Starting phenix.real_space_refine on Thu Sep 18 08:31:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssz_25417/09_2025/7ssz_25417.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssz_25417/09_2025/7ssz_25417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ssz_25417/09_2025/7ssz_25417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssz_25417/09_2025/7ssz_25417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssz_25417/09_2025/7ssz_25417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssz_25417/09_2025/7ssz_25417.map" } resolution = 3.25 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= 0.003 sd= 0.062 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 K 3 8.98 5 S 60 5.16 5 C 9924 2.51 5 N 2564 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 3.44, per 1000 atoms: 0.23 Number of scatterers: 15283 At special positions: 0 Unit cell: (120.132, 120.132, 152.508, 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) K 3 19.00 S 60 16.00 O 2732 8.00 N 2564 7.00 C 9924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.05 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: 1.39 Conformation dependent library (CDL) restraints added in 732.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3520 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 52.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 256 removed outlier: 3.778A pdb=" N THR A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.302A pdb=" N GLU A 262 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.711A pdb=" N VAL A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 394 through 419 Processing helix chain 'A' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP A 433 " --> pdb=" O SER A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.880A pdb=" N ARG B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 256 removed outlier: 3.778A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.301A pdb=" N GLU B 262 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 347 Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.710A pdb=" N VAL B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 372 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 394 through 419 Processing helix chain 'B' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP B 433 " --> pdb=" O SER B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.789A pdb=" N TYR C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 256 removed outlier: 3.779A pdb=" N THR C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 4.302A pdb=" N GLU C 262 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 347 Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.710A pdb=" N VAL C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE C 372 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 394 through 419 Processing helix chain 'C' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP C 433 " --> pdb=" O SER C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 256 removed outlier: 3.779A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.303A pdb=" N GLU D 262 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 347 Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.711A pdb=" N VAL D 371 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 372 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG D 373 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 394 through 419 Processing helix chain 'D' and resid 430 through 433 removed outlier: 3.620A pdb=" N ASP D 433 " --> pdb=" O SER D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.887A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 146 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 26 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 26 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER E 34 " --> pdb=" O TRP E 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E 35 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 26 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 26 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.663A pdb=" N SER F 34 " --> pdb=" O TRP F 99 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA F 35 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 13 Processing sheet with id=AB1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 26 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 26 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER G 34 " --> pdb=" O TRP G 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA G 