Starting phenix.real_space_refine on Mon Aug 25 04:47:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v48_42968/08_2025/8v48_42968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v48_42968/08_2025/8v48_42968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v48_42968/08_2025/8v48_42968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v48_42968/08_2025/8v48_42968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v48_42968/08_2025/8v48_42968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v48_42968/08_2025/8v48_42968.map" } resolution = 3.68 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= 0.013 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 97 5.16 5 C 16134 2.51 5 N 4235 2.21 5 O 4850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25334 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3320 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} Chain breaks: 4 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3218 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 389} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "C" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "H" Number of atoms: 2371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2371 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 4 Chain: "G" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "K" Number of atoms: 2371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2371 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 4 Chain: "J" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.80, per 1000 atoms: 0.27 Number of scatterers: 25334 At special positions: 0 Unit cell: (100.98, 199.155, 175.78, 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 97 16.00 P 18 15.00 O 4850 8.00 N 4235 7.00 C 16134 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=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 53.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.665A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.569A pdb=" N ALA A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.162A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.529A pdb=" N LYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.612A pdb=" N VAL A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 319 removed outlier: 3.806A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.573A pdb=" N VAL A 365 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.743A pdb=" N GLU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.621A pdb=" N ALA B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 199 through 237 removed outlier: 3.543A pdb=" N PHE B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.648A pdb=" N VAL B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.674A pdb=" N SER B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.691A pdb=" N ALA B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.961A pdb=" N ASP B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 42 removed outlier: 3.737A pdb=" N PHE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 59 through 64 removed outlier: 4.299A pdb=" N LYS D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 143 through 172 removed outlier: 4.680A pdb=" N SER D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.804A pdb=" N ALA D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 226 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 236 through 257 removed outlier: 3.585A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 275 through 291 Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'C' and resid 38 through 51 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.675A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.579A pdb=" N ALA C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 199 through 234 removed outlier: 3.899A pdb=" N PHE C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.542A pdb=" N ASN C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 269 " --> pdb=" O ILE C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 269' Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.837A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 319 removed outlier: 3.524A pdb=" N ALA C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.554A pdb=" N VAL C 365 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.845A pdb=" N GLU C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.677A pdb=" N ALA F 58 " --> pdb=" O ILE F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 151 through 161 Processing helix chain 'F' and resid 177 through 189 Processing helix chain 'F' and resid 199 through 235 removed outlier: 4.442A pdb=" N PHE F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 235 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 264 removed outlier: 3.609A pdb=" N LYS F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 287 removed outlier: 3.885A pdb=" N VAL F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 319 Processing helix chain 'F' and resid 319 through 331 Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.503A pdb=" N VAL F 365 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.692A pdb=" N GLU F 404 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU F 407 " --> pdb=" O GLN F 403 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 102 through 114 removed outlier: 3.807A pdb=" N ILE H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 137 Processing helix chain 'H' and resid 151 through 161 Processing helix chain 'H' and resid 177 through 189 Processing helix chain 'H' and resid 322 through 333 removed outlier: 4.094A pdb=" N PHE H 332 " --> pdb=" O SER H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 381 Processing helix chain 'H' and resid 399 through 405 removed outlier: 3.794A pdb=" N GLU H 404 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP H 405 " --> pdb=" O ASP H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 412 removed outlier: 3.537A pdb=" N ARG H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 Processing helix chain 'G' and resid 27 through 42 removed outlier: 3.697A pdb=" N PHE G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.400A pdb=" N LYS G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 120 through 126 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 143 through 172 removed outlier: 3.573A pdb=" N GLU G 153 " --> pdb=" O GLU G 149 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER G 157 " --> pdb=" O GLU G 153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA G 160 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 182 removed outlier: 3.965A pdb=" N ALA G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 226 Proline residue: G 221 - end of helix Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 236 through 257 Processing helix chain 'G' and resid 260 through 273 Processing helix chain 'G' and resid 275 through 291 Processing helix chain 'G' and resid 300 through 307 Processing helix chain 'K' and resid 38 