Starting phenix.real_space_refine on Wed Mar 4 18:03:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssz_25417/03_2026/7ssz_25417.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssz_25417/03_2026/7ssz_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_25417/03_2026/7ssz_25417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssz_25417/03_2026/7ssz_25417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssz_25417/03_2026/7ssz_25417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssz_25417/03_2026/7ssz_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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15283 Number of models: 1 Model: "" Number of chains: 9 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: "F" 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: "G" 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: "H" 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: "B" 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: "C" 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: "D" 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: "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} Time building chain proxies: 3.49, 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: 1.35 Conformation dependent library (CDL) restraints added in 566.6 milliseconds 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: 0.54 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: 2.56 Time building geometry restraints manager: 1.79 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: 4.980 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: 0.050 Set scattering table: 0.040 Process input model: 14.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- 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 are 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 : 0.573 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: 0.7219 (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: 0.6975 (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: 0.7056 (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: 0.6705 (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: 0.7633 (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: 0.1707 time to fit residues: 80.2106 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 : 0.600 ------------------------------------------------------------------------------- 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 = 0.213227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189167 restraints weight = 17425.224| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.21 r_work: 0.3584 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2239 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 : 0.656 6.761 21200 Z= 0.357 Chirality : 0.045 0.208 2332 Planarity : 0.006 0.055 2700 Dihedral : 8.771 59.771 2240 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.73 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 are not related in a simple way. whole: -0.56 (0.19), residues: 1876 helix: -0.02 (0.17), residues: 956 sheet: 1.42 (0.46), residues: 136 loop : -1.04 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 39 TYR 0.017 0.002 TYR C 447 PHE 0.016 0.001 PHE F 68 TRP 0.008 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 0.65597 (21192) SS BOND : bond 0.00420 ( 4) SS BOND : angle 0.81577 ( 8) hydrogen bonds : bond 0.06349 ( 808) hydrogen bonds : angle 4.92031 ( 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 259 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASP cc_start: 0.8366 (m-30) cc_final: 0.7991 (m-30) REVERT: A 368 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7798 (tt) REVERT: A 395 MET cc_start: 0.7874 (mmm) cc_final: 0.7668 (mmt) REVERT: A 450 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6290 (mmt) REVERT: A 469 VAL cc_start: 0.8244 (p) cc_final: 0.7677 (t) REVERT: E 26 SER cc_start: 0.7692 (m) cc_final: 0.7322 (p) REVERT: F 26 SER cc_start: 0.7586 (m) cc_final: 0.7270 (p) REVERT: G 26 SER cc_start: 0.7526 (m) cc_final: 0.7230 (p) REVERT: H 26 SER cc_start: 0.7546 (m) cc_final: 0.7267 (p) REVERT: B 332 ASP cc_start: 0.8381 (m-30) cc_final: 0.7974 (m-30) REVERT: B 368 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7774 (tt) REVERT: B 395 MET cc_start: 0.7894 (mmm) cc_final: 0.7641 (mmt) REVERT: B 450 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6408 (mmt) REVERT: B 469 VAL cc_start: 0.8412 (p) cc_final: 0.7872 (t) REVERT: C 332 ASP cc_start: 0.8420 (m-30) cc_final: 0.8001 (m-30) REVERT: C 368 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7639 (tt) REVERT: C 395 MET cc_start: 0.7792 (mmm) cc_final: 0.7547 (mmt) REVERT: C 450 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6254 (mmt) REVERT: C 469 VAL cc_start: 0.8373 (p) cc_final: 0.7825 (t) REVERT: D 332 ASP cc_start: 0.8343 (m-30) cc_final: 0.7930 (m-30) REVERT: D 368 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7682 (tt) REVERT: D 395 MET cc_start: 0.7779 (mmm) cc_final: 0.7533 (mmt) REVERT: D 469 VAL cc_start: 0.8409 (p) cc_final: 0.7855 (t) outliers start: 57 outliers final: 25 residues processed: 240 average time/residue: 0.1377 time to fit residues: 47.8192 Evaluate side-chains 199 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 218 ARG 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 218 ARG 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 218 ARG 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: 4.