35 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 26 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 26 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER H 34 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG H 39 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB9, first strand: chain 'B' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 146 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 146 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 146 " --> pdb=" O ASP D 141 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2408 1.31 - 1.43: 4505 1.43 - 1.56: 8647 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 15652 Sorted by residual: bond pdb=" CA SER B 426 " pdb=" CB SER B 426 " ideal model delta sigma weight residual 1.528 1.451 0.077 1.61e-02 3.86e+03 2.28e+01 bond pdb=" CA SER A 426 " pdb=" CB SER A 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.23e+01 bond pdb=" CA SER D 426 " pdb=" CB SER D 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.22e+01 bond pdb=" CA SER C 426 " pdb=" CB SER C 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.21e+01 bond pdb=" N TYR C 265 " pdb=" CA TYR C 265 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.09e+01 ... (remaining 15647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 17387 2.13 - 4.26: 3205 4.26 - 6.39: 476 6.39 - 8.52: 98 8.52 - 10.64: 26 Bond angle restraints: 21192 Sorted by residual: angle pdb=" N VAL B 445 " pdb=" CA VAL B 445 " pdb=" C VAL B 445 " ideal model delta sigma weight residual 110.42 100.34 10.08 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 110.42 100.35 10.07 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL D 445 " pdb=" CA VAL D 445 " pdb=" C VAL D 445 " ideal model delta sigma weight residual 110.42 100.37 10.05 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL C 445 " pdb=" CA VAL C 445 " pdb=" C VAL C 445 " ideal model delta sigma weight residual 110.42 100.39 10.03 9.60e-01 1.09e+00 1.09e+02 angle pdb=" N GLU B 262 " pdb=" CA GLU B 262 " pdb=" C GLU B 262 " ideal model delta sigma weight residual 113.28 104.88 8.40 1.22e+00 6.72e-01 4.74e+01 ... (remaining 21187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8180 17.92 - 35.85: 801 35.85 - 53.77: 211 53.77 - 71.70: 24 71.70 - 89.62: 4 Dihedral angle restraints: 9220 sinusoidal: 3728 harmonic: 5492 Sorted by residual: dihedral pdb=" C THR D 444 " pdb=" N THR D 444 " pdb=" CA THR D 444 " pdb=" CB THR D 444 " ideal model delta harmonic sigma weight residual -122.00 -144.18 22.18 0 2.50e+00 1.60e-01 7.87e+01 dihedral pdb=" C THR B 444 " pdb=" N THR B 444 " pdb=" CA THR B 444 " pdb=" CB THR B 444 " ideal model delta harmonic sigma weight residual -122.00 -144.16 22.16 0 2.50e+00 1.60e-01 7.86e+01 dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -144.14 22.14 0 2.50e+00 1.60e-01 7.84e+01 ... (remaining 9217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 2014 0.167 - 0.334: 298 0.334 - 0.501: 12 0.501 - 0.669: 4 0.669 - 0.836: 4 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CA THR D 444 " pdb=" N THR D 444 " pdb=" C THR D 444 " pdb=" CB THR D 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 2329 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 201 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C GLU C 201 " 0.078 2.00e-02 2.50e+03 pdb=" O GLU C 201 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY C 202 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 201 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C GLU A 201 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU A 201 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY A 202 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 418 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C PHE A 418 " -0.078 2.00e-02 2.50e+03 pdb=" O PHE A 418 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 419 " 0.026 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.40: 24 1.40 - 2.34: 36 2.34 - 3.27: 15754 3.27 - 4.21: 42056 4.21 - 5.14: 83500 Warning: very small nonbonded interaction distances. Nonbonded interactions: 141370 Sorted by model distance: nonbonded pdb=" CZ ARG E 53 " pdb=" OD2 ASP B 261 " model vdw 0.467 3.270 nonbonded pdb=" OD2 ASP A 261 " pdb=" CZ ARG H 53 " model vdw 0.475 3.270 nonbonded pdb=" CZ ARG G 53 " pdb=" OD2 ASP D 261 " model vdw 0.475 3.270 nonbonded pdb=" CZ ARG F 53 " pdb=" OD2 ASP C 261 " model vdw 0.485 3.270 nonbonded pdb=" NH1 ARG E 53 " pdb=" CG ASP B 261 " model vdw 0.950 3.350 ... (remaining 141365 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 103 through 491) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.410 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.014 0.092 15656 Z= 0.838 Angle : 1.698 10.644 21200 Z= 1.181 Chirality : 0.119 0.836 2332 Planarity : 0.009 0.078 2700 Dihedral : 14.901 89.621 5688 Min Nonbonded Distance : 0.467 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.31 % Allowed : 10.68 % Favored : 83.01 % Cbeta Deviations : 1.14 % 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: -2.29 (0.17), residues: 1876 helix: -1.92 (0.14), residues: 928 sheet: 1.08 (0.53), residues: 120 loop : -1.26 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 260 TYR 0.033 0.003 TYR D 447 PHE 0.033 0.004 PHE C 224 TRP 0.016 0.003 TRP B 436 HIS 0.009 0.004 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.01376 (15652) covalent geometry : angle 1.69869 (21192) SS BOND : bond 0.01663 ( 4) SS BOND : angle 0.28903 ( 8) hydrogen bonds : bond 0.26093 ( 808) hydrogen bonds : angle 8.36931 ( 2364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 272 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7255 (pt0) REVERT: A 119 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7833 (tp) REVERT: A 147 TYR cc_start: 0.7351 (m-80) cc_final: 0.6917 (m-80) REVERT: A 170 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7194 (mmt-90) REVERT: A 187 TYR cc_start: 0.7294 (m-80) cc_final: 0.7055 (m-80) REVERT: A 198 ARG cc_start: 0.7218 (tpp-160) cc_final: 0.7014 (tpp-160) REVERT: A 218 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.5101 (ptt180) REVERT: A 328 MET cc_start: 0.7027 (mtm) cc_final: 0.6721 (mtm) REVERT: A 332 ASP cc_start: 0.7890 (m-30) cc_final: 0.7370 (m-30) REVERT: A 368 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7398 (tt) REVERT: A 395 MET cc_start: 0.7638 (mmm) cc_final: 0.7250 (mmt) REVERT: A 450 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6154 (mmt) REVERT: E 37 TRP cc_start: 0.6240 (OUTLIER) cc_final: 0.5895 (m-90) REVERT: F 37 TRP cc_start: 0.6321 (OUTLIER) cc_final: 0.5915 (m-90) REVERT: G 29 LEU cc_start: 0.7428 (mt) cc_final: 0.7193 (mp) REVERT: G 37 TRP cc_start: 0.6358 (OUTLIER) cc_final: 0.5966 (m-90) REVERT: G 78 THR cc_start: 0.7901 (p) cc_final: 0.7697 (p) REVERT: H 37 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.5963 (m-90) REVERT: H 78 THR cc_start: 0.7913 (p) cc_final: 0.7708 (p) REVERT: B 104 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7288 (pt0) REVERT: B 119 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 147 TYR cc_start: 0.7334 (m-80) cc_final: 0.6959 (m-80) REVERT: B 170 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7494 (mmt-90) REVERT: B 218 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.5061 (ptt180) REVERT: B 328 MET cc_start: 0.7104 (mtm) cc_final: 0.6800 (mtm) REVERT: B 332 ASP cc_start: 0.7913 (m-30) cc_final: 0.7334 (m-30) REVERT: B 368 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7369 (tt) REVERT: B 395 MET cc_start: 0.7730 (mmm) cc_final: 0.7290 (mmt) REVERT: B 450 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6364 (mmt) REVERT: C 104 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7458 (tt0) REVERT: C 147 TYR cc_start: 0.7330 (m-80) cc_final: 0.7055 (m-80) REVERT: C 170 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7499 (mmt-90) REVERT: C 218 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.5059 (ptt180) REVERT: C 328 MET cc_start: 0.7057 (mtm) cc_final: 0.6706 (mtm) REVERT: C 332 ASP cc_start: 0.7762 (m-30) cc_final: 0.7189 (m-30) REVERT: C 368 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7395 (tt) REVERT: C 395 MET cc_start: 0.7692 (mmm) cc_final: 0.7275 (mmt) REVERT: C 450 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6321 (mmt) REVERT: D 104 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7452 (tt0) REVERT: D 147 TYR cc_start: 0.7338 (m-80) cc_final: 0.7070 (m-80) REVERT: D 170 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7044 (mmt-90) REVERT: D 218 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5069 (ptt180) REVERT: D 328 MET cc_start: 0.7022 (mtm) cc_final: 0.6643 (mtm) REVERT: D 332 ASP cc_start: 0.7734 (m-30) cc_final: 0.7187 (m-30) REVERT: D 368 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7381 (tt) REVERT: D 395 MET cc_start: 0.7634 (mmm) cc_final: 0.7219 (mmt) REVERT: D 450 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6423 (mmt) outliers start: 104 outliers final: 28 residues