0.7272 (m-30) REVERT: F 228 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8591 (mp) REVERT: F 325 ASP cc_start: 0.7388 (m-30) cc_final: 0.7055 (m-30) REVERT: F 388 MET cc_start: 0.5718 (ptm) cc_final: 0.4263 (mmt) outliers start: 53 outliers final: 33 residues processed: 286 average time/residue: 0.4678 time to fit residues: 155.3742 Evaluate side-chains 267 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 54 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 210 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN ** F 132 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 = 0.4715 r_free = 0.4715 target = 0.190798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.166937 restraints weight = 24575.591| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 1.96 r_work: 0.4335 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 19494 Z= 0.258 Angle : 0.820 12.627 26472 Z= 0.409 Chirality : 0.052 0.326 2994 Planarity : 0.006 0.071 3399 Dihedral : 9.803 77.289 2820 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 26.14 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.26 (0.17), residues: 2415 helix: -0.07 (0.15), residues: 1122 sheet: -1.10 (0.28), residues: 321 loop : -1.55 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 46 TYR 0.038 0.003 TYR C 403 PHE 0.043 0.003 PHE A 191 TRP 0.034 0.003 TRP E 23 HIS 0.006 0.002 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00593 (19485) covalent geometry : angle 0.81962 (26472) hydrogen bonds : bond 0.05285 ( 904) hydrogen bonds : angle 5.70268 ( 2682) Misc. bond : bond 0.00573 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 242 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: A 381 ARG cc_start: 0.7081 (ptm-80) cc_final: 0.6863 (ptm-80) REVERT: B 353 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8074 (m-10) REVERT: B 355 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5434 (pm20) REVERT: C 151 PHE cc_start: 0.7404 (t80) cc_final: 0.7138 (t80) REVERT: D 90 SER cc_start: 0.4537 (m) cc_final: 0.4018 (p) REVERT: D 94 LYS cc_start: 0.3935 (OUTLIER) cc_final: 0.3451 (tmtt) REVERT: D 291 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6903 (ptp-110) REVERT: E 341 ARG cc_start: 0.6888 (ttp-110) cc_final: 0.6295 (tmm-80) REVERT: F 31 THR cc_start: 0.5896 (OUTLIER) cc_final: 0.5409 (t) REVERT: F 106 TYR cc_start: 0.6516 (t80) cc_final: 0.5881 (t80) REVERT: F 158 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5365 (pm20) REVERT: F 160 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.3713 (m-10) REVERT: F 184 TYR cc_start: 0.6596 (m-10) cc_final: 0.6288 (m-10) REVERT: F 224 ASP cc_start: 0.7621 (m-30) cc_final: 0.7341 (m-30) REVERT: F 228 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8800 (mp) REVERT: F 325 ASP cc_start: 0.7846 (m-30) cc_final: 0.7503 (m-30) REVERT: F 388 MET cc_start: 0.6317 (ptm) cc_final: 0.4638 (mmt) outliers start: 57 outliers final: 36 residues processed: 283 average time/residue: 0.4707 time to fit residues: 154.2966 Evaluate side-chains 269 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 125 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.194522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.171137 restraints weight = 24692.532| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 2.00 r_work: 0.4376 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19494 Z= 0.174 Angle : 0.754 12.568 26472 Z= 0.373 Chirality : 0.048 0.250 2994 Planarity : 0.005 0.060 3399 Dihedral : 9.484 74.163 2820 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.73 % Allowed : 26.79 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.23 (0.17), residues: 2415 helix: -0.02 (0.15), residues: 1122 sheet: -1.01 (0.29), residues: 312 loop : -1.61 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 46 TYR 0.037 0.002 TYR C 187 PHE 0.033 0.002 PHE A 191 TRP 0.033 0.002 TRP D 102 HIS 0.005 0.001 HIS D 8 Details of bonding type rmsd covalent geometry : bond 0.00400 (19485) covalent geometry : angle 0.75379 (26472) hydrogen bonds : bond 0.04711 ( 904) hydrogen bonds : angle 5.56438 ( 2682) Misc. bond : bond 0.00410 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.38 seconds wall clock time: 99 minutes 30.07 seconds (5970.07 seconds total)