Starting phenix.real_space_refine on Sat Jul 4 06:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7quq_14151/07_2026/7quq_14151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7quq_14151/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7quq_14151/07_2026/7quq_14151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7quq_14151/07_2026/7quq_14151.cif" model { file = "/net/cci-nas-00/data/ceres_data/7quq_14151/07_2026/7quq_14151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7quq_14151/07_2026/7quq_14151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7quq_14151/07_2026/7quq_14151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7quq_14151/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 3.88, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 711.6 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: 0.36 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: 2.40 Time building geometry restraints manager: 1.78 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 - 15.89: 10369 15.89 - 31.78: 959 31.78 - 47.66: 186 47.66 - 63.55: 25 63.55 - 79.44: 14 Dihedral angle restraints: 11553 sinusoidal: 4509 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 11550 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.670 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 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 : 12.926 79.439 7011 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/Z covalent geometry : bond 0.00904 / 0.45 (19485) covalent geometry : angle 0.93760 / 0.44 (26472) hydrogen bonds : bond 0.16562 / 11.21 ( 904) hydrogen bonds : angle 7.41342 / 5.27 ( 2682) Misc. bond : bond 0.00301 / 0.13 ( 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 : 0.530 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: 0.5022 time to fit residues: 276.0762 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 : 0.727 ------------------------------------------------------------------------------- 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... A 5 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 263 ASN B 285 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 = 0.4819 r_free = 0.4819 target = 0.203276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.178072 restraints weight = 24105.417| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 2.10 r_work: 0.4442 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19494 Z= 0.180 Angle : 0.731 12.740 26472 Z= 0.365 Chirality : 0.048 0.220 2994 Planarity : 0.005 0.053 3399 Dihedral : 6.157 56.824 2656 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 3.12 % Allowed : 14.09 % Favored : 82.79 % 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: -0.41 (0.27), residues: 357 loop : -1.50 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 46 TYR 0.018 0.002 TYR A 403 PHE 0.034 0.002 PHE D 299 TRP 0.030 0.002 TRP E 349 HIS 0.004 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (19485) covalent geometry : angle 0.73054 / 0.37 (26472) hydrogen bonds : bond 0.05460 / 3.72 ( 904) hydrogen bonds : angle 5.81103 / 4.17 ( 2682) Misc. bond : bond 0.00430 / 0.19 ( 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 387 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 324 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.6018 (t80) cc_final: 0.5575 (t80) REVERT: A 209 GLU cc_start: 0.7753 (pp20) cc_final: 0.7534 (pm20) REVERT: A 244 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7748 (mtm) REVERT: A 312 MET cc_start: 0.6516 (mmt) cc_final: 0.6025 (mmp) REVERT: A 315 ARG cc_start: 0.6334 (tpp-160) cc_final: 0.4668 (ptt180) REVERT: B 70 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5913 (pp20) REVERT: B 88 GLU cc_start: 0.4883 (mp0) cc_final: 0.4672 (mp0) REVERT: C 245 ARG cc_start: 0.7374 (ttp80) cc_final: 0.7038 (mtp85) REVERT: D 291 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6135 (ptp-110) REVERT: D 299 PHE cc_start: 0.7201 (m-80) cc_final: 0.6771 (m-80) REVERT: E 219 TRP cc_start: 0.6291 (t-100) cc_final: 0.6086 (t-100) REVERT: E 341 ARG cc_start: 0.6345 (ttp-110) cc_final: 0.5730 (tmm-80) REVERT: F 169 SER cc_start: 0.8897 (m) cc_final: 0.8634 (p) REVERT: F 175 LEU cc_start: 0.7460 (pt) cc_final: 0.7260 (pp) REVERT: F 224 ASP cc_start: 0.7772 (m-30) cc_final: 0.7541 (m-30) REVERT: F 228 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (mp) REVERT: F 388 MET cc_start: 0.5815 (ptm) cc_final: 0.3813 (mmt) outliers start: 63 outliers final: 17 residues processed: 366 average time/residue: 0.5033 time to fit residues: 211.7459 Evaluate side-chains 281 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 150 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN A 16 ASN A 48 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 247 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.200944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.175767 restraints weight = 24220.475| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 