processed: 345 average time/residue: 0.1761 time to fit residues: 82.9713 Evaluate side-chains 235 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 48 PHE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 450 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN A 164 GLN A 217 GLN E 84 ASN F 84 ASN G 84 ASN H 84 ASN B 124 GLN B 164 GLN B 217 GLN C 124 GLN C 164 GLN C 217 GLN D 124 GLN D 145 ASN D 217 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.213261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.189268 restraints weight = 17430.487| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.21 r_work: 0.3680 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15656 Z= 0.152 Angle : 0.660 6.748 21200 Z= 0.358 Chirality : 0.045 0.208 2332 Planarity : 0.006 0.055 2700 Dihedral : 8.778 59.830 2240 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.46 % Allowed : 15.29 % Favored : 81.25 % 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: -0.56 (0.19), residues: 1876 helix: -0.02 (0.17), residues: 956 sheet: 1.41 (0.46), residues: 136 loop : -1.04 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 39 TYR 0.016 0.002 TYR B 447 PHE 0.016 0.001 PHE F 68 TRP 0.007 0.001 TRP E 99 HIS 0.002 0.001 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00317 (15652) covalent geometry : angle 0.65951 (21192) SS BOND : bond 0.00448 ( 4) SS BOND : angle 0.78234 ( 8) hydrogen bonds : bond 0.06348 ( 808) hydrogen bonds : angle 4.92198 ( 2364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 332 ASP cc_start: 0.8075 (m-30) cc_final: 0.7762 (m-30) REVERT: A 368 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 450 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5655 (mmt) REVERT: A 469 VAL cc_start: 0.8207 (p) cc_final: 0.7643 (t) REVERT: B 309 GLU cc_start: 0.7230 (tt0) cc_final: 0.6952 (tt0) REVERT: B 332 ASP cc_start: 0.8095 (m-30) cc_final: 0.7762 (m-30) REVERT: B 368 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 450 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5739 (mmt) REVERT: B 469 VAL cc_start: 0.8388 (p) cc_final: 0.7858 (t) REVERT: C 332 ASP cc_start: 0.8124 (m-30) cc_final: 0.7772 (m-30) REVERT: C 368 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (tt) REVERT: C 450 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5696 (mmt) REVERT: C 469 VAL cc_start: 0.8351 (p) cc_final: 0.7808 (t) REVERT: D 332 ASP cc_start: 0.8044 (m-30) cc_final: 0.7693 (m-30) REVERT: D 368 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7489 (tt) REVERT: D 469 VAL cc_start: 0.8404 (p) cc_final: 0.7855 (t) outliers start: 57 outliers final: 22 residues processed: 242 average time/residue: 0.1464 time to fit residues: 51.2136 Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 92 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 186 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 164 GLN B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.205731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178603 restraints weight = 17650.810| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.31 r_work: 0.3586 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15656 Z= 0.181 Angle : 0.626 6.062 21200 Z= 0.339 Chirality : 0.045 0.178 2332 Planarity : 0.005 0.054 2700 Dihedral : 7.031 59.641 2171 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.07 % Allowed : 14.87 % Favored : 81.07 % 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: -0.11 (0.19), residues: 1876 helix: 0.48 (0.17), residues: 960 sheet: 1.49 (0.44), residues: 136 loop : -1.00 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 313 TYR 0.022 0.002 TYR B 447 PHE 0.013 0.002 PHE D 306 TRP 0.007 0.001 TRP A 221 HIS 0.002 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00431 (15652) covalent geometry : angle 0.62619 (21192) SS BOND : bond 0.00452 ( 4) SS BOND : angle 0.62667 ( 8) hydrogen bonds : bond 0.06551 ( 808) hydrogen bonds : angle 4.57203 ( 2364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 218 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.6231 (ptt180) REVERT: A 332 ASP cc_start: 0.8260 (m-30) cc_final: 0.7956 (m-30) REVERT: A 368 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 450 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6311 (mmt) REVERT: A 469 VAL cc_start: 0.8491 (p) cc_final: 0.7871 (t) REVERT: B 332 ASP cc_start: 0.8257 (m-30) cc_final: 0.7941 (m-30) REVERT: B 368 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7826 (tt) REVERT: B 469 VAL cc_start: 0.8547 (p) cc_final: 0.7946 (t) REVERT: C 332 ASP cc_start: 0.8268 (m-30) cc_final: 0.7948 (m-30) REVERT: C 368 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7701 (tt) REVERT: C 469 VAL cc_start: 0.8519 (p) cc_final: 0.7912 (t) REVERT: D 332 ASP cc_start: 0.8233 (m-30) cc_final: 0.7904 (m-30) REVERT: D 368 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7732 (tt) REVERT: D 450 MET cc_start: 0.7050 (mtm) cc_final: 0.6732 (mtt) REVERT: D 469 VAL cc_start: 0.8558 (p) cc_final: 0.7940 (t) outliers start: 67 outliers final: 41 residues processed: 213 average time/residue: 0.1203 time to fit residues: 39.2763 Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 62 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 48 PHE Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.205873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177771 restraints weight = 17629.548| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.33 r_work: 0.3583 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15656 Z= 0.162 Angle : 0.573 5.653 21200 Z= 0.309 Chirality : 0.043 0.155 2332 Planarity : 0.005 0.050 2700 Dihedral : 6.580 59.745 2161 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.46 % Allowed : 15.84 % Favored : 80.70 % 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: 0.19 (0.20), residues: 1876 helix: 0.86 (0.18), residues: 944 sheet: 0.69 (0.33), residues: 232 loop : -1.02 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 313 TYR 0.017 0.001 TYR B 447 PHE 0.012 0.001 PHE A 406 TRP 0.005 0.001 TRP B 221 HIS 0.002 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00388 (15652) covalent geometry : angle 0.57249 (21192) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.66846 ( 8) hydrogen bonds : bond 0.05989 ( 808) hydrogen bonds : angle 4.34336 ( 2364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.704 Fit side-chains REVERT: A 218 ARG cc_start: 0.6322 (ptt180) cc_final: 0.5982 (ptt180) REVERT: A 332 ASP cc_start: 0.7983 (m-30) cc_final: 0.7712 (m-30) REVERT: A 368 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 450 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5831 (mmt) REVERT: A 469 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.7916 (t) REVERT: B 332 ASP cc_start: 0.7995 (m-30) cc_final: 0.7711 (m-30) REVERT: B 368 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7835 (tt) REVERT: B 450 MET cc_start: 0.6232 (mpp) cc_final: 0.5906 (mtt) REVERT: B 469 VAL cc_start: 0.8570 (p) cc_final: 0.7963 (t) REVERT: C 332 ASP cc_start: 0.7997 (m-30) cc_final: 0.7722 (m-30) REVERT: C 368 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7749 (tt) REVERT: C 469 VAL cc_start: 0.8587 (p) cc_final: 0.7983 (t) REVERT: D 332 ASP cc_start: 0.7983 (m-30) cc_final: 0.7702 (m-30) REVERT: D 368 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7764 (tt) REVERT: D 450 MET cc_start: 0.6314 (mtm) cc_final: 0.6059 (mtt) REVERT: D 469 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.7972 (t) outliers start: 57 outliers final: 38 residues processed: 201 average time/residue: 0.1290 time to fit residues: 39.5302 Evaluate side-chains 195 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 128 optimal weight: 0.0370 chunk 129 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.209393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179561 restraints weight = 17750.337| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.39 r_work: 0.3571 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15656 Z= 0.116 Angle : 0.524 5.740 21200 Z= 0.281 Chirality : 0.041 0.145 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.219 59.521 2153 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.49 % Allowed : 17.11 % Favored : 80.40 % 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: 0.68 (0.20), residues: 1876 helix: 1.37 (0.18), residues: 920 sheet: 0.82 (0.34), residues: 232 loop : -0.84 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.014 0.001 TYR A 447 PHE 0.008 0.001 PHE B 406 TRP 0.010 0.001 TRP G 99 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00250 (15652) covalent geometry : angle 0.52361 (21192) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.54715 ( 8) hydrogen bonds : bond 0.04841 ( 808) hydrogen bonds : angle 4.12334 ( 2364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.595 Fit side-chains REVERT: A 218 ARG cc_start: 0.6379 (ptt180) cc_final: 0.6149 (ptt180) REVERT: A 332 ASP cc_start: 0.7970 (m-30) cc_final: 0.7664 (m-30) REVERT: A 368 