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.207689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182751 restraints weight = 17671.735| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.20 r_work: 0.3605 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15656 Z= 0.200 Angle : 0.644 6.147 21200 Z= 0.348 Chirality : 0.045 0.165 2332 Planarity : 0.006 0.054 2700 Dihedral : 7.272 59.612 2183 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.13 % Allowed : 14.87 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1876 helix: 0.43 (0.17), residues: 960 sheet: 1.47 (0.44), residues: 136 loop : -1.02 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 313 TYR 0.025 0.002 TYR B 447 PHE 0.014 0.002 PHE C 306 TRP 0.008 0.001 TRP D 221 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00485 (15652) covalent geometry : angle 0.64366 (21192) SS BOND : bond 0.00462 ( 4) SS BOND : angle 0.64187 ( 8) hydrogen bonds : bond 0.06882 ( 808) hydrogen bonds : angle 4.61489 ( 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 232 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 164 time to evaluate : 0.514 Fit side-chains REVERT: A 218 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6291 (ptt180) REVERT: A 332 ASP cc_start: 0.8275 (m-30) cc_final: 0.7974 (m-30) REVERT: A 368 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 395 MET cc_start: 0.8070 (mmm) cc_final: 0.7858 (mmt) REVERT: A 450 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6502 (mmt) REVERT: A 469 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.7893 (t) REVERT: B 218 ARG cc_start: 0.6458 (OUTLIER) cc_final: 0.6226 (ptt180) REVERT: B 332 ASP cc_start: 0.8245 (m-30) cc_final: 0.7934 (m-30) REVERT: B 368 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7789 (tt) REVERT: B 395 MET cc_start: 0.8128 (mmm) cc_final: 0.7917 (mmt) REVERT: B 469 VAL cc_start: 0.8589 (p) cc_final: 0.7962 (t) REVERT: C 218 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.6224 (ptt180) REVERT: C 332 ASP cc_start: 0.8283 (m-30) cc_final: 0.7969 (m-30) REVERT: C 368 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7699 (tt) REVERT: C 395 MET cc_start: 0.8070 (mmm) cc_final: 0.7869 (mmt) REVERT: C 469 VAL cc_start: 0.8582 (p) cc_final: 0.7951 (t) REVERT: D 218 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.6238 (ptt180) REVERT: D 332 ASP cc_start: 0.8259 (m-30) cc_final: 0.7938 (m-30) REVERT: D 368 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7725 (tt) REVERT: D 395 MET cc_start: 0.8034 (mmm) cc_final: 0.7812 (mmt) REVERT: D 450 MET cc_start: 0.7246 (mtm) cc_final: 0.6925 (mtt) REVERT: D 469 VAL cc_start: 0.8587 (p) cc_final: 0.7960 (t) outliers start: 68 outliers final: 43 residues processed: 217 average time/residue: 0.1059 time to fit residues: 35.7133 Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 469 VAL 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 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 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 218 ARG Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP 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 218 ARG 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 218 ARG 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: 0.4980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 0.0040 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.206461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.181363 restraints weight = 17438.410| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.24 r_work: 0.3615 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15656 Z= 0.139 Angle : 0.553 5.563 21200 Z= 0.298 Chirality : 0.042 0.141 2332 Planarity : 0.005 0.049 2700 Dihedral : 6.806 59.725 2175 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.46 % Allowed : 16.14 % 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 are not related in a simple way. whole: 0.38 (0.20), residues: 1876 helix: 1.09 (0.18), residues: 920 sheet: 0.67 (0.34), residues: 232 loop : -0.95 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.014 0.001 TYR B 447 PHE 0.010 0.001 PHE A 406 TRP 0.005 0.001 TRP D 436 HIS 0.002 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00321 (15652) covalent geometry : angle 0.55250 (21192) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.60910 ( 8) hydrogen bonds : bond 0.05492 ( 808) hydrogen bonds : angle 4.28583 ( 