2.10 r_work: 0.4422 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19494 Z= 0.170 Angle : 0.696 13.334 26472 Z= 0.348 Chirality : 0.047 0.245 2994 Planarity : 0.005 0.051 3399 Dihedral : 6.085 59.543 2652 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.47 % Allowed : 17.76 % Favored : 78.77 % 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: -1.10 (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 0.011 0.001 ARG E 46 TYR 0.018 0.002 TYR C 403 PHE 0.025 0.002 PHE D 299 TRP 0.019 0.002 TRP E 349 HIS 0.004 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19485) covalent geometry : angle 0.69636 / 0.35 (26472) hydrogen bonds : bond 0.05108 / 3.47 ( 904) hydrogen bonds : angle 5.65399 / 4.05 ( 2682) Misc. bond : bond 0.00431 / 0.18 ( 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 360 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 290 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.6623 (t-100) REVERT: A 244 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: A 312 MET cc_start: 0.6465 (mmt) cc_final: 0.6028 (mmp) REVERT: A 315 ARG cc_start: 0.6468 (tpp-160) cc_final: 0.4844 (ptt180) REVERT: B 70 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: B 88 GLU cc_start: 0.4918 (mp0) cc_final: 0.4706 (mp0) REVERT: B 355 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5364 (pm20) REVERT: D 76 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.6005 (mpp-170) REVERT: D 291 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6170 (ptp-110) REVERT: E 81 VAL cc_start: 0.7335 (t) cc_final: 0.7128 (m) REVERT: E 219 TRP cc_start: 0.6357 (t-100) cc_final: 0.6154 (t-100) REVERT: E 341 ARG cc_start: 0.6335 (ttp-110) cc_final: 0.5750 (tmm-80) REVERT: F 106 TYR cc_start: 0.6398 (t80) cc_final: 0.6168 (t80) REVERT: F 169 SER cc_start: 0.9003 (m) cc_final: 0.8732 (p) REVERT: F 182 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: F 224 ASP cc_start: 0.7773 (m-30) cc_final: 0.7485 (m-30) REVERT: F 228 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (mp) REVERT: F 320 ASP cc_start: 0.7304 (t70) cc_final: 0.7090 (t0) REVERT: F 325 ASP cc_start: 0.7177 (m-30) cc_final: 0.6911 (m-30) REVERT: F 388 MET cc_start: 0.5820 (ptm) cc_final: 0.3814 (mmt) outliers start: 70 outliers final: 25 residues processed: 336 average time/residue: 0.4833 time to fit residues: 188.7325 Evaluate side-chains 280 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 382 ILE 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 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: 0.8980 chunk 135 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 ASN B 338 ASN C 80 ASN 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.200503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.176599 restraints weight = 24380.729| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 1.97 r_work: 0.4417 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2992 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= 0.157 Angle : 0.675 12.256 26472 Z= 0.335 Chirality : 0.046 0.188 2994 Planarity : 0.005 0.051 3399 Dihedral : 6.002 58.329 2652 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.27 % Allowed : 20.44 % Favored : 75.30 % 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: 0.04 (0.15), residues: 1134 sheet: -0.64 (0.27), residues: 360 loop : -1.38 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 46 TYR 0.020 0.002 TYR B 398 PHE 0.033 0.002 PHE A 191 TRP 0.017 0.002 TRP A 219 HIS 0.004 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (19485) covalent geometry : angle 0.67482 / 0.34 (26472) hydrogen bonds : bond 0.04771 / 3.24 ( 904) hydrogen bonds : angle 5.49965 / 3.94 ( 2682) Misc. bond : bond 0.00380 / 0.17 ( 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 375 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5994 (t80) cc_final: 0.5532 (t80) REVERT: A 244 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7818 (mtm) REVERT: A 312 MET cc_start: 0.6486 (mmt) cc_final: 0.6238 (mmt) REVERT: A 315 ARG cc_start: 0.6424 (tpp-160) cc_final: 0.4956 (ptt180) REVERT: A 330 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.7054 (pmtt) REVERT: B 70 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5732 (pp20) REVERT: B 112 LYS cc_start: 0.7181 (ptpp) cc_final: 0.6866 (ptpp) REVERT: B 355 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5274 (pm20) REVERT: B 398 TYR cc_start: 0.5527 (m-80) cc_final: 0.5264 (m-80) REVERT: C 3 VAL cc_start: 0.7467 (m) cc_final: 0.7198 (p) REVERT: D 76 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5830 (mpp-170) REVERT: D 291 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6136 (ptp-110) REVERT: D 420 GLN cc_start: 0.5159 (OUTLIER) cc_final: 0.4953 (tp-100) REVERT: E 341 ARG cc_start: 0.6392 (ttp-110) cc_final: 0.5866 (tmm-80) REVERT: F 106 TYR cc_start: 0.6648 (t80) cc_final: 0.6408 (t80) REVERT: F 224 ASP cc_start: 0.7691 (m-30) cc_final: 0.7427 (m-30) REVERT: F 228 