through 50 Processing helix chain 'K' and resid 53 through 59 removed outlier: 3.573A pdb=" N ARG K 56 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 114 Processing helix chain 'K' and resid 125 through 138 Processing helix chain 'K' and resid 151 through 159 removed outlier: 3.822A pdb=" N SER K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 189 Processing helix chain 'K' and resid 322 through 333 removed outlier: 4.467A pdb=" N PHE K 332 " --> pdb=" O SER K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 366 removed outlier: 3.969A pdb=" N VAL K 365 " --> pdb=" O PRO K 362 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU K 366 " --> pdb=" O ILE K 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 362 through 366' Processing helix chain 'K' and resid 367 through 379 removed outlier: 3.932A pdb=" N ALA K 379 " --> pdb=" O THR K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 412 Processing helix chain 'K' and resid 432 through 434 No H-bonds generated for 'chain 'K' and resid 432 through 434' Processing helix chain 'J' and resid 8 through 18 Processing helix chain 'J' and resid 27 through 42 removed outlier: 3.673A pdb=" N PHE J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 64 removed outlier: 4.402A pdb=" N LYS J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 120 through 126 Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 143 through 172 removed outlier: 4.619A pdb=" N SER J 156 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE J 159 " --> pdb=" O ILE J 155 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA J 160 " --> pdb=" O SER J 156 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL J 161 " --> pdb=" O SER J 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 182 removed outlier: 3.960A pdb=" N ALA J 180 " --> pdb=" O GLY J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 225 Proline residue: J 221 - end of helix Processing helix chain 'J' and resid 227 through 232 Processing helix chain 'J' and resid 236 through 257 removed outlier: 3.669A pdb=" N LEU J 242 " --> pdb=" O HIS J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 273 Processing helix chain 'J' and resid 275 through 291 Processing helix chain 'J' and resid 300 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 5.342A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 148 removed outlier: 7.293A pdb=" N ALA A 387 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ILE A 420 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 389 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N CYS A 422 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 391 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A 437 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 30 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 439 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N HIS A 32 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.826A pdb=" N GLU B 64 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 11 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 66 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 9 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 68 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 148 removed outlier: 8.424A pdb=" N ILE B 420 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 437 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.172A pdb=" N LEU D 23 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR D 114 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE D 85 " --> pdb=" O TYR D 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 3.710A pdb=" N GLU C 64 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 13 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 442 " --> pdb=" O ASN C 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.148A pdb=" N SER C 146 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP C 392 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 148 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 389 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N CYS C 422 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 391 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 437 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 439 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N HIS C 32 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 341 Processing sheet with id=AB3, first strand: chain 'F' and resid 97 through 101 removed outlier: 3.655A pdb=" N GLU F 64 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 20 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS F 13 " --> pdb=" O TYR F 18 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR F 18 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 146 through 148 removed outlier: 5.915A pdb=" N VAL F 389 " --> pdb=" O ILE F 420 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS F 422 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE F 391 " --> pdb=" O CYS F 422 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE F 437 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL F 30 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 337 through 341 Processing sheet with id=AB6, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.542A pdb=" N GLU H 64 " --> pdb=" O SER H 12 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS H 13 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR H 18 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 146 through 148 removed outlier: 5.888A pdb=" N VAL H 389 " --> pdb=" O ILE H 420 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS H 422 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE H 391 " --> pdb=" O CYS H 422 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE H 437 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL H 30 " --> pdb=" O ILE H 437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 337 through 339 removed outlier: 3.797A pdb=" N ALA H 339 " --> pdb=" O GLY H 352 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY H 352 " --> pdb=" O ALA H 339 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.297A pdb=" N LYS G 21 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP G 50 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU G 23 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 94 through 96 Processing sheet with id=AC2, first strand: chain 'K' and resid 97 through 101 removed outlier: 3.616A pdb=" N PHE K 87 " --> pdb=" O ASP K 80 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 64 " --> pdb=" O SER K 12 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS K 13 " --> pdb=" O TYR K 18 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR K 18 " --> pdb=" O LYS K 13 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 147 through 148 removed outlier: 3.505A pdb=" N ILE K 420 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS K 422 " --> pdb=" O ILE K 391 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE K 437 " --> pdb=" O LEU K 28 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL K 30 " --> pdb=" O ILE K 437 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 6 through 7 removed outlier: 6.670A pdb=" N TYR J 6 " --> pdb=" O LYS J 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 48 through 51 removed outlier: 6.005A pdb=" N LEU J 23 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG J 22 " --> pdb=" O SER J 84 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU J 86 " --> pdb=" O ARG J 22 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU J 24 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP J 115 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR J 108 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 94 through 95 1333 hydrogen bonds defined for protein. 