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 210 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.602 Fit side-chains REVERT: A 218 ARG cc_start: 0.6237 (ptt180) cc_final: 0.5934 (ptt180) REVERT: A 332 ASP cc_start: 0.7951 (m-30) cc_final: 0.7680 (m-30) REVERT: A 368 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 450 MET cc_start: 0.6084 (mmt) cc_final: 0.5859 (mmt) REVERT: A 469 VAL cc_start: 0.8444 (p) cc_final: 0.7865 (t) REVERT: B 218 ARG cc_start: 0.6176 (ptt180) cc_final: 0.5886 (ptt180) REVERT: B 332 ASP cc_start: 0.7946 (m-30) cc_final: 0.7664 (m-30) REVERT: B 368 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7786 (tt) REVERT: B 450 MET cc_start: 0.6123 (mpp) cc_final: 0.5800 (mtm) REVERT: B 469 VAL cc_start: 0.8524 (p) cc_final: 0.7938 (t) REVERT: C 218 ARG cc_start: 0.6201 (ptt180) cc_final: 0.5934 (ptt180) REVERT: C 332 ASP cc_start: 0.7955 (m-30) cc_final: 0.7675 (m-30) REVERT: C 368 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7710 (tt) REVERT: C 450 MET cc_start: 0.6039 (mpp) cc_final: 0.5741 (mtm) REVERT: C 469 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.7926 (t) REVERT: D 218 ARG cc_start: 0.6194 (ptt180) cc_final: 0.5909 (ptt180) REVERT: D 332 ASP cc_start: 0.7934 (m-30) cc_final: 0.7647 (m-30) REVERT: D 368 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7717 (tt) REVERT: D 450 MET cc_start: 0.6238 (mtm) cc_final: 0.5992 (mtt) REVERT: D 469 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.7954 (t) outliers start: 57 outliers final: 39 residues processed: 198 average time/residue: 0.1156 time to fit residues: 35.0085 Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 3 VAL Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 37 TRP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TRP Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 TRP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 230 SER 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 423 ASP 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 230 SER Chi-restraints excluded: chain C residue 300 THR 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 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 230 SER 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: 2.9990 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.207425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177984 restraints weight = 17624.643| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.38 r_work: 0.3554 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15656 Z= 0.133 Angle : 0.531 4.888 21200 Z= 0.286 Chirality : 0.042 0.133 2332 Planarity : 0.005 0.047 2700 Dihedral : 6.284 59.994 2148 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.09 % Allowed : 16.93 % 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 are not related in a simple way. whole: 0.63 (0.20), residues: 1876 helix: 1.32 (0.18), residues: 920 sheet: 0.75 (0.34), residues: 232 loop : -0.83 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.016 0.001 TYR A 447 PHE 0.010 0.001 PHE D 406 TRP 0.005 0.001 TRP D 436 HIS 0.003 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00307 (15652) covalent geometry : angle 0.53105 (21192) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.55461 ( 8) hydrogen bonds : bond 0.05355 ( 808) hydrogen bonds : angle 4.18066 ( 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 214 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 332 ASP cc_start: 0.7949 (m-30) cc_final: 0.7651 (m-30) REVERT: A 368 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7881 (tt) REVERT: A 450 MET cc_start: 0.6178 (mmt) cc_final: 0.5910 (mmt) REVERT: A 469 VAL cc_start: 0.8498 (p) cc_final: 0.7906 (t) REVERT: B 218 ARG cc_start: 0.6366 (ptt180) cc_final: 0.6000 (ptt180) REVERT: B 332 ASP cc_start: 0.7929 (m-30) cc_final: 0.7624 (m-30) REVERT: B 368 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 450 MET cc_start: 0.6175 (mpp) cc_final: 0.5940 (mtm) REVERT: B 469 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.7970 (t) REVERT: C 218 ARG cc_start: 0.6358 (ptt180) cc_final: 0.5998 (ptt180) REVERT: C 332 ASP cc_start: 0.7932 (m-30) cc_final: 0.7632 (m-30) REVERT: C 368 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7795 (tt) REVERT: C 450 MET cc_start: 0.6194 (mpp) cc_final: 0.5968 (mtm) REVERT: C 469 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.7958 (t) REVERT: D 218 ARG cc_start: 0.6343 (ptt180) cc_final: 0.6038 (ptm160) REVERT: D 332 ASP cc_start: 0.7931 (m-30) cc_final: 0.7635 (m-30) REVERT: D 368 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7851 (tt) REVERT: D 450 MET cc_start: 0.6337 (mtm) cc_final: 0.6136 (mtt) REVERT: D 469 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.7978 (t) outliers start: 51 outliers final: 40 residues processed: 199 average time/residue: 0.1255 time to fit residues: 37.5131 Evaluate side-chains 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 