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8471 (mp) REVERT: F 325 ASP cc_start: 0.7260 (m-30) cc_final: 0.6955 (m-30) REVERT: F 388 MET cc_start: 0.5607 (ptm) cc_final: 0.3850 (mmt) outliers start: 86 outliers final: 30 residues processed: 349 average time/residue: 0.4278 time to fit residues: 173.9262 Evaluate side-chains 282 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 330 LYS 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 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 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 166 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 279 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: 6.9990 chunk 190 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.198713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.175778 restraints weight = 24661.401| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 1.89 r_work: 0.4420 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4298 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19494 Z= 0.164 Angle : 0.681 12.308 26472 Z= 0.338 Chirality : 0.047 0.233 2994 Planarity : 0.005 0.051 3399 Dihedral : 6.023 59.276 2652 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.61 % Allowed : 21.78 % Favored : 73.61 % 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: -0.94 (0.17), residues: 2415 helix: 0.13 (0.15), residues: 1134 sheet: -0.80 (0.27), residues: 372 loop : -1.38 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 46 TYR 0.026 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/Z covalent geometry : bond 0.00373 / 0.16 (19485) covalent geometry : angle 0.68105 / 0.34 (26472) hydrogen bonds : bond 0.04749 / 3.23 ( 904) hydrogen bonds : angle 5.44662 / 3.90 ( 2682) Misc. bond : bond 0.00391 / 0.17 ( 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: 93 poor density : 263 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.6020 (t80) cc_final: 0.5521 (t80) REVERT: A 244 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: A 312 MET cc_start: 0.6694 (mmt) cc_final: 0.6490 (mmt) REVERT: A 315 ARG cc_start: 0.6590 (tpp-160) cc_final: 0.5079 (ptt180) REVERT: B 70 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5624 (pp20) REVERT: B 355 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5322 (pm20) REVERT: B 398 TYR cc_start: 0.5641 (m-80) cc_final: 0.5344 (m-80) REVERT: C 3 VAL cc_start: 0.7547 (m) cc_final: 0.7268 (p) REVERT: C 151 PHE cc_start: 0.7068 (t80) cc_final: 0.6855 (t80) REVERT: D 76 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5912 (mpp-170) REVERT: D 291 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6442 (ptp-110) REVERT: D 387 ILE cc_start: 0.7369 (mt) cc_final: 0.7156 (tt) REVERT: E 74 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5737 (pt0) REVERT: E 341 ARG cc_start: 0.6625 (ttp-110) cc_final: 0.6083 (tmm-80) REVERT: F 106 TYR cc_start: 0.6532 (t80) cc_final: 0.6239 (t80) REVERT: F 184 TYR cc_start: 0.6471 (m-10) cc_final: 0.6212 (m-10) REVERT: F 224 ASP cc_start: 0.7688 (m-30) cc_final: 0.7372 (m-30) REVERT: F 228 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8598 (mp) REVERT: F 325 ASP cc_start: 0.7655 (m-30) cc_final: 0.7319 (m-30) REVERT: F 388 MET cc_start: 0.5908 (ptm) cc_final: 0.4039 (mmt) outliers start: 93 outliers final: 38 residues processed: 333 average time/residue: 0.4857 time to fit residues: 187.4084 Evaluate side-chains 281 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 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 285 ASN Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 355 GLU 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 74 GLU 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 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: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 193 optimal weight: 0.3980 chunk 15 optimal weight: 0.0170 chunk 234 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 306 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.201806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.179119 restraints weight = 24465.620| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 1.88 r_work: 0.4451 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4330 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19494 Z= 0.138 Angle : 0.659 12.055 26472 Z= 0.326 Chirality : 0.045 0.204 2994 Planarity : 0.004 0.051 3399 Dihedral : 5.825 58.055 2652 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.22 % Allowed : 22.27 % Favored : 73.51 % 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: -0.84 (0.17), residues: 2415 helix: 0.27 (0.15), residues: 1122 sheet: -0.87 (0.27), residues: 363 loop : -1.33 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 46 TYR 0.021 0.002 TYR C 403 PHE 0.023 0.001 PHE A 191 TRP 0.025 0.002 TRP D 102 HIS 0.004 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (19485) covalent geometry : angle 0.65894 / 0.33 (26472) hydrogen bonds : bond 0.04478 / 3.04 ( 