3813 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: 5.07 Time building geometry restraints manager: 2.98 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: 8034 1.34 - 1.46: 5398 1.46 - 1.58: 12193 1.58 - 1.70: 16 1.70 - 1.81: 167 Bond restraints: 25808 Sorted by residual: bond pdb=" O3A ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 1.592 1.531 0.061 3.00e-02 1.11e+03 4.11e+00 bond pdb=" CA HIS A 32 " pdb=" CB HIS A 32 " ideal model delta sigma weight residual 1.536 1.497 0.038 2.08e-02 2.31e+03 3.42e+00 bond pdb=" C LEU J 220 " pdb=" N PRO J 221 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.21e+00 bond pdb=" C LEU G 177 " pdb=" N PRO G 178 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.10e+00 bond pdb=" C LEU J 177 " pdb=" N PRO J 178 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.02e+00 ... (remaining 25803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33395 1.63 - 3.25: 1246 3.25 - 4.88: 137 4.88 - 6.50: 18 6.50 - 8.13: 20 Bond angle restraints: 34816 Sorted by residual: angle pdb=" C ASP K 83 " pdb=" N GLU K 84 " pdb=" CA GLU K 84 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ASP H 83 " pdb=" N GLU H 84 " pdb=" CA GLU H 84 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ASP A 83 " pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CA GLU C 433 " pdb=" CB GLU C 433 " pdb=" CG GLU C 433 " ideal model delta sigma weight residual 114.10 106.19 7.91 2.00e+00 2.50e-01 1.56e+01 angle pdb=" C ASP C 343 " pdb=" CA ASP C 343 " pdb=" CB ASP C 343 " ideal model delta sigma weight residual 115.89 111.41 4.48 1.32e+00 5.74e-01 1.15e+01 ... (remaining 34811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 14752 17.75 - 35.50: 723 35.50 - 53.25: 161 53.25 - 71.00: 54 71.00 - 88.75: 15 Dihedral angle restraints: 15705 sinusoidal: 6451 harmonic: 9254 Sorted by residual: dihedral pdb=" CA ILE K 14 " pdb=" C ILE K 14 " pdb=" N HIS K 15 " pdb=" CA HIS K 15 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TRP H 360 " pdb=" C TRP H 360 " pdb=" N SER H 361 " pdb=" CA SER H 361 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE K 363 " pdb=" C ILE K 363 " pdb=" N ARG K 364 " pdb=" CA ARG K 364 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 15702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2657 0.047 - 0.094: 924 0.094 - 0.141: 256 0.141 - 0.189: 36 0.189 - 0.236: 5 Chirality restraints: 3878 Sorted by residual: chirality pdb=" CB VAL D 255 " pdb=" CA VAL D 255 " pdb=" CG1 VAL D 255 " pdb=" CG2 VAL D 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU F 187 " pdb=" CB LEU F 187 " pdb=" CD1 LEU F 187 " pdb=" CD2 LEU F 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB VAL G 255 " pdb=" CA VAL G 255 " pdb=" CG1 VAL G 255 " pdb=" CG2 VAL G 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3875 not shown) Planarity restraints: 4396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 223 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C SER B 223 " 0.051 2.00e-02 2.50e+03 pdb=" O SER B 223 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 224 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 312 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C GLN C 312 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN C 312 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP C 313 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 237 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C GLY G 237 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY G 237 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS G 238 " -0.014 2.00e-02 2.50e+03 ... (remaining 4393 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4534 2.77 - 3.30: 23595 3.30 - 3.83: 43025 3.83 - 4.37: 49910 4.37 - 4.90: 86158 Nonbonded interactions: 207222 Sorted by model distance: nonbonded pdb=" OE1 GLU B 222 " pdb=" OG SER C 223 " model vdw 2.235 3.040 nonbonded pdb=" O ASN B 177 " pdb=" OG SER B 181 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASN K 177 " pdb=" OG SER K 181 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR H 5 " pdb=" OG SER H 70 " model vdw 2.292 3.040 nonbonded pdb=" O ALA A 380 " pdb=" OG SER A 415 " model vdw 2.297 3.040 ... (remaining 207217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444 or r \ esid 501)) selection = (chain 'B' and (resid 3 through 236 or resid 249 through 288 or resid 295 throug \ h 501)) selection = (chain 'C' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444 or r \ esid 501)) selection = (chain 'F' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444 or r \ esid 501)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.006 0.061 25808 Z= 0.272 Angle : 0.734 8.128 34816 Z= 0.418 Chirality : 0.051 0.236 3878 Planarity : 0.005 0.050 4396 Dihedral : 11.859 88.752 9691 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.49 % Allowed : 4.80 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3073 helix: 0.17 (0.12), residues: 1544 sheet: 0.16 (0.24), residues: 496 loop : -0.83 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.030 0.002 TYR A 18 PHE 0.021 0.002 PHE B 226 TRP 0.023 0.002 TRP B 402 HIS 0.010 0.002 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00588 (25808) covalent geometry : angle 0.73437 (34816) hydrogen bonds : bond 0.16624 ( 1333) hydrogen bonds : angle 6.35359 ( 3813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 39 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8802 (mtmm) REVERT: A 53 ASP cc_start: 0.8912 (t0) cc_final: 0.8414 (t0) REVERT: A 104 GLU cc_start: 0.9108 (tt0) cc_final: 0.8830 (tp30) REVERT: A 154 MET cc_start: 0.9096 (ttt) cc_final: 0.8886 (ttm) REVERT: A 209 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8851 (mm-30) REVERT: A 338 MET cc_start: 0.8442 (ttp) cc_final: 0.7749 (ttt) REVERT: A 347 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7380 (mmtt) REVERT: A 376 MET cc_start: 0.9371 (mtm) cc_final: 0.9031 (mtp) REVERT: B 230 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8129 (m-80) REVERT: B 308 LEU cc_start: 0.8554 (mt) cc_final: 0.8337 (tp) REVERT: D 62 MET cc_start: 0.8890 (ttp) cc_final: 0.8483 (tpp) REVERT: D 87 CYS cc_start: 