369 VAL 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 26 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 230 SER 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 423 ASP 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 230 SER 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 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 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 469 VAL 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: 0.7980 chunk 55 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.203680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.174177 restraints weight = 17530.466| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.38 r_work: 0.3545 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15656 Z= 0.222 Angle : 0.606 5.357 21200 Z= 0.326 Chirality : 0.045 0.141 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.370 59.836 2148 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.82 % Allowed : 16.93 % Favored : 79.25 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1876 helix: 1.00 (0.18), residues: 932 sheet: 0.69 (0.34), residues: 232 loop : -0.93 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.021 0.002 TYR B 447 PHE 0.015 0.002 PHE A 406 TRP 0.014 0.001 TRP H 107 HIS 0.004 0.002 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00560 (15652) covalent geometry : angle 0.60614 (21192) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.58540 ( 8) hydrogen bonds : bond 0.06869 ( 808) hydrogen bonds : angle 4.39297 ( 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 214 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ARG cc_start: 0.6394 (ptt180) cc_final: 0.6151 (ptt180) REVERT: A 332 ASP cc_start: 0.8043 (m-30) cc_final: 0.7763 (m-30) REVERT: A 368 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 450 MET cc_start: 0.6362 (mmt) cc_final: 0.6056 (mmt) REVERT: B 332 ASP cc_start: 0.8038 (m-30) cc_final: 0.7727 (m-30) REVERT: B 368 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8047 (tt) REVERT: B 450 MET cc_start: 0.6491 (mpp) cc_final: 0.6137 (mtt) REVERT: C 332 ASP cc_start: 0.8030 (m-30) cc_final: 0.7718 (m-30) REVERT: C 368 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8040 (tt) REVERT: C 450 MET cc_start: 0.6443 (mpp) cc_final: 0.6116 (mtt) REVERT: D 332 ASP cc_start: 0.8018 (m-30) cc_final: 0.7738 (m-30) REVERT: D 368 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8056 (tt) outliers start: 63 outliers final: 53 residues processed: 193 average time/residue: 0.1193 time to fit residues: 35.1995 Evaluate side-chains 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 481 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 37 TRP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain F residue 3 VAL 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 H residue 52 ILE 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 300 THR 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 369 VAL Chi-restraints excluded: chain B residue 423 ASP 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 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 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.206845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.178930 restraints weight = 17383.573| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.31 r_work: 0.3568 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15656 Z= 0.133 Angle : 0.524 4.858 21200 Z= 0.283 Chirality : 0.041 0.137 2332 Planarity : 0.005 0.047 2700 Dihedral : 6.195 59.765 2148 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.28 % Allowed : 17.78 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1876 helix: 1.27 (0.18), residues: 932 sheet: 0.61 (0.34), residues: 236 loop : -0.81 (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 0.010 0.001 PHE A 406 TRP 0.010 0.001 TRP E 99 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00305 (15652) covalent geometry : angle 0.52426 (21192) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.52945 ( 8) hydrogen bonds : bond 0.05420 ( 808) hydrogen bonds : angle 4.14764 ( 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 208 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.6116 (ptt180) REVERT: A 332 ASP cc_start: 0.7923 (m-30) cc_final: 0.7629 (m-30) REVERT: A 368 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 450 MET cc_start: 0.6015 (mmt) cc_final: 0.5771 (mmt) REVERT: A 469 VAL cc_start: 0.8580 (p) cc_final: 0.8000 (t) REVERT: B 332 ASP cc_start: 0.7894 (m-30) cc_final: 0.7596 (m-30) REVERT: B 368 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8063 (tt) REVERT: B 450 MET cc_start: 0.6163 (mpp) cc_final: 0.5878 (mtt) REVERT: B 469 VAL cc_start: 0.8650 (p) cc_final: 0.8058 (t) REVERT: C 332 ASP cc_start: 0.7886 (m-30) cc_final: 0.7590 (m-30) REVERT: C 368 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8038 (tt) REVERT: C 450 MET cc_start: 0.6174 (mpp) cc_final: 