904) hydrogen bonds : angle 5.35784 / 3.84 ( 2682) Misc. bond : bond 0.00315 / 0.14 ( 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 356 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 271 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5811 (t80) cc_final: 0.5424 (t80) REVERT: A 312 MET cc_start: 0.6682 (mmt) cc_final: 0.6449 (mmt) REVERT: B 355 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5285 (pm20) REVERT: B 361 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: B 398 TYR cc_start: 0.5486 (m-80) cc_final: 0.5199 (m-80) REVERT: C 3 VAL cc_start: 0.7487 (m) cc_final: 0.7234 (p) REVERT: C 121 MET cc_start: 0.6668 (mmm) cc_final: 0.6208 (mmm) REVERT: C 151 PHE cc_start: 0.7012 (t80) cc_final: 0.6774 (t80) REVERT: D 76 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5905 (mpp-170) REVERT: D 291 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6335 (ptp-110) REVERT: D 420 GLN cc_start: 0.5141 (pt0) cc_final: 0.4869 (tp-100) REVERT: E 341 ARG cc_start: 0.6683 (ttp-110) cc_final: 0.6066 (tmm-80) REVERT: F 106 TYR cc_start: 0.6597 (t80) cc_final: 0.6374 (t80) REVERT: F 224 ASP cc_start: 0.7642 (m-30) cc_final: 0.7312 (m-30) REVERT: F 228 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8560 (mp) REVERT: F 325 ASP cc_start: 0.7384 (m-30) cc_final: 0.7060 (m-30) REVERT: F 388 MET cc_start: 0.5779 (ptm) cc_final: 0.3841 (mmt) outliers start: 85 outliers final: 32 residues processed: 336 average time/residue: 0.4337 time to fit residues: 170.7508 Evaluate side-chains 272 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 289 LEU 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 251 THR Chi-restraints excluded: chain C residue 260 LEU 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 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 355 GLU 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 247 SER Chi-restraints excluded: chain E residue 251 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 298 ASN E 401 ASN F 14 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.200223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.176242 restraints weight = 24412.776| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 1.97 r_work: 0.4422 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19494 Z= 0.151 Angle : 0.679 12.175 26472 Z= 0.334 Chirality : 0.046 0.220 2994 Planarity : 0.005 0.069 3399 Dihedral : 5.880 59.740 2652 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.87 % Allowed : 23.66 % Favored : 72.47 % 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: -0.84 (0.17), residues: 2415 helix: 0.28 (0.15), residues: 1122 sheet: -0.89 (0.27), residues: 363 loop : -1.35 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 46 TYR 0.024 0.002 TYR C 403 PHE 0.027 0.002 PHE A 191 TRP 0.029 0.002 TRP D 102 HIS 0.011 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (19485) covalent geometry : angle 0.67870 / 0.33 (26472) hydrogen bonds : bond 0.04525 / 3.07 ( 904) hydrogen bonds : angle 5.36072 / 3.83 ( 2682) Misc. bond : bond 0.00359 / 0.16 ( 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 326 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7587 (p) REVERT: B 355 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5257 (pm20) REVERT: B 361 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.4545 (m-80) REVERT: B 399 GLU cc_start: 0.5670 (mp0) cc_final: 0.5420 (mp0) REVERT: C 3 VAL cc_start: 0.7491 (m) cc_final: 0.7230 (p) REVERT: C 151 PHE cc_start: 0.6848 (t80) cc_final: 0.6597 (t80) REVERT: C 428 GLN cc_start: 0.4364 (OUTLIER) cc_final: 0.3920 (mm-40) REVERT: D 291 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6293 (ptp-110) REVERT: E 341 ARG cc_start: 0.6568 (ttp-110) cc_final: 0.6068 (tmm-80) REVERT: F 106 TYR cc_start: 0.6551 (t80) cc_final: 0.6337 (t80) REVERT: F 154 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6339 (mm-30) REVERT: F 158 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5244 (pm20) REVERT: F 224 ASP cc_start: 0.7594 (m-30) cc_final: 0.7279 (m-30) REVERT: F 228 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8610 (mp) REVERT: F 325 ASP cc_start: 0.7494 (m-30) cc_final: 0.7140 (m-30) REVERT: F 388 MET cc_start: 0.5659 (ptm) cc_final: 0.4032 (mmt) outliers start: 78 outliers final: 39 residues processed: 308 average time/residue: 0.4749 time to fit residues: 169.9483 Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 234 THR Chi-restraints excluded: chain A residue 249 PHE 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 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 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 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 355 GLU 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 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 356 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 148 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 285 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 