0.8903 (m) cc_final: 0.8700 (m) REVERT: C 16 ASN cc_start: 0.8769 (m-40) cc_final: 0.8171 (p0) REVERT: C 110 ARG cc_start: 0.8998 (ttt-90) cc_final: 0.8543 (tpp-160) REVERT: C 191 PHE cc_start: 0.7955 (t80) cc_final: 0.7641 (t80) REVERT: C 225 THR cc_start: 0.9268 (m) cc_final: 0.8526 (p) REVERT: C 326 MET cc_start: 0.8833 (mtt) cc_final: 0.8036 (mmm) REVERT: C 374 LEU cc_start: 0.9391 (tp) cc_final: 0.9175 (tp) REVERT: C 393 GLN cc_start: 0.8698 (mt0) cc_final: 0.8497 (mm-40) REVERT: F 60 LEU cc_start: 0.7372 (tp) cc_final: 0.7067 (tt) REVERT: F 191 PHE cc_start: 0.5860 (t80) cc_final: 0.5526 (p90) REVERT: F 280 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8291 (pt0) REVERT: F 286 ASN cc_start: 0.7285 (t0) cc_final: 0.6888 (m-40) REVERT: F 378 TYR cc_start: 0.6622 (t80) cc_final: 0.6335 (t80) REVERT: H 22 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (t) REVERT: H 49 ILE cc_start: 0.8440 (mt) cc_final: 0.8186 (mm) REVERT: H 54 PHE cc_start: 0.8480 (m-80) cc_final: 0.7838 (m-80) REVERT: H 155 LEU cc_start: 0.9199 (tp) cc_final: 0.8946 (tt) REVERT: H 340 TYR cc_start: 0.1614 (p90) cc_final: 0.1360 (t80) REVERT: G 23 LEU cc_start: 0.8270 (tp) cc_final: 0.8037 (tp) REVERT: G 101 GLU cc_start: 0.9326 (tt0) cc_final: 0.9036 (mp0) REVERT: K 43 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8959 (pt) REVERT: K 175 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5142 (p90) REVERT: K 340 TYR cc_start: -0.2416 (OUTLIER) cc_final: -0.2845 (p90) outliers start: 69 outliers final: 12 residues processed: 490 average time/residue: 0.2034 time to fit residues: 149.8069 Evaluate side-chains 231 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 HIS B 15 HIS B 177 ASN B 295 ASN B 424 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 312 GLN C 315 GLN F 32 HIS F 177 ASN F 262 GLN F 312 GLN F 315 GLN ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS H 51 ASN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 399 HIS ** G 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS K 32 HIS K 85 GLN ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 HIS J 306 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.110877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074828 restraints weight = 120109.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.076122 restraints weight = 56324.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.075870 restraints weight = 30004.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.075946 restraints weight = 31748.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.076049 restraints weight = 27637.591| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25808 Z= 0.272 Angle : 0.661 9.775 34816 Z= 0.350 Chirality : 0.044 0.213 3878 Planarity : 0.005 0.053 4396 Dihedral : 9.559 89.665 3654 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.85 % Allowed : 9.82 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3073 helix: 1.41 (0.13), residues: 1533 sheet: 0.09 (0.25), residues: 488 loop : -0.24 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 89 TYR 0.018 0.002 TYR D 143 PHE 0.025 0.002 PHE B 226 TRP 0.016 0.002 TRP B 402 HIS 0.011 0.002 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00591 (25808) covalent geometry : angle 0.66078 (34816) hydrogen bonds : bond 0.04024 ( 1333) hydrogen bonds : angle 4.86737 ( 3813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 208 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8399 (p0) REVERT: A 53 ASP cc_start: 0.8852 (t0) cc_final: 0.8367 (t0) REVERT: A 106 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8862 (mpp) REVERT: A 154 MET cc_start: 0.9012 (ttt) cc_final: 0.8766 (ttm) REVERT: A 262 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8055 (mm110) REVERT: A 326 MET cc_start: 0.8910 (mmm) cc_final: 0.8420 (mmm) REVERT: A 338 MET cc_start: 0.8372 (ttp) cc_final: 0.7551 (ttm) REVERT: A 347 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7672 (mmtt) REVERT: B 252 LEU cc_start: 0.9210 (tp) cc_final: 0.8943 (tp) REVERT: B 377 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9360 (mm) REVERT: D 62 MET cc_start: 0.8750 (ttp) cc_final: 0.8445 (tpp) REVERT: D 87 CYS cc_start: 0.8778 (m) cc_final: 0.8548 (m) REVERT: C 106 MET cc_start: 0.9426 (mtm) cc_final: 0.9110 (mpp) REVERT: C 110 ARG cc_start: 0.8951 (ttt-90) cc_final: 0.8659 (tpp-160) REVERT: C 326 MET cc_start: 0.9386 (mtt) cc_final: 0.8931 (mmm) REVERT: C 338 MET cc_start: 0.8647 (ttp) cc_final: 0.8209 (ttp) REVERT: C 348 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: C 374 LEU cc_start: 0.9494 (tp) cc_final: 0.9270 (tp) REVERT: C 393 GLN cc_start: 0.9200 (mt0) cc_final: 0.8870 (mm-40) REVERT: F 280 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8134 (pt0) REVERT: F 286 ASN cc_start: 0.7224 (t0) cc_final: 0.6749 (m-40) REVERT: F 326 MET cc_start: 0.8854 (mmm) cc_final: 0.8608 (mmm) REVERT: H 340 TYR cc_start: 0.1061 (p90) cc_final: 0.0393 (t80) REVERT: H 383 MET cc_start: 0.8588 (mpp) cc_final: 0.8361 (mpp) REVERT: H 390 LEU cc_start: 0.9328 (mt) cc_final: 0.9127 (mp) REVERT: G 17 MET cc_start: 0.8264 (mmm) cc_final: 0.7861 (mmm) REVERT: G 35 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: K 175 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5207 (p90) REVERT: K 340 TYR cc_start: -0.2542 (OUTLIER) cc_final: -0.3358 (p90) REVERT: K 376 MET cc_start: 0.9351 (mtt) cc_final: 0.9030 (mmt) REVERT: J 200 ASP cc_start: 0.7897 (m-30) cc_final: 0.7655 (t0) outliers start: 79 outliers final: 41 residues processed: 272 average time/residue: 0.1729 time to fit residues: 75.4071 Evaluate side-chains 213 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain J residue 35 TYR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 142 optimal weight: 0.0370 chunk 200 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 309 optimal weight: 50.0000 chunk 251 optimal weight: 0.7980 overall best weight: 3.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.110569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074796 restraints weight = 120372.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.075999 restraints weight = 59123.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.075693 restraints weight = 33243.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.075932 restraints weight = 32903.