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7884 (tt) REVERT: A 450 MET cc_start: 0.6093 (mmt) cc_final: 0.5852 (mmt) REVERT: A 469 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.7861 (t) REVERT: B 332 ASP cc_start: 0.7948 (m-30) cc_final: 0.7642 (m-30) REVERT: B 368 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 469 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.7908 (t) REVERT: C 332 ASP cc_start: 0.7958 (m-30) cc_final: 0.7649 (m-30) REVERT: C 368 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7830 (tt) REVERT: C 469 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.7901 (t) REVERT: D 332 ASP cc_start: 0.7929 (m-30) cc_final: 0.7626 (m-30) REVERT: D 368 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7823 (tt) REVERT: D 469 VAL cc_start: 0.8451 (p) cc_final: 0.7910 (t) outliers start: 41 outliers final: 30 residues processed: 186 average time/residue: 0.1328 time to fit residues: 36.8524 Evaluate side-chains 181 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.201385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.173061 restraints weight = 17569.736| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.37 r_work: 0.3482 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15656 Z= 0.296 Angle : 0.686 6.521 21200 Z= 0.368 Chirality : 0.048 0.156 2332 Planarity : 0.006 0.050 2700 Dihedral : 6.402 59.158 2146 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.40 % Allowed : 16.63 % Favored : 79.98 % 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: 0.05 (0.20), residues: 1876 helix: 0.77 (0.18), residues: 932 sheet: 0.47 (0.33), residues: 236 loop : -1.05 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 53 TYR 0.026 0.002 TYR A 447 PHE 0.017 0.002 PHE B 406 TRP 0.009 0.002 TRP D 221 HIS 0.004 0.002 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00749 (15652) covalent geometry : angle 0.68620 (21192) SS BOND : bond 0.00415 ( 4) SS BOND : angle 0.66384 ( 8) hydrogen bonds : bond 0.07897 ( 808) hydrogen bonds : angle 4.56908 ( 2364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.659 Fit side-chains REVERT: A 218 ARG cc_start: 0.6441 (ptt180) cc_final: 0.6169 (ptt180) REVERT: A 332 ASP cc_start: 0.7990 (m-30) cc_final: 0.7694 (m-30) REVERT: A 368 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8126 (tt) REVERT: A 450 MET cc_start: 0.6336 (mmt) cc_final: 0.6059 (mmt) REVERT: A 480 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8684 (t) REVERT: B 332 ASP cc_start: 0.7963 (m-30) cc_final: 0.7670 (m-30) REVERT: B 368 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8100 (tt) REVERT: C 332 ASP cc_start: 0.7996 (m-30) cc_final: 0.7695 (m-30) REVERT: C 368 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8071 (tt) REVERT: D 332 ASP cc_start: 0.7993 (m-30) cc_final: 0.7703 (m-30) REVERT: D 368 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8057 (tt) REVERT: D 480 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8685 (t) outliers start: 56 outliers final: 43 residues processed: 196 average time/residue: 0.1175 time to fit residues: 35.7913 Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** H 33 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 = 0.4253 r_free = 0.4253 target = 0.205472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175567 restraints weight = 17354.331| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.44 r_work: 0.3681 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15656 Z= 0.145 Angle : 0.553 5.934 21200 Z= 0.298 Chirality : 0.042 0.138 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.193 59.398 2146 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.16 % Allowed : 16.87 % Favored : 79.98 % 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: 0.38 (0.20), residues: 1876 helix: 1.10 (0.18), residues: 932 sheet: 0.46 (0.34), residues: 236 loop : -0.91 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 53 TYR 0.015 0.001 TYR A 447 PHE 0.011 0.001 PHE B 406 TRP 0.009 0.001 TRP E 99 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00335 (15652) covalent geometry : angle 0.55346 (21192) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.55634 ( 8) hydrogen bonds : bond 0.05902 ( 808) hydrogen bonds : angle 4.25663 ( 2364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.592 Fit side-chains REVERT: A 332 ASP cc_start: 0.8120 (m-30) cc_final: 0.7846 (m-30) REVERT: A 368 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 450 MET cc_start: 0.6600 (mmt) cc_final: 0.6346 (mmt) REVERT: A 469 VAL cc_start: 