7 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 138 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 296 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.199916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.176685 restraints weight = 24535.576| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 1.87 r_work: 0.4436 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4317 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19494 Z= 0.147 Angle : 0.679 12.147 26472 Z= 0.333 Chirality : 0.046 0.192 2994 Planarity : 0.005 0.054 3399 Dihedral : 5.842 57.833 2652 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.32 % Allowed : 24.55 % Favored : 72.12 % 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: -0.88 (0.17), residues: 2415 helix: 0.30 (0.16), residues: 1122 sheet: -0.86 (0.29), residues: 318 loop : -1.46 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 46 TYR 0.023 0.002 TYR C 403 PHE 0.028 0.001 PHE A 191 TRP 0.033 0.002 TRP D 102 HIS 0.004 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (19485) covalent geometry : angle 0.67881 / 0.33 (26472) hydrogen bonds : bond 0.04459 / 3.03 ( 904) hydrogen bonds : angle 5.31800 / 3.80 ( 2682) Misc. bond : bond 0.00350 / 0.16 ( 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 314 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7665 (p) REVERT: B 320 ASP cc_start: 0.7602 (t0) cc_final: 0.7399 (OUTLIER) REVERT: B 355 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5104 (pm20) REVERT: B 398 TYR cc_start: 0.5539 (m-80) cc_final: 0.5306 (m-80) REVERT: C 3 VAL cc_start: 0.7537 (m) cc_final: 0.7321 (p) REVERT: C 151 PHE cc_start: 0.7046 (t80) cc_final: 0.6811 (t80) REVERT: D 182 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: E 341 ARG cc_start: 0.6712 (ttp-110) cc_final: 0.6110 (tmm-80) REVERT: F 158 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5273 (pm20) REVERT: F 184 TYR cc_start: 0.6339 (m-10) cc_final: 0.5975 (m-10) REVERT: F 224 ASP cc_start: 0.7721 (m-30) cc_final: 0.7366 (m-30) REVERT: F 228 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8569 (mp) REVERT: F 325 ASP cc_start: 0.7378 (m-30) cc_final: 0.7052 (m-30) REVERT: F 388 MET cc_start: 0.6024 (ptm) cc_final: 0.4255 (mmt) outliers start: 67 outliers final: 41 residues processed: 297 average time/residue: 0.4582 time to fit residues: 158.0828 Evaluate side-chains 275 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 235 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU 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 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 182 GLU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 355 GLU 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 247 SER 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 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 26 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.198696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.174935 restraints weight = 24347.155| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 1.97 r_work: 0.4418 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19494 Z= 0.158 Angle : 0.698 12.214 26472 Z= 0.344 Chirality : 0.047 0.191 2994 Planarity : 0.005 0.075 3399 Dihedral : 5.897 57.419 2652 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.32 % Allowed : 24.75 % 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: -0.89 (0.17), residues: 2415 helix: 0.31 (0.16), residues: 1122 sheet: -0.88 (0.29), residues: 318 loop : -1.48 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 46 TYR 0.024 0.002 TYR C 403 PHE 0.031 0.002 PHE A 191 TRP 0.035 0.002 TRP D 102 HIS 0.006 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (19485) covalent geometry : angle 0.69775 / 0.34 (26472) hydrogen bonds : bond 0.04530 / 3.07 ( 904) hydrogen bonds : angle 5.36232 / 3.84 ( 2682) Misc. bond : bond 0.00374 / 0.17 ( 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 309 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.6029 (t80) cc_final: 0.5438 (t80) REVERT: A 234 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7645 (p) REVERT: A 244 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7816 (mtm) REVERT: B 355 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5109 (pm20) REVERT: C 151 PHE cc_start: 0.6833 (t80) cc_final: 0.6575 (t80) REVERT: E 341 ARG cc_start: 0.6506 (ttp-110) cc_final: 0.6031 (tmm-80) REVERT: F 31 THR cc_start: 0.5780 (OUTLIER) cc_final: 0.5306 (t) REVERT: F 224 ASP cc_start: 0.7601 (m-30) cc_final: 0.7250 (m-30) REVERT: F 228 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8555 (mp) REVERT: F 325 ASP cc_start: 0.7284 (m-30) cc_final: 0.6948 (m-30) REVERT: F 388 MET cc_start: 0.5754 (ptm) cc_final: 0.4159 (mmt) outliers start: 67 outliers final: 39 residues processed: 291 average time/residue: 0.4448 time to fit residues: 151.2573 Evaluate side-chains 271 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 