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.076030 restraints weight = 28069.678| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25808 Z= 0.220 Angle : 0.591 9.029 34816 Z= 0.313 Chirality : 0.044 0.267 3878 Planarity : 0.004 0.036 4396 Dihedral : 8.735 89.211 3637 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.74 % Allowed : 11.26 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.15), residues: 3073 helix: 1.77 (0.13), residues: 1502 sheet: -0.06 (0.25), residues: 488 loop : -0.05 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 309 TYR 0.019 0.002 TYR A 278 PHE 0.025 0.002 PHE B 226 TRP 0.012 0.001 TRP J 287 HIS 0.020 0.002 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00480 (25808) covalent geometry : angle 0.59140 (34816) hydrogen bonds : bond 0.03673 ( 1333) hydrogen bonds : angle 4.69287 ( 3813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 177 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8817 (t0) cc_final: 0.8526 (t0) REVERT: A 96 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8851 (mmtm) REVERT: A 106 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8662 (mpp) REVERT: A 154 MET cc_start: 0.8967 (ttt) cc_final: 0.8703 (ttm) REVERT: A 326 MET cc_start: 0.8929 (mmm) cc_final: 0.8441 (mmm) REVERT: A 338 MET cc_start: 0.8008 (ttp) cc_final: 0.7413 (ttm) REVERT: A 377 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 252 LEU cc_start: 0.9186 (tp) cc_final: 0.8910 (tp) REVERT: D 62 MET cc_start: 0.8702 (ttp) cc_final: 0.8380 (tpp) REVERT: D 87 CYS cc_start: 0.8748 (m) cc_final: 0.8543 (m) REVERT: C 110 ARG cc_start: 0.8981 (ttt-90) cc_final: 0.8767 (tpp-160) REVERT: C 326 MET cc_start: 0.9401 (mtt) cc_final: 0.8949 (mmm) REVERT: C 338 MET cc_start: 0.8581 (ttp) cc_final: 0.8102 (ttp) REVERT: C 393 GLN cc_start: 0.9257 (mt0) cc_final: 0.8894 (mm-40) REVERT: F 201 MET cc_start: 0.9446 (mmp) cc_final: 0.8369 (tmm) REVERT: F 280 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8024 (mt-10) REVERT: F 286 ASN cc_start: 0.7095 (t0) cc_final: 0.6611 (m-40) REVERT: F 304 TYR cc_start: 0.8480 (t80) cc_final: 0.7959 (t80) REVERT: H 54 PHE cc_start: 0.8872 (m-80) cc_final: 0.8023 (m-80) REVERT: H 340 TYR cc_start: 0.1082 (p90) cc_final: 0.0530 (t80) REVERT: H 366 LEU cc_start: 0.8946 (mt) cc_final: 0.8404 (pt) REVERT: H 374 LEU cc_start: 0.9560 (tt) cc_final: 0.9352 (pp) REVERT: G 17 MET cc_start: 0.8059 (mmm) cc_final: 0.7504 (mmm) REVERT: G 35 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: K 175 PHE cc_start: 0.6358 (OUTLIER) cc_final: 0.5346 (p90) REVERT: K 340 TYR cc_start: -0.2300 (OUTLIER) cc_final: -0.3061 (p90) REVERT: J 17 MET cc_start: 0.7804 (ttt) cc_final: 0.7141 (mtp) REVERT: J 20 LYS cc_start: 0.5524 (OUTLIER) cc_final: 0.5135 (tppt) REVERT: J 121 LEU cc_start: 0.7494 (tp) cc_final: 0.7174 (mt) REVERT: J 200 ASP cc_start: 0.7898 (m-30) cc_final: 0.7685 (t0) outliers start: 76 outliers final: 50 residues processed: 236 average time/residue: 0.1556 time to fit residues: 59.7577 Evaluate side-chains 213 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 444 ILE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 35 TYR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 297 optimal weight: 50.0000 chunk 156 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 301 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.111451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071317 restraints weight = 120049.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.073101 restraints weight = 50851.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074086 restraints weight = 31387.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.074530 restraints weight = 23808.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.074877 restraints weight = 20952.162| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25808 Z= 0.118 Angle : 0.510 11.876 34816 Z= 0.268 Chirality : 0.042 0.222 3878 Planarity : 0.003 0.043 4396 Dihedral : 7.821 89.848 3632 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 12.06 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.16), residues: 3073 helix: 1.79 (0.13), residues: 1556 sheet: 0.20 (0.25), residues: 463 loop : -0.18 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 309 TYR 0.014 0.001 TYR A 278 PHE 0.023 0.001 PHE B 226 TRP 0.015 0.001 TRP G 287 HIS 0.018 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00255 (25808) covalent geometry : angle 0.50961 (34816) hydrogen bonds : bond 0.03149 ( 1333) hydrogen bonds : angle 4.35599 ( 3813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8842 (t0) cc_final: 0.8387 (t0) REVERT: A 154 MET cc_start: 0.8950 (ttt) cc_final: 0.8675 (ttm) REVERT: A 326 MET cc_start: 0.9035 (mmm) cc_final: 0.8574 (mmm) REVERT: A 338 MET cc_start: 0.8054 (ttp) cc_final: 0.7424 (ttm) REVERT: A 347 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7364 (mmtt) REVERT: A 376 MET cc_start: 0.9055 (mtp) cc_final: 0.8747 (mtp) REVERT: A 377 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 252 LEU cc_start: 0.9279 (tp) cc_final: 0.8977 (tp) REVERT: B 326 MET cc_start: 0.9013 (mmm) cc_final: 0.8585 (mmm) REVERT: B 377 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9262 (mm) REVERT: D 62 MET cc_start: 0.8678 (ttp) cc_final: 0.8279 (tpp) REVERT: D 87 CYS cc_start: 0.8713 (m) cc_final: 0.8471 (m) REVERT: C 205 ASP cc_start: 0.9156 (m-30) cc_final: 0.8938 (m-30) REVERT: C 326 MET cc_start: 0.9469 (mtt) cc_final: 0.8945 (mmm) REVERT: C 338 MET cc_start: 0.8362 (ttp) cc_final: 0.7921 (ttp) REVERT: C 393 GLN cc_start: 0.9248 (mt0) cc_final: 0.8877 (mm-40) REVERT: F 280 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7951 (mt-10) REVERT: F 286 ASN cc_start: 0.7218 (t0) cc_final: 0.6655 (m-40) REVERT: F 304 TYR cc_start: 0.8500 (t80) cc_final: 0.8164 (t80) REVERT: H 54 PHE cc_start: 0.8678 (m-80) cc_final: 0.7840 (m-80) REVERT: H 366 LEU cc_start: 0.9036 (mt) cc_final: 0.8506 (pt) REVERT: G 17 MET cc_start: 0.8044 (mmm) cc_final: 0.7613 (mmm) REVERT: G 35 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: K 175 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5316 (p90) REVERT: K 340 TYR cc_start: -0.2478 (OUTLIER) cc_final: -0.3413 (p90) REVERT: K 373 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9015 (pp) REVERT: K 393 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7847 (mm-40) outliers start: 70 outliers final: 38 residues processed: 235 average time/residue: 0.1547 time to fit residues: 58.2727 Evaluate side-chains 198 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 106 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 255 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 245 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN K 35 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.109723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068893 restraints weight = 118342.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070364 restraints weight = 52551.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071288 restraints weight = 32482.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.071946 restraints weight = 25489.