0.8610 (p) cc_final: 0.7971 (t) REVERT: B 332 ASP cc_start: 0.8071 (m-30) cc_final: 0.7772 (m-30) REVERT: B 368 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 469 VAL cc_start: 0.8653 (p) cc_final: 0.8041 (t) REVERT: C 332 ASP cc_start: 0.8120 (m-30) cc_final: 0.7813 (m-30) REVERT: C 368 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8105 (tt) REVERT: C 469 VAL cc_start: 0.8648 (p) cc_final: 0.8038 (t) REVERT: D 332 ASP cc_start: 0.8103 (m-30) cc_final: 0.7835 (m-30) REVERT: D 368 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8117 (tt) REVERT: D 469 VAL cc_start: 0.8657 (p) cc_final: 0.8040 (t) outliers start: 52 outliers final: 40 residues processed: 192 average time/residue: 0.1168 time to fit residues: 35.0028 Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 77 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN G 33 ASN H 33 ASN C 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.210782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182807 restraints weight = 17644.254| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.36 r_work: 0.3609 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15656 Z= 0.121 Angle : 0.516 6.829 21200 Z= 0.277 Chirality : 0.041 0.145 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.025 59.667 2146 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.91 % Allowed : 17.29 % Favored : 79.79 % 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: 0.66 (0.20), residues: 1876 helix: 1.34 (0.18), residues: 932 sheet: 0.61 (0.34), residues: 236 loop : -0.80 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 313 TYR 0.013 0.001 TYR A 447 PHE 0.008 0.001 PHE D 406 TRP 0.009 0.001 TRP E 99 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00273 (15652) covalent geometry : angle 0.51585 (21192) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.54145 ( 8) hydrogen bonds : bond 0.04989 ( 808) hydrogen bonds : angle 4.09159 ( 2364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.607 Fit side-chains REVERT: A 332 ASP cc_start: 0.8134 (m-30) cc_final: 0.7819 (m-30) REVERT: A 368 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 450 MET cc_start: 0.6666 (mmt) cc_final: 0.6426 (mmt) REVERT: A 469 VAL cc_start: 0.8581 (p) cc_final: 0.8020 (t) REVERT: B 332 ASP cc_start: 0.8094 (m-30) cc_final: 0.7780 (m-30) REVERT: B 368 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 469 VAL cc_start: 0.8589 (p) cc_final: 0.8035 (t) REVERT: C 332 ASP cc_start: 0.8073 (m-30) cc_final: 0.7759 (m-30) REVERT: C 368 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (tt) REVERT: C 469 VAL cc_start: 0.8604 (p) cc_final: 0.8052 (t) REVERT: D 332 ASP cc_start: 0.8092 (m-30) cc_final: 0.7771 (m-30) REVERT: D 368 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8187 (tt) REVERT: D 469 VAL cc_start: 0.8623 (p) cc_final: 0.8066 (t) outliers start: 48 outliers final: 40 residues processed: 197 average time/residue: 0.1187 time to fit residues: 36.6213 Evaluate side-chains 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 chunk 32 optimal weight: 0.0060 chunk 20 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.210055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.180850 restraints weight = 17432.300| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.37 r_work: 0.3623 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15656 Z= 0.102 Angle : 0.490 5.827 21200 Z= 0.262 Chirality : 0.040 0.151 2332 Planarity : 0.005 0.047 2700 Dihedral : 5.889 59.830 2146 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.00 % Allowed : 17.66 % Favored : 80.34 % 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: 0.96 (0.21), residues: 1876 helix: 1.60 (0.18), residues: 932 sheet: 0.59 (0.34), residues: 244 loop : -0.62 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 364 TYR 0.016 0.001 TYR C 163 PHE 0.007 0.001 PHE B 406 TRP 0.010 0.001 TRP F 99 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00214 (15652) covalent geometry : angle 0.49029 (21192) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.55519 ( 8) hydrogen bonds : bond 0.04202 ( 808) hydrogen bonds : angle 3.91338 ( 2364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.597 Fit side-chains REVERT: A 332 ASP cc_start: 0.7746 (m-30) cc_final: 0.7460 (m-30) REVERT: A 368 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 469 VAL cc_start: 0.8381 (p) cc_final: 0.7928 (t) REVERT: B 332 ASP cc_start: 0.7741 (m-30) cc_final: 0.7464 (m-30) REVERT: B 368 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8060 (tt) REVERT: B 469 VAL cc_start: 0.8391 (p) cc_final: 0.7967 (t) REVERT: B 490 GLU cc_start: 0.6298 (pp20) cc_final: 0.6092 (mm-30) REVERT: C 332 ASP cc_start: 0.7762 (m-30) cc_final: 0.7483 (m-30) REVERT: C 368 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8032 (tt) REVERT: C 469 VAL cc_start: 0.8391 (p) cc_final: 0.7960 (t) REVERT: D 332 ASP cc_start: 0.7747 (m-30) cc_final: 0.7471 (m-30) REVERT: D 368 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8028 (tt) REVERT: D 469 VAL cc_start: 0.8418 (p) cc_final: 0.7976 (t) outliers start: 33 outliers final: 27 residues processed: 184 average time/residue: 0.1162 time to fit residues: 33.2889 Evaluate side-chains 174 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 128 optimal weight: 0.7980 chunk 186 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 169 optimal weight: 0.4980 chunk 176 optimal weight: 0.8980 chunk 141 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN D 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.210089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.179387 restraints weight = 17560.357| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.42 r_work: 0.3728 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15656 Z= 0.109 Angle : 0.508 9.106 21200 Z= 0.268 Chirality : 0.040 0.141 2332 Planarity : 0.005 0.047 2700 Dihedral : 5.848 59.769 2146 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.76 % Allowed : 17.96 % Favored : 80.28 % 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: 0.93 (0.21), residues: 1876 helix: 1.61 (0.18), residues: 932 sheet: 0.23 (0.34), residues: 264 loop : -0.55 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 53 TYR 0.013 0.001 TYR A 161 PHE 0.008 0.001 PHE B 406 TRP 0.019 0.001 TRP G 107 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00235 (15652) covalent geometry : angle 0.50766 (21192) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.45766 ( 8) hydrogen bonds : bond 0.04379 ( 808) hydrogen bonds : angle 3.91633 ( 2364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.576 Fit side-chains REVERT: A 332 ASP cc_start: 0.7922 (m-30) cc_final: 0.7630 (m-30) REVERT: A 368 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 469 VAL cc_start: 0.8402 (p) cc_final: 0.7932 (t) REVERT: A 490 GLU cc_start: 0.6399 (pp20) cc_final: 0.6163 (mm-30) REVERT: B 332 ASP cc_start: 0.7889 (m-30) cc_final: 0.7612 (m-30) REVERT: B 368 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 469 VAL cc_start: 0.8460 (p) cc_final: 0.8021 (t) REVERT: B 490 GLU cc_start: 0.6397 (pp20) cc_final: 0.6110 (mm-30) REVERT: C 332 ASP cc_start: 0.7918 (m-30) cc_final: 0.7634 (m-30) REVERT: C 368 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8089 (tt) REVERT: C 469 VAL cc_start: 0.8440 (p) cc_final: 0.8000 (t) REVERT: D 332 ASP cc_start: 0.7931 (m-30) cc_final: 0.7651 (m-30) REVERT: D 368 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8114 (tt) REVERT: D 469 VAL cc_start: 0.8434 (p) cc_final: 0.7976 (t) outliers start: 29 outliers final: 25 residues processed: 162 average time/residue: 0.1199 time to fit residues: 29.9026 Evaluate side-chains 166 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 136 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 187 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 140 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.209504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181479 restraints weight = 17407.916| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.32 r_work: 0.3600 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15656 Z= 0.118 Angle : 0.512 7.937 21200 Z= 0.271 Chirality : 0.041 0.137 2332 Planarity : 0.005 0.047 2700 Dihedral : 5.843 59.900 2146 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.88 % Allowed : 18.14 % Favored : 79.98 % 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: 0.95 (0.21), residues: 1876 helix: 1.62 (0.18), residues: 932 sheet: 0.23 (0.33), residues: 272 loop : -0.54 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.013 0.001 TYR A 447 PHE 0.009 0.001 PHE D 406 TRP 0.015 0.001 TRP G 107 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00267 (15652) covalent geometry : angle 0.51186 (21192) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.50240 ( 8) hydrogen bonds : bond 0.04668 ( 808) hydrogen bonds : angle 3.93122 ( 2364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.49 seconds wall clock time: 63 minutes 59.46 seconds (3839.46 seconds total)