Starting phenix.real_space_refine on Sat Mar 7 06:00:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sml_10243/03_2026/6sml_10243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sml_10243/03_2026/6sml_10243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sml_10243/03_2026/6sml_10243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sml_10243/03_2026/6sml_10243.map" model { file = "/net/cci-nas-00/data/ceres_data/6sml_10243/03_2026/6sml_10243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sml_10243/03_2026/6sml_10243.cif" } resolution = 3.4 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21184 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 14056 2.51 5 N 3720 2.21 5 O 4294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 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: 22152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 7134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 911, 7126 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 911, 7126 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 7280 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 65 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, '5PL:plan-2': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: D, E, F Time building chain proxies: 10.53, per 1000 atoms: 0.48 Number of scatterers: 22152 At special positions: 0 Unit cell: (151.94, 127.33, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 4294 8.00 N 3720 7.00 C 14056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 28 sheets defined 20.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 38 through 56 removed outlier: 3.696A pdb=" N ASN A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.687A pdb=" N GLU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 105 through 133 removed outlier: 3.611A pdb=" N ASN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 167 removed outlier: 3.870A pdb=" N ILE A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.873A pdb=" N GLU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.830A pdb=" N VAL A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.670A pdb=" N ALA A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.786A pdb=" N TYR A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.540A pdb=" N ALA B 141 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 143 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 194 through 195 No H-bonds generated for 'chain 'B' and resid 194 through 195' Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.795A pdb=" N LEU B 256 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.897A pdb=" N ASP B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 411 through 417 removed outlier: 3.540A pdb=" N MET B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 895 through 898 Processing helix chain 'B' and resid 911 through 915 removed outlier: 3.684A pdb=" N LEU B 914 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 939 No H-bonds generated for 'chain 'B' and resid 937 through 939' Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.696A pdb=" N ASN D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 67 removed outlier: 3.687A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 86 Processing helix chain 'D' and resid 105 through 133 removed outlier: 3.611A pdb=" N ASN D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 167 removed outlier: 3.870A pdb=" N ILE D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.873A pdb=" N GLU D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 247 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.830A pdb=" N VAL D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 381 through 396 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.670A pdb=" N ALA D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 437 through 445 Processing helix chain 'D' and resid 477 through 481 removed outlier: 3.786A pdb=" N TYR D 480 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 143 removed outlier: 3.540A pdb=" N ALA E 141 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 194 through 195 No H-bonds generated for 'chain 'E' and resid 194 through 195' Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 253 through 257 removed outlier: 3.795A pdb=" N LEU E 256 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 272 removed outlier: 3.897A pdb=" N ASP E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 411 through 417 removed outlier: 3.540A pdb=" N MET E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 453 Processing helix chain 'E' and resid 895 through 898 Processing helix chain 'E' and resid 911 through 915 removed outlier: 3.684A pdb=" N LEU E 914 " --> pdb=" O ASP E 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 939 No H-bonds generated for 'chain 'E' and resid 937 through 939' Processing sheet with id=1, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.838A pdb=" N ASP A 30 " --> pdb=" O VAL B 673 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=4, first strand: chain 'A' and resid 287 through 290 removed outlier: 6.951A pdb=" N ILE A 287 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER A 380 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 289 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=6, first strand: chain 'A' and resid 342 through 346 removed outlier: 5.863A pdb=" N GLY A 351 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.535A pdb=" N SER B 202 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 227 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 179 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 226 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 181 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR B 228 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR B 180 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=9, first strand: chain 'B' and resid 983 through 985 removed outlier: 3.610A pdb=" N GLN B 333 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG B 396 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 457 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY B 507 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 628 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER B 751 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 864 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 878 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 954 " --> pdb=" O SER B 878 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 880 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 952 " --> pdb=" O ASP B 880 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP B 882 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 433 through 434 Processing sheet with id=11, first strand: chain 'B' and resid 731 through 732 Processing sheet with id=12, first strand: chain 'B' and resid 795 through 796 removed outlier: 4.228A pdb=" N PHE B 813 " --> pdb=" O ILE B 856 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 830 through 831 Processing sheet with id=14, first strand: chain 'B' and resid 941 through 943 removed outlier: 8.408A pdb=" N TRP B 890 " --> pdb=" O ASN B 997 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY B 999 " --> pdb=" O TRP B 890 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 892 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.838A pdb=" N ASP D 30 " --> pdb=" O VAL E 673 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 71 through 73 Processing sheet with id=17, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=18, first strand: chain 'D' and resid 287 through 290 removed outlier: 6.951A pdb=" N ILE D 287 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER D 380 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE D 289 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=20, first strand: chain 'D' and resid 342 through 346 removed outlier: 5.863A pdb=" N GLY D 351 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.535A pdb=" N SER E 202 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 227 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU E 179 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE E 226 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE E 181 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR E 228 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR E 180 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 149 through 152 Processing sheet with id=23, first strand: chain 'E' and resid 983 through 985 removed outlier: 3.610A pdb=" N GLN E 333 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG E 396 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER E 457 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY E 507 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR E 628 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER E 751 " --> pdb=" O THR E 787 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 864 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER E 878 " --> pdb=" O LEU E 954 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU E 954 " --> pdb=" O SER E 878 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP E 880 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU E 952 " --> pdb=" O ASP E 880 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP E 882 " --> pdb=" O LYS E 950 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 433 through 434 Processing sheet with id=25, first strand: chain 'E' and resid 731 through 732 Processing sheet with id=26, first strand: chain 'E' and resid 795 through 796 removed outlier: 4.228A pdb=" N PHE E 813 " --> pdb=" O ILE E 856 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 830 through 831 Processing sheet with id=28, first strand: chain 'E' and resid 941 through 943 removed outlier: 8.408A pdb=" N TRP E 890 " --> pdb=" O ASN E 997 