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072132 restraints weight = 22284.338| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25808 Z= 0.231 Angle : 0.610 13.050 34816 Z= 0.319 Chirality : 0.044 0.348 3878 Planarity : 0.004 0.040 4396 Dihedral : 7.732 85.559 3627 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.82 % Allowed : 12.49 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.15), residues: 3073 helix: 1.67 (0.13), residues: 1532 sheet: -0.21 (0.24), residues: 487 loop : -0.06 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 236 TYR 0.018 0.002 TYR A 278 PHE 0.020 0.002 PHE B 226 TRP 0.016 0.001 TRP G 287 HIS 0.005 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00506 (25808) covalent geometry : angle 0.60956 (34816) hydrogen bonds : bond 0.03504 ( 1333) hydrogen bonds : angle 4.70460 ( 3813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 155 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9030 (ttt) cc_final: 0.8763 (ttm) REVERT: A 326 MET cc_start: 0.9034 (mmm) cc_final: 0.8475 (mmm) REVERT: A 338 MET cc_start: 0.8152 (ttp) cc_final: 0.7416 (ttm) REVERT: A 377 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8893 (mm) REVERT: B 252 LEU cc_start: 0.9346 (tp) cc_final: 0.9032 (tp) REVERT: B 377 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9325 (mm) REVERT: C 84 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: C 326 MET cc_start: 0.9462 (mtt) cc_final: 0.9142 (mtp) REVERT: C 393 GLN cc_start: 0.9316 (mt0) cc_final: 0.8885 (mm-40) REVERT: F 201 MET cc_start: 0.9365 (mmp) cc_final: 0.8363 (tmm) REVERT: F 280 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8081 (pt0) REVERT: F 286 ASN cc_start: 0.7151 (t0) cc_final: 0.6631 (m-40) REVERT: F 304 TYR cc_start: 0.8580 (t80) cc_final: 0.8234 (t80) REVERT: F 319 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8848 (t80) REVERT: H 54 PHE cc_start: 0.8705 (m-80) cc_final: 0.7849 (m-80) REVERT: H 154 MET cc_start: 0.7696 (ttt) cc_final: 0.7120 (ttt) REVERT: H 366 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8487 (pt) REVERT: G 17 MET cc_start: 0.8045 (mmm) cc_final: 0.7618 (mmm) REVERT: G 35 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: K 175 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.5820 (p90) REVERT: K 340 TYR cc_start: -0.2337 (OUTLIER) cc_final: -0.3446 (p90) REVERT: K 393 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7997 (mm-40) REVERT: J 17 MET cc_start: 0.8162 (ttt) cc_final: 0.6682 (mtp) outliers start: 78 outliers final: 50 residues processed: 216 average time/residue: 0.1539 time to fit residues: 54.3231 Evaluate side-chains 204 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 400 ILE Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.111247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070998 restraints weight = 120551.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072606 restraints weight = 51884.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.073618 restraints weight = 31303.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074004 restraints weight = 24109.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074662 restraints weight = 21419.638| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25808 Z= 0.112 Angle : 0.533 13.094 34816 Z= 0.275 Chirality : 0.042 0.297 3878 Planarity : 0.003 0.034 4396 Dihedral : 7.270 86.448 3627 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.95 % Allowed : 13.86 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.16), residues: 3073 helix: 1.78 (0.13), residues: 1540 sheet: 0.13 (0.25), residues: 450 loop : -0.12 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 309 TYR 0.021 0.001 TYR F 378 PHE 0.019 0.001 PHE B 226 TRP 0.018 0.001 TRP G 287 HIS 0.005 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00240 (25808) covalent geometry : angle 0.53262 (34816) hydrogen bonds : bond 0.03063 ( 1333) hydrogen bonds : angle 4.41887 ( 3813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8558 (mtm-85) REVERT: A 53 ASP cc_start: 0.8859 (t0) cc_final: 0.8308 (t0) REVERT: A 154 MET cc_start: 0.8929 (ttt) cc_final: 0.8656 (ttm) REVERT: A 338 MET cc_start: 0.8032 (ttp) cc_final: 0.7817 (ttm) REVERT: A 347 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7044 (mmtt) REVERT: A 376 MET cc_start: 0.9271 (mtp) cc_final: 0.9019 (mtp) REVERT: A 377 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 252 LEU cc_start: 0.9322 (tp) cc_final: 0.9013 (tp) REVERT: B 377 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9242 (mm) REVERT: D 62 MET cc_start: 0.8774 (ttp) cc_final: 0.8210 (tpp) REVERT: C 16 ASN cc_start: 0.9089 (m-40) cc_final: 0.8346 (p0) REVERT: C 84 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: C 326 MET cc_start: 0.9492 (mtt) cc_final: 0.8818 (mtt) REVERT: C 393 GLN cc_start: 0.9282 (mt0) cc_final: 0.8882 (mm-40) REVERT: C 436 MET cc_start: 0.8941 (ptt) cc_final: 0.8625 (ppp) REVERT: F 201 MET cc_start: 0.9329 (mmp) cc_final: 0.8282 (tmm) REVERT: F 280 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8027 (pt0) REVERT: F 286 ASN cc_start: 0.7129 (t0) cc_final: 0.6678 (m-40) REVERT: F 304 TYR cc_start: 0.8652 (t80) cc_final: 0.8312 (t80) REVERT: H 17 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7472 (mtm180) REVERT: H 54 PHE cc_start: 0.8694 (m-80) cc_final: 0.7868 (m-80) REVERT: H 366 LEU cc_start: 0.8870 (mt) cc_final: 0.8455 (pt) REVERT: G 24 LEU cc_start: 0.9063 (tp) cc_final: 0.8474 (mp) REVERT: G 35 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: K 175 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5757 (p90) REVERT: K 340 TYR cc_start: -0.2374 (OUTLIER) cc_final: -0.3300 (p90) REVERT: J 17 MET cc_start: 0.8143 (ttt) cc_final: 0.7656 (mtp) outliers start: 54 outliers final: 40 residues processed: 201 average time/residue: 0.1675 time to fit residues: 55.3511 Evaluate side-chains 196 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 306 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.111438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071411 restraints weight = 119746.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.073160 restraints weight = 51337.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.074124 restraints weight = 31054.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.074663 restraints weight = 23651.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.074825 restraints weight = 20792.789| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25808 Z= 0.105 Angle : 0.522 13.055 34816 Z= 0.268 Chirality : 0.042 0.246 3878 Planarity : 0.003 0.036 4396 Dihedral : 7.050 86.114 3627 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.84 % Allowed : 14.12 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.16), residues: 3073 helix: 1.82 (0.13), residues: 1539 sheet: 0.02 (0.25), residues: 471 loop : -0.00 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 309 TYR 0.015 0.001 TYR F 378 PHE 0.018 0.001 PHE B 226 TRP 0.019 0.001 TRP G 287 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00225 (25808) covalent geometry : angle 0.52157 (34816) hydrogen bonds : bond 0.02952 ( 1333) hydrogen bonds : angle 4.29875 ( 3813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (mtm-85) REVERT: A 53 ASP cc_start: 0.8855 (t0) cc_final: 0.8303 (t0) REVERT: A 154 MET cc_start: 0.8940 (ttt) cc_final: 0.8700 (ttm) REVERT: A 326 MET cc_start: 0.8955 (mmm) cc_final: 0.8562 (mmm) REVERT: A 338 MET cc_start: 0.7923 (ttp) cc_final: 0.7631 (ttm) REVERT: A 347 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7168 (mmpt) REVERT: A 376 MET cc_start: 0.9166 (mtp) cc_final: 0.8924 (mtp) REVERT: A 377 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8855 (mm) REVERT: B 53 ASP cc_start: 0.8725 (t0) cc_final: 0.7991 (p0) REVERT: B 252 LEU cc_start: 0.9291 (tp) cc_final: 0.8992 (tp) REVERT: B 377 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9200 (mm) REVERT: D 62 MET cc_start: 0.8793 (ttp) cc_final: 0.8219 (tpp) REVERT: C 16 ASN cc_start: 0.9054 (m-40) cc_final: 0.8342 (p0) REVERT: C 154 MET cc_start: 0.8831 (ptm) cc_final: 0.8607 (ptm) REVERT: C 326 MET cc_start: 0.9491 (mtt) cc_final: 0.9197 (mtt) REVERT: C 393 GLN cc_start: 0.9273 (mt0) cc_final: 0.8888 (mm-40) REVERT: C 436 MET cc_start: 0.8894 (ptt) cc_final: 0.8590 (ppp) REVERT: F 201 MET cc_start: 0.9276 (mmp) cc_final: 0.8276 (tmm) REVERT: F 280 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8075 (pt0) REVERT: F 286 ASN cc_start: 0.7048 (t0) cc_final: 0.6627 (m-40) REVERT: F 304 TYR cc_start: 0.8723 (t80) cc_final: 0.8376 (t80) REVERT: F 383 MET cc_start: 0.6237 (mpp) cc_final: 0.6013 (mmt) REVERT: H 17 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7358 (mtm180) REVERT: H 54 PHE cc_start: 0.8727 (m-80) cc_final: 0.7931 (m-80) REVERT: H 366 LEU cc_start: 0.8861 (mt) cc_final: 0.8472 (pt) REVERT: G 24 LEU cc_start: 0.9027 (tp) cc_final: 0.8450 (mp) REVERT: G 35 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: K 175 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.5670 (p90) REVERT: K 340 TYR cc_start: -0.2426 (OUTLIER) cc_final: -0.3593 (p90) REVERT: J 17 MET cc_start: 0.7989 (ttt) cc_final: 0.7472 (mtp) outliers start: 51 outliers final: 34 residues processed: 198 average time/residue: 0.1558 time to fit residues: 51.1352 Evaluate side-chains 195 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 400 ILE Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 67 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 274 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.109944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.069159 restraints weight = 120035.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.070703 restraints weight = 51705.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071595 restraints weight = 32100.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072057 restraints weight = 25136.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072360 restraints weight = 21888.640| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25808 Z= 0.193 Angle : 0.593 12.421 34816 Z= 0.307 Chirality : 0.043 0.277 3878 Planarity : 0.003 0.036 4396 Dihedral : 7.188 87.573 3627 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.35 % Allowed : 13.86 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.16), residues: 3073 helix: 1.80 (0.13), residues: 1522 sheet: -0.15 (0.24), residues: 492 loop : 0.05 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 309 TYR 0.017 0.001 TYR B 432 PHE 0.018 0.001 PHE B 230 TRP 0.020 0.001 TRP G 287 HIS 0.009 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00424 (25808) covalent geometry : angle 0.59339 (34816) hydrogen bonds : bond 0.03294 ( 1333) hydrogen bonds : angle 4.54671 ( 3813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 154 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8937 (t0) cc_final: 0.8391 (t0) REVERT: A 154 MET cc_start: 0.9035 (ttt) cc_final: 0.8691 (ttt) REVERT: A 326 MET cc_start: 0.8998 (mmm) cc_final: 0.8342 (mmm) REVERT: A 338 MET cc_start: 0.8077 (ttp) cc_final: 0.7679 (ttm) REVERT: A 347 LYS cc_start: 0.7482 (mmtt) cc_final: 0.6944 (mmtt) REVERT: A 377 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 252 LEU cc_start: 0.9270 (tp) cc_final: 0.8970 (tp) REVERT: B 377 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9306 (mm) REVERT: C 16 ASN cc_start: 0.9130 (m-40) cc_final: 0.8380 (p0) REVERT: C 84 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: C 326 MET cc_start: 0.9441 (mtt) cc_final: 0.9205 (mtt) REVERT: C 393 GLN cc_start: 0.9319 (mt0) cc_final: 0.8899 (mm-40) REVERT: C 436 MET cc_start: 0.8857 (ptt) cc_final: 0.8610 (ppp) REVERT: F 201 MET cc_start: 0.9297 (mmp) cc_final: 0.8281 (tmm) REVERT: F 280 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8047 (pt0) REVERT: F 286 ASN cc_start: 0.7071 (t0) cc_final: 0.6630 (m-40) REVERT: F 304 TYR cc_start: 0.8736 (t80) cc_final: 0.8409 (t80) REVERT: F 383 MET cc_start: 0.6271 (mpp) cc_final: 0.6063 (mmt) REVERT: H 54 PHE cc_start: 0.8767 (m-80) cc_final: 0.7938 (m-80) REVERT: H 366 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8496 (pt) REVERT: G 24 LEU cc_start: 0.9114 (tp) cc_final: 0.8525 (mp) REVERT: G 35 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: K 175 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.5941 (p90) REVERT: K 340 TYR cc_start: -0.2165 (OUTLIER) cc_final: -0.3352 (p90) REVERT: J 17 MET cc_start: 0.8104 (ttt) cc_final: 0.7515 (mtp) outliers start: 65 outliers final: 45 residues processed: 204 average time/residue: 0.1515 time to fit residues: 51.4268 Evaluate side-chains 198 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 400 ILE Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 293 optimal weight: 30.0000 chunk 140 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.110679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.074044 restraints weight = 121489.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.075861 restraints weight = 53726.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.075632 restraints weight = 34677.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.076006 restraints weight = 25466.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.076169 restraints weight = 24669.421| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25808 Z= 0.138 Angle : 0.561 12.357 34816 Z= 0.289 Chirality : 0.043 0.268 3878 Planarity : 0.003 0.032 4396 Dihedral : 7.063 87.808 3627 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.09 % Allowed : 14.30 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.16), residues: 3073 helix: 1.84 (0.13), residues: 1522 sheet: -0.17 (0.24), residues: 482 loop : 0.10 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 309 TYR 0.015 0.001 TYR B 97 PHE 0.023 0.001 PHE H 355 TRP 0.021 0.001 TRP G 287 HIS 0.007 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00302 (25808) covalent geometry : angle 0.56107 (34816) hydrogen bonds : bond 0.03101 ( 1333) hydrogen bonds : angle 4.44509 ( 3813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8802 (t0) cc_final: 0.8242 (t0) REVERT: A 154 MET cc_start: 0.8959 (ttt) cc_final: 0.8687 (ttm) REVERT: A 326 MET cc_start: 0.9027 (mmm) cc_final: 0.8456 (mmm) REVERT: A 338 MET cc_start: 0.8012 (ttp) cc_final: 0.7743 (ttm) REVERT: A 347 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6979 (mmtt) REVERT: A 377 