0.5895 (mtt) REVERT: C 469 VAL cc_start: 0.8660 (p) cc_final: 0.8055 (t) REVERT: D 332 ASP cc_start: 0.7895 (m-30) cc_final: 0.7599 (m-30) REVERT: D 368 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8036 (tt) REVERT: D 469 VAL cc_start: 0.8673 (p) cc_final: 0.8056 (t) outliers start: 54 outliers final: 46 residues processed: 195 average time/residue: 0.1197 time to fit residues: 36.0972 Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 218 ARG 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 369 VAL 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 H residue 54 MET 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 369 VAL Chi-restraints excluded: chain B residue 423 ASP 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 218 ARG 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: 0.4980 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 chunk 167 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.208386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.178736 restraints weight = 17592.842| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.41 r_work: 0.3577 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3747 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= 0.116 Angle : 0.504 4.977 21200 Z= 0.272 Chirality : 0.041 0.138 2332 Planarity : 0.005 0.047 2700 Dihedral : 6.093 59.984 2148 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.16 % Allowed : 17.72 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1876 helix: 1.44 (0.18), residues: 932 sheet: 0.53 (0.34), residues: 244 loop : -0.70 (0.24), residues: 700 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 C 406 TRP 0.018 0.001 TRP G 107 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00256 (15652) covalent geometry : angle 0.50361 (21192) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.49618 ( 8) hydrogen bonds : bond 0.04854 ( 808) hydrogen bonds : angle 4.04072 ( 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 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASP cc_start: 0.7887 (m-30) cc_final: 0.7587 (m-30) REVERT: A 368 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8047 (tt) REVERT: B 332 ASP cc_start: 0.7887 (m-30) cc_final: 0.7580 (m-30) REVERT: B 368 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8068 (tt) REVERT: B 450 MET cc_start: 0.6138 (mpp) cc_final: 0.5876 (mtt) REVERT: B 469 VAL cc_start: 0.8577 (p) cc_final: 0.8015 (t) REVERT: C 332 ASP cc_start: 0.7868 (m-30) cc_final: 0.7566 (m-30) REVERT: C 368 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 450 MET cc_start: 0.6139 (mpp) cc_final: 0.5880 (mtt) REVERT: C 469 VAL cc_start: 0.8581 (p) cc_final: 0.8017 (t) REVERT: D 332 ASP cc_start: 0.7889 (m-30) cc_final: 0.7593 (m-30) REVERT: D 368 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8055 (tt) REVERT: D 469 VAL cc_start: 0.8588 (p) cc_final: 0.8044 (t) outliers start: 52 outliers final: 44 residues processed: 191 average time/residue: 0.1170 time to fit residues: 34.3313 Evaluate side-chains 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 218 ARG Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 262 GLU 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 369 VAL Chi-restraints excluded: chain B residue 423 ASP 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 218 ARG 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 481 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.203723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.175605 restraints weight = 17418.711| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.37 r_work: 0.3509 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15656 Z= 0.208 Angle : 0.578 5.254 21200 Z= 0.311 Chirality : 0.044 0.133 2332 Planarity : 0.005 0.049 2700 Dihedral : 6.194 59.220 2148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.22 % Allowed : 17.54 % Favored : 79.25 % 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 are not related in a simple way. whole: 0.51 (0.20), residues: 1876 helix: 1.17 (0.18), residues: 936 sheet: 0.51 (0.34), residues: 244 loop : -0.80 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.020 0.002 TYR A 447 PHE 0.014 0.002 PHE C 406 TRP 0.015 0.001 TRP E 107 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00520 (15652) covalent geometry : angle 0.57765 (21192) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.54728 ( 8) hydrogen bonds : bond 0.06550 ( 808) hydrogen bonds : angle 4.24522 ( 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 204 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASP cc_start: 0.7955 (m-30) cc_final: 0.7645 (m-30) REVERT: A 368 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 469 VAL cc_start: 0.8710 (p) cc_final: 0.8085 (t) REVERT: B 332 ASP cc_start: 0.7923 (m-30) cc_final: 0.7634 (m-30) REVERT: B 368 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (tt) REVERT: B 450 MET cc_start: 0.6359 (mpp) cc_final: 0.6090 (mtt) REVERT: B 469 VAL cc_start: 0.8675 (p) cc_final: 0.8059 (t) REVERT: C 332 ASP cc_start: 0.7912 (m-30) cc_final: 0.7626 (m-30) REVERT: C 368 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8144 (tt) REVERT: C 450 MET cc_start: 0.6412 (mpp) cc_final: 0.6130 (mtt) REVERT: C 469 VAL cc_start: 0.8680 (p) cc_final: 0.8061 (t) REVERT: D 332 ASP cc_start: 0.7923 (m-30) cc_final: 0.7635 (m-30) REVERT: D 368 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8125 (tt) REVERT: D 469 VAL cc_start: 0.8687 (p) cc_final: 0.8071 (t) outliers start: 53 outliers final: 46 residues processed: 195 average time/residue: 0.1072 time to fit residues: 32.3657 Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 369 VAL 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 3 VAL 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 300 THR 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 369 VAL Chi-restraints excluded: chain B residue 423 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 128 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.208576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.180218 restraints weight = 17458.833| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.36 r_work: 0.3552 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15656 Z= 0.153 Angle : 0.534 4.956 21200 Z= 0.287 Chirality : 0.042 0.132 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.116 58.958 2148 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.03 % Allowed : 17.90 % Favored : 79.07 % 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 are not related in a simple way. whole: 0.57 (0.20), residues: 1876 helix: 1.25 (0.18), residues: 936 sheet: 0.52 (0.34), residues: 244 loop : -0.81 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 53 TYR 0.015 0.001 TYR B 163 PHE 0.011 0.001 PHE A 406 TRP 0.013 0.001 TRP E 107 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00369 (15652) covalent geometry : angle 0.53358 (21192) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.52727 ( 8) hydrogen bonds : bond 0.05733 ( 808) hydrogen bonds : angle 4.13404 ( 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 198 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASP cc_start: 0.7966 (m-30) cc_final: 0.7665 (m-30) REVERT: A 368 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8147 (tt) REVERT: A 469 VAL cc_start: 0.8658 (p) cc_final: 0.8072 (t) REVERT: B 332 ASP cc_start: 0.7967 (m-30) cc_final: 0.7669 (m-30) REVERT: B 368 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 450 MET cc_start: 0.6327 (mpp) cc_final: 0.6081 (mtt) REVERT: B 469 VAL cc_start: 0.8665 (p) cc_final: 0.8068 (t) REVERT: C 332 ASP cc_start: 0.7957 (m-30) cc_final: 0.7662 (m-30) REVERT: C 368 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8140 (tt) REVERT: C 450 MET cc_start: 0.6260 (mpp) cc_final: 0.6022 (mtt) REVERT: C 469 VAL cc_start: 0.8669 (p) cc_final: 0.8070 (t) REVERT: D 332 ASP cc_start: 0.7989 (m-30) cc_final: 0.7692 (m-30) REVERT: D 368 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8135 (tt) REVERT: D 469 VAL cc_start: 0.8672 (p) cc_final: 0.8076 (t) outliers start: 50 outliers final: 45 residues processed: 188 average time/residue: 0.1130 time to fit residues: 32.8394 Evaluate side-chains 197 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 218 ARG 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 369 VAL 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 173 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 300 THR 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 369 VAL Chi-restraints excluded: chain B residue 423 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 136 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 140 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.207816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178637 restraints weight = 17285.120| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.37 r_work: 0.3560 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3928 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= 0.121 Angle : 0.502 4.898 21200 Z= 0.270 Chirality : 0.041 0.137 2332 Planarity : 0.005 0.048 2700 Dihedral : 6.016 59.271 2148 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.16 % Allowed : 17.84 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1876 helix: 1.42 (0.18), residues: 936 sheet: 0.56 (0.35), residues: 244 loop : -0.73 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 53 TYR 0.013 0.001 TYR A 163 PHE 0.009 0.001 PHE C 406 TRP 0.014 0.001 TRP E 107 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00277 (15652) covalent geometry : angle 0.50197 (21192) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.49944 ( 8) hydrogen bonds : bond 0.04986 ( 808) hydrogen bonds : angle 4.01143 ( 2364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3299.76 seconds wall clock time: 57 minutes 14.95 seconds (3434.95 seconds total)