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 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 235 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU 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 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 355 GLU 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 247 SER 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 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: 3.9990 chunk 16 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 228 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 210 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 151 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN D 100 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN E 188 ASN E 401 ASN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.198959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.176013 restraints weight = 24372.602| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 1.89 r_work: 0.4431 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4309 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19494 Z= 0.152 Angle : 0.704 12.671 26472 Z= 0.347 Chirality : 0.047 0.274 2994 Planarity : 0.005 0.066 3399 Dihedral : 5.877 57.544 2652 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.53 % Allowed : 26.04 % Favored : 71.43 % 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: 0.30 (0.16), residues: 1122 sheet: -1.10 (0.30), residues: 294 loop : -1.44 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 46 TYR 0.026 0.002 TYR E 187 PHE 0.032 0.001 PHE A 191 TRP 0.039 0.002 TRP B 102 HIS 0.006 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19485) covalent geometry : angle 0.70433 / 0.35 (26472) hydrogen bonds : bond 0.04474 / 3.03 ( 904) hydrogen bonds : angle 5.35872 / 3.84 ( 2682) Misc. bond : bond 0.00356 / 0.16 ( 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 289 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.6009 (t80) cc_final: 0.5418 (t80) REVERT: A 234 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 381 ARG cc_start: 0.6759 (ptm-80) cc_final: 0.6513 (ptm-80) REVERT: B 175 LEU cc_start: 0.7690 (pt) cc_final: 0.7490 (tp) REVERT: B 320 ASP cc_start: 0.7619 (t0) cc_final: 0.7363 (t0) REVERT: B 355 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5139 (pm20) REVERT: C 109 TYR cc_start: 0.6464 (t80) cc_final: 0.6151 (t80) REVERT: C 110 LEU cc_start: 0.6347 (mm) cc_final: 0.6102 (mm) REVERT: C 151 PHE cc_start: 0.7032 (t80) cc_final: 0.6778 (t80) REVERT: E 340 MET cc_start: 0.5755 (ttp) cc_final: 0.5351 (tpp) REVERT: E 341 ARG cc_start: 0.6595 (ttp-110) cc_final: 0.6027 (tmm-80) REVERT: F 31 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.5260 (t) REVERT: F 184 TYR cc_start: 0.6444 (m-10) cc_final: 0.6148 (m-10) REVERT: F 224 ASP cc_start: 0.7636 (m-30) cc_final: 0.7237 (m-30) REVERT: F 228 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (mp) REVERT: F 325 ASP cc_start: 0.7445 (m-30) cc_final: 0.7126 (m-30) REVERT: F 388 MET cc_start: 0.6045 (ptm) cc_final: 0.4296 (mmt) outliers start: 51 outliers final: 37 residues processed: 275 average time/residue: 0.4509 time to fit residues: 145.7425 Evaluate side-chains 269 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 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 B residue 400 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU 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 219 SER Chi-restraints excluded: chain D residue 355 GLU 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 247 SER 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 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: 7.9990 chunk 152 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 247 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.196659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.173561 restraints weight = 24626.120| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 1.90 r_work: 0.4403 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3890 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= 0.178 Angle : 0.732 12.754 26472 Z= 0.361 Chirality : 0.048 0.314 2994 Planarity : 0.005 0.068 3399 Dihedral : 6.000 57.217 2652 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.68 % Allowed : 26.09 % Favored : 71.23 % 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: 0.25 (0.16), residues: 1122 sheet: -0.85 (0.29), residues: 318 loop : -1.46 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 46 TYR 0.036 0.002 TYR C 187 PHE 0.033 0.002 PHE A 191 TRP 0.037 0.003 TRP B 102 HIS 0.006 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (19485) covalent geometry : angle 0.73245 / 0.36 (26472) hydrogen bonds : bond 0.04658 / 3.16 ( 904) hydrogen bonds : angle 5.42677 / 3.89 ( 2682) Misc. bond : bond 0.00411 / 0.19 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.02 seconds wall clock time: 101 minutes 44.77 seconds (6104.77 seconds total)