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 252 LEU cc_start: 0.9263 (tp) cc_final: 0.8959 (tp) REVERT: B 377 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9233 (mm) REVERT: C 16 ASN cc_start: 0.9280 (m-40) cc_final: 0.8629 (p0) REVERT: C 326 MET cc_start: 0.9441 (mtt) cc_final: 0.9200 (mtt) REVERT: C 393 GLN cc_start: 0.9373 (mt0) cc_final: 0.8919 (mm-40) REVERT: C 436 MET cc_start: 0.8927 (ptt) cc_final: 0.8698 (ppp) REVERT: F 201 MET cc_start: 0.9313 (mmp) cc_final: 0.8290 (tmm) REVERT: F 280 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8123 (pt0) REVERT: F 286 ASN cc_start: 0.6915 (t0) cc_final: 0.6516 (m-40) REVERT: F 304 TYR cc_start: 0.8877 (t80) cc_final: 0.8567 (t80) REVERT: H 54 PHE cc_start: 0.8975 (m-80) cc_final: 0.8054 (m-80) REVERT: H 366 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8331 (pt) REVERT: H 371 ARG cc_start: 0.8789 (ttm170) cc_final: 0.8420 (mtt180) REVERT: G 24 LEU cc_start: 0.9034 (tp) cc_final: 0.8381 (mp) REVERT: G 35 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: K 175 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5970 (p90) REVERT: K 340 TYR cc_start: -0.2631 (OUTLIER) cc_final: -0.3735 (p90) REVERT: J 17 MET cc_start: 0.7727 (ttt) cc_final: 0.7097 (mtp) outliers start: 58 outliers final: 44 residues processed: 199 average time/residue: 0.1623 time to fit residues: 52.8172 Evaluate side-chains 198 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 400 ILE Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 270 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 295 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 310 optimal weight: 0.0970 chunk 85 optimal weight: 0.0020 chunk 70 optimal weight: 0.8980 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.110360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.069562 restraints weight = 120323.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070915 restraints weight = 53353.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071855 restraints weight = 33050.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.072505 restraints weight = 25577.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072764 restraints weight = 22282.143| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25808 Z= 0.162 Angle : 0.590 13.924 34816 Z= 0.303 Chirality : 0.043 0.375 3878 Planarity : 0.003 0.033 4396 Dihedral : 7.052 86.909 3627 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.95 % Allowed : 14.62 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.16), residues: 3073 helix: 1.84 (0.13), residues: 1508 sheet: -0.25 (0.24), residues: 496 loop : 0.12 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 345 TYR 0.015 0.001 TYR B 97 PHE 0.045 0.001 PHE C 191 TRP 0.023 0.001 TRP G 287 HIS 0.007 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00357 (25808) covalent geometry : angle 0.59012 (34816) hydrogen bonds : bond 0.03165 ( 1333) hydrogen bonds : angle 4.51969 ( 3813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6146 Ramachandran restraints generated. 3073 Oldfield, 0 Emsley, 3073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8897 (t0) cc_final: 0.8342 (t0) REVERT: A 154 MET cc_start: 0.8989 (ttt) cc_final: 0.8730 (ttt) REVERT: A 326 MET cc_start: 0.9016 (mmm) cc_final: 0.8429 (mmm) REVERT: A 338 MET cc_start: 0.8028 (ttp) cc_final: 0.7733 (ttm) REVERT: A 347 LYS cc_start: 0.7346 (mmtt) cc_final: 0.6867 (mmtt) REVERT: A 377 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8827 (mm) REVERT: B 252 LEU cc_start: 0.9257 (tp) cc_final: 0.8955 (tp) REVERT: B 377 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9257 (mm) REVERT: C 16 ASN cc_start: 0.9070 (m-40) cc_final: 0.8343 (p0) REVERT: C 326 MET cc_start: 0.9448 (mtt) cc_final: 0.9220 (mtt) REVERT: C 393 GLN cc_start: 0.9365 (mt0) cc_final: 0.8905 (mm-40) REVERT: C 436 MET cc_start: 0.8943 (ptt) cc_final: 0.8697 (ppp) REVERT: F 201 MET cc_start: 0.9291 (mmp) cc_final: 0.8282 (tmm) REVERT: F 280 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8020 (pt0) REVERT: F 286 ASN cc_start: 0.7028 (t0) cc_final: 0.6591 (m-40) REVERT: F 304 TYR cc_start: 0.8767 (t80) cc_final: 0.8445 (t80) REVERT: H 23 ASP cc_start: 0.8491 (m-30) cc_final: 0.7856 (t0) REVERT: H 366 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8483 (pt) REVERT: H 376 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8971 (ptt) REVERT: H 410 MET cc_start: 0.8820 (mmp) cc_final: 0.8306 (mmm) REVERT: G 24 LEU cc_start: 0.9052 (tp) cc_final: 0.8483 (mp) REVERT: G 35 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: K 175 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6042 (p90) REVERT: K 340 TYR cc_start: -0.2536 (OUTLIER) cc_final: -0.3741 (p90) REVERT: J 17 MET cc_start: 0.8106 (ttt) cc_final: 0.7590 (mtp) outliers start: 54 outliers final: 44 residues processed: 187 average time/residue: 0.1546 time to fit residues: 47.8845 Evaluate side-chains 194 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 97 TYR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 338 MET Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 374 LEU Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain H residue 397 SER Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 35 TYR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 340 TYR Chi-restraints excluded: chain K residue 363 ILE Chi-restraints excluded: chain K residue 373 LEU Chi-restraints excluded: chain K residue 400 ILE Chi-restraints excluded: chain K residue 430 THR Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 214 optimal weight: 0.0010 chunk 7 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 245 GLN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068715 restraints weight = 120746.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069785 restraints weight = 53901.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070810 restraints weight = 33697.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071216 restraints weight = 25991.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071499 restraints weight = 23054.120| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25808 Z= 0.173 Angle : 0.605 13.660 34816 Z= 0.310 Chirality : 0.043 0.348 3878 Planarity : 0.003 0.035 4396 Dihedral : 7.084 87.067 3627 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.09 % Allowed : 14.58 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.16), residues: 3073 helix: 1.77 (0.13), residues: 1514 sheet: -0.29 (0.24), residues: 496 loop : 0.14 (0.21), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 287 TYR 0.016 0.001 TYR B 97 PHE 0.021 0.001 PHE B 230 TRP 0.022 0.001 TRP G 287 HIS 0.009 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00380 (25808) covalent geometry : angle 0.60467 (34816) hydrogen bonds : bond 0.03227 ( 1333) hydrogen bonds : angle 4.58439 ( 3813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6703.95 seconds wall clock time: 115 minutes 42.69 seconds (6942.69 seconds total)