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLY E 999 " --> pdb=" O TRP E 890 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE E 892 " --> pdb=" O GLY E 999 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2692 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: 4.27 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3744 1.30 - 1.42: 6148 1.42 - 1.55: 12564 1.55 - 1.68: 36 1.68 - 1.80: 158 Bond restraints: 22650 Sorted by residual: bond pdb=" CBU 5PL A 601 " pdb=" OCK 5PL A 601 " ideal model delta sigma weight residual 1.328 1.409 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CBU 5PL D 601 " pdb=" OCK 5PL D 601 " ideal model delta sigma weight residual 1.328 1.409 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CBL 5PL A 601 " pdb=" OCL 5PL A 601 " ideal model delta sigma weight residual 1.329 1.407 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CBL 5PL D 601 " pdb=" OCL 5PL D 601 " ideal model delta sigma weight residual 1.329 1.407 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CA SER B 591 " pdb=" CB SER B 591 " ideal model delta sigma weight residual 1.533 1.490 0.043 1.66e-02 3.63e+03 6.81e+00 ... (remaining 22645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 29704 2.52 - 5.03: 818 5.03 - 7.55: 100 7.55 - 10.07: 24 10.07 - 12.58: 12 Bond angle restraints: 30658 Sorted by residual: angle pdb=" C GLY E 996 " pdb=" N ASN E 997 " pdb=" CA ASN E 997 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C GLY B 996 " pdb=" N ASN B 997 " pdb=" CA ASN B 997 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C LYS D 348 " pdb=" N ASP D 349 " pdb=" CA ASP D 349 " ideal model delta sigma weight residual 123.93 131.89 -7.96 1.54e+00 4.22e-01 2.67e+01 angle pdb=" C LYS A 348 " pdb=" N ASP A 349 " pdb=" CA ASP A 349 " ideal model delta sigma weight residual 123.93 131.89 -7.96 1.54e+00 4.22e-01 2.67e+01 angle pdb=" C PRO B 799 " pdb=" N ASN B 800 " pdb=" CA ASN B 800 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 ... (remaining 30653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 11962 17.64 - 35.28: 1182 35.28 - 52.92: 218 52.92 - 70.56: 36 70.56 - 88.20: 20 Dihedral angle restraints: 13418 sinusoidal: 5296 harmonic: 8122 Sorted by residual: dihedral pdb=" CA GLY E 691 " pdb=" C GLY E 691 " pdb=" N ASN E 692 " pdb=" CA ASN E 692 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLY B 691 " pdb=" C GLY B 691 " pdb=" N ASN B 692 " pdb=" CA ASN B 692 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG B 495 " pdb=" C ARG B 495 " pdb=" N MET B 496 " pdb=" CA MET B 496 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 13415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2154 0.051 - 0.102: 822 0.102 - 0.152: 222 0.152 - 0.203: 50 0.203 - 0.254: 6 Chirality restraints: 3254 Sorted by residual: chirality pdb=" CA ASP A 349 " pdb=" N ASP A 349 " pdb=" C ASP A 349 " pdb=" CB ASP A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP D 349 " pdb=" N ASP D 349 " pdb=" C ASP D 349 " pdb=" CB ASP D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU D 22 " pdb=" CB LEU D 22 " pdb=" CD1 LEU D 22 " pdb=" CD2 LEU D 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3251 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 82 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 83 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 82 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO D 83 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 83 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 83 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 33 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO D 34 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 34 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 34 " -0.031 5.00e-02 4.00e+02 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5053 2.77 - 3.31: 17380 3.31 - 3.84: 34309 3.84 - 4.37: 40291 4.37 - 4.90: 76014 Nonbonded interactions: 173047 Sorted by model distance: nonbonded pdb=" OG SER B 171 " pdb=" OE2 GLU B 698 " model vdw 2.243 3.040 nonbonded pdb=" OG SER E 171 " pdb=" OE2 GLU E 698 " model vdw 2.243 3.040 nonbonded pdb=" O THR B 471 " pdb=" OG1 THR B 471 " model vdw 2.273 3.040 nonbonded pdb=" O THR E 471 " pdb=" OG1 THR E 471 " model vdw 2.273 3.040 nonbonded pdb=" O TYR D 249 " pdb=" OG SER D 391 " model vdw 2.293 3.040 ... (remaining 173042 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.740 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.930 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 22654 Z= 0.390 Angle : 1.019 12.584 30658 Z= 0.551 Chirality : 0.059 0.254 3254 Planarity : 0.006 0.066 4016 Dihedral : 14.589 88.204 8266 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.85 % 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: -3.42 (0.13), residues: 2796 helix: -2.98 (0.15), residues: 584 sheet: -0.72 (0.17), residues: 808 loop : -2.96 (0.13), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 378 TYR 0.023 0.003 TYR E 514 PHE 0.027 0.003 PHE B1017 TRP 0.023 0.002 TRP D 161 HIS 0.020 0.002 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00912 (22650) covalent geometry : angle 1.01918 (30658) hydrogen bonds : bond 0.13016 ( 944) hydrogen bonds : angle 6.22492 ( 2692) Misc. bond : bond 0.00052 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 0.817 Fit side-chains REVERT: A 22 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 278 TYR cc_start: 0.8747 (t80) cc_final: 0.8419 (t80) REVERT: A 359 GLU cc_start: 0.7460 (pt0) cc_final: 0.7193 (pt0) REVERT: B 312 PRO cc_start: 0.9108 (Cg_endo) cc_final: 0.8904 (Cg_exo) REVERT: B 774 TYR cc_start: 0.7922 (p90) cc_final: 0.7630 (p90) REVERT: B 783 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7363 (ttp-170) REVERT: E 227 GLN cc_start: 0.7487 (tp40) cc_final: 0.7282 (tp40) REVERT: E 279 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7490 (mm110) REVERT: E 314 ASP cc_start: 0.7666 (t0) cc_final: 0.7378 (p0) REVERT: E 370 SER cc_start: 0.8529 (p) cc_final: 0.8290 (t) REVERT: E 374 ASN cc_start: 0.8316 (m-40) cc_final: 0.8074 (m-40) REVERT: E 783 ARG cc_start: 0.7448 (ptm160) cc_final: 0.7132 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.1540 time to fit residues: 81.9292 Evaluate side-chains 241 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 86 ASN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 283 ASN A 465 ASN B 198 ASN B 343 GLN B 395 ASN B 463 ASN B 469 GLN B 621 ASN B 638 ASN B 704 ASN B 713 ASN B 714 ASN B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN B 980 ASN B1002 GLN D 32 GLN D 64 GLN D 86 ASN D 283 ASN D 465 ASN E 343 GLN E 395 ASN E 469 GLN E 582 HIS E 621 ASN E 638 ASN E 713 ASN E 714 ASN E 747 GLN E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN E 967 ASN E 980 ASN E1002 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.143338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.109824 restraints weight = 36102.635| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.82 r_work: 0.2698 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22654 Z= 0.114 Angle : 0.582 13.316 30658 Z= 0.305 Chirality : 0.042 0.176 3254 Planarity : 0.004 0.055 4016 Dihedral : 5.236 47.205 3148 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.24 % Allowed : 12.96 % Favored : 85.80 % 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: -2.34 (0.14), residues: 2796 helix: -1.31 (0.19), residues: 564 sheet: -0.40 (0.17), residues: 844 loop : -2.45 (0.14), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 509 TYR 0.017 0.001 TYR E 514 PHE 0.016 0.001 PHE E 868 TRP 0.012 0.001 TRP B 321 HIS 0.005 0.001 HIS E 582 Details of bonding type rmsd covalent geometry : bond 0.00250 (22650) covalent geometry : angle 0.58248 (30658) hydrogen bonds : bond 0.03370 ( 944) hydrogen bonds : angle 4.97634 ( 2692) Misc. bond : bond 0.00024 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 0.817 Fit side-chains REVERT: A 22 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 30 ASP cc_start: 0.9011 (t0) cc_final: 0.8811 (t0) REVERT: A 60 MET cc_start: 0.8886 (mmp) cc_final: 0.8571 (mmt) REVERT: B 172 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8250 (pp) REVERT: B 541 MET cc_start: 0.8762 (ptp) cc_final: 0.8227 (ptt) REVERT: B 598 TYR cc_start: 0.8680 (t80) cc_final: 0.8230 (t80) REVERT: B 783 ARG cc_start: 0.8303 (ptm160) cc_final: 0.7851 (ttt90) REVERT: B 797 MET cc_start: 0.8349 (pmm) cc_final: 0.7874 (ttt) REVERT: D 22 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7945 (pp) REVERT: D 406 LYS cc_start: 0.8855 (mttt) cc_final: 0.8500 (mmmt) REVERT: E 172 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8352 (pp) REVERT: E 279 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8061 (mm-40) REVERT: E 283 LYS cc_start: 0.8611 (tttp) cc_final: 0.8394 (tttp) REVERT: E 446 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8136 (mm-30) REVERT: E 713 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8288 (t0) REVERT: E 797 MET cc_start: 0.8231 (pmm) cc_final: 0.7797 (ttt) outliers start: 29 outliers final: 14 residues processed: 323 average time/residue: 0.1418 time to fit residues: 72.4614 Evaluate side-chains 266 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 713 ASN Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 967 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 264 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 575 ASN B 582 HIS B 638 ASN B 713 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 463 ASN E 575 ASN E 677 ASN E 748 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106618 restraints weight = 29247.290| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.01 r_work: 0.2697 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22654 Z= 0.153 Angle : 0.605 14.822 30658 Z= 0.315 Chirality : 0.043 0.180 3254 Planarity : 0.004 0.066 4016 Dihedral : 5.164 51.373 3148 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.88 % Allowed : 14.97 % Favored : 83.15 % 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: -1.83 (0.15), residues: 2796 helix: -0.45 (0.21), residues: 566 sheet: -0.30 (0.17), residues: 866 loop : -2.20 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 490 TYR 0.019 0.001 TYR E 514 PHE 0.017 0.001 PHE E 712 TRP 0.013 0.001 TRP E 874 HIS 0.006 0.001 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00357 (22650) covalent geometry : angle 0.60502 (30658) hydrogen bonds : bond 0.03804 ( 944) hydrogen bonds : angle 4.82461 ( 2692) Misc. bond : bond 0.00027 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.829 Fit side-chains REVERT: A 22 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8275 (pp) REVERT: A 60 MET cc_start: 0.8891 (mmp) cc_final: 0.8586 (mmt) REVERT: A 313 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7817 (tptt) REVERT: B 172 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 342 SER cc_start: 0.8373 (m) cc_final: 0.8172 (m) REVERT: B 436 MET cc_start: 0.8610 (mtt) cc_final: 0.8354 (mtt) REVERT: B 541 MET cc_start: 0.8552 (ptp) cc_final: 0.8070 (ptt) REVERT: B 774 TYR cc_start: 0.8340 (p90) cc_final: 0.8076 (p90) REVERT: B 783 ARG cc_start: 0.8263 (ptm160) cc_final: 0.7947 (ttt90) REVERT: D 22 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8203 (pp) REVERT: D 406 LYS cc_start: 0.8889 (mttt) cc_final: 0.8556 (mmmt) REVERT: D 421 MET cc_start: 0.6462 (tpt) cc_final: 0.5990 (tpt) REVERT: E 142 LEU cc_start: 0.8604 (mp) cc_final: 0.8365 (mt) REVERT: E 172 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8260 (pp) REVERT: E 283 LYS cc_start: 0.8717 (tttp) cc_final: 0.8465 (tttp) REVERT: E 446 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8146 (mm-30) REVERT: E 547 GLU cc_start: 0.8603 (tt0) cc_final: 0.8345 (tt0) REVERT: E 753 LYS cc_start: 0.8623 (pttp) cc_final: 0.8396 (ptmt) REVERT: E 797 MET cc_start: 0.8296 (pmm) cc_final: 0.7945 (ttt) REVERT: E 894 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8768 (t160) outliers start: 44 outliers final: 25 residues processed: 277 average time/residue: 0.1351 time to fit residues: 61.1436 Evaluate side-chains 256 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 894 ASN Chi-restraints excluded: chain E residue 926 ASP Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 277 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 220 optimal weight: 0.2980 chunk 176 optimal weight: 9.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 343 GLN B 465 ASN B 481 GLN B 575 ASN B 638 ASN B 713 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 318 ASN E 198 ASN E 282 GLN E 343 GLN E 535 HIS E 575 ASN E 704 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.135562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.101845 restraints weight = 36732.188| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.84 r_work: 0.2560 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 22654 Z= 0.282 Angle : 0.700 16.704 30658 Z= 0.361 Chirality : 0.047 0.180 3254 Planarity : 0.005 0.086 4016 Dihedral : 5.781 62.291 3148 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 2.87 % Allowed : 16.42 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.15), residues: 2796 helix: -0.29 (0.22), residues: 566 sheet: -0.40 (0.17), residues: 878 loop : -2.13 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.023 0.002 TYR B1003 PHE 0.022 0.002 PHE B1017 TRP 0.017 0.001 TRP E 874 HIS 0.006 0.002 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00675 (22650) covalent geometry : angle 0.69960 (30658) hydrogen bonds : bond 0.04634 ( 944) hydrogen bonds : angle 5.05049 ( 2692) Misc. bond : bond 0.00050 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 0.718 Fit side-chains REVERT: A 22 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8294 (pp) REVERT: B 172 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8283 (pp) REVERT: B 282 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8676 (tp-100) REVERT: B 783 ARG cc_start: 0.8454 (ptm160) cc_final: 0.7964 (ttt90) REVERT: D 22 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8367 (pp) REVERT: D 313 LYS cc_start: 0.8391 (tppt) cc_final: 0.8123 (tppt) REVERT: D 406 LYS cc_start: 0.8985 (mttt) cc_final: 0.8680 (mmmt) REVERT: D 421 MET cc_start: 0.6416 (tpt) cc_final: 0.5951 (tpt) REVERT: E 172 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8254 (pp) REVERT: E 282 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8315 (tp-100) REVERT: E 640 PHE cc_start: 0.7479 (m-10) cc_final: 0.7173 (m-10) outliers start: 67 outliers final: 42 residues processed: 278 average time/residue: 0.1420 time to fit residues: 63.5220 Evaluate side-chains 260 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 757 VAL Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 23 optimal weight: 0.7980 chunk 270 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 543 HIS B 575 ASN B 713 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 575 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.137009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.103245 restraints weight = 38413.330| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.95 r_work: 0.2570 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22654 Z= 0.199 Angle : 0.626 15.049 30658 Z= 0.324 Chirality : 0.044 0.181 3254 Planarity : 0.004 0.092 4016 Dihedral : 5.403 51.700 3148 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 2.87 % Allowed : 16.89 % Favored : 80.24 % 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: -1.61 (0.15), residues: 2796 helix: -0.08 (0.22), residues: 566 sheet: -0.35 (0.17), residues: 878 loop : -2.02 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 490 TYR 0.019 0.002 TYR E 514 PHE 0.014 0.001 PHE E 868 TRP 0.012 0.001 TRP E 697 HIS 0.005 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00474 (22650) covalent geometry : angle 0.62632 (30658) hydrogen bonds : bond 0.03959 ( 944) hydrogen bonds : angle 4.89020 ( 2692) Misc. bond : bond 0.00035 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 0.919 Fit side-chains REVERT: A 22 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 313 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7736 (tptt) REVERT: B 172 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8235 (pp) REVERT: B 282 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8721 (tp-100) REVERT: B 774 TYR cc_start: 0.8404 (p90) cc_final: 0.8093 (p90) REVERT: B 783 ARG cc_start: 0.8447 (ptm160) cc_final: 0.7941 (ttt90) REVERT: D 22 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8404 (pp) REVERT: D 348 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8909 (mmmm) REVERT: D 421 MET cc_start: 0.6550 (tpt) cc_final: 0.6095 (tpt) REVERT: E 172 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8224 (pp) REVERT: E 282 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8348 (tp-100) REVERT: E 283 LYS cc_start: 0.8825 (tttp) cc_final: 0.8573 (tttp) REVERT: E 547 GLU cc_start: 0.8809 (tt0) cc_final: 0.8565 (tt0) REVERT: E 598 TYR cc_start: 0.8789 (t80) cc_final: 0.8507 (t80) REVERT: E 640 PHE cc_start: 0.7504 (m-10) cc_final: 0.7164 (m-10) REVERT: E 778 ASN cc_start: 0.8962 (p0) cc_final: 0.8743 (p0) REVERT: E 797 MET cc_start: 0.8464 (pmm) cc_final: 0.8089 (ttt) outliers start: 67 outliers final: 44 residues processed: 282 average time/residue: 0.1407 time to fit residues: 63.8563 Evaluate side-chains 272 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 757 VAL Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 26 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 156 GLN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 HIS E 575 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN E 916 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.141208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.108123 restraints weight = 27408.338| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.85 r_work: 0.2749 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22654 Z= 0.099 Angle : 0.533 11.482 30658 Z= 0.277 Chirality : 0.041 0.179 3254 Planarity : 0.004 0.054 4016 Dihedral : 4.656 46.758 3148 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.18 % Allowed : 18.22 % Favored : 79.60 % 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: -1.22 (0.15), residues: 2796 helix: 0.17 (0.22), residues: 578 sheet: -0.11 (0.17), residues: 862 loop : -1.74 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 973 TYR 0.014 0.001 TYR B 514 PHE 0.012 0.001 PHE E 990 TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00220 (22650) covalent geometry : angle 0.53302 (30658) hydrogen bonds : bond 0.02924 ( 944) hydrogen bonds : angle 4.58547 ( 2692) Misc. bond : bond 0.00011 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.811 Fit side-chains REVERT: A 22 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8316 (pp) REVERT: A 30 ASP cc_start: 0.8872 (t0) cc_final: 0.8628 (t0) REVERT: A 60 MET cc_start: 0.8858 (mmp) cc_final: 0.8543 (mmt) REVERT: A 182 ASP cc_start: 0.8161 (t0) cc_final: 0.7829 (t0) REVERT: A 313 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7837 (tptt) REVERT: B 172 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8095 (pp) REVERT: B 185 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8631 (ptt) REVERT: B 342 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8084 (m) REVERT: B 537 LEU cc_start: 0.8341 (mp) cc_final: 0.8118 (mp) REVERT: B 598 TYR cc_start: 0.8685 (t80) cc_final: 0.8138 (t80) REVERT: B 774 TYR cc_start: 0.8274 (p90) cc_final: 0.7977 (p90) REVERT: B 783 ARG cc_start: 0.8265 (ptm160) cc_final: 0.7900 (ttt90) REVERT: D 30 ASP cc_start: 0.8873 (t0) cc_final: 0.8639 (t0) REVERT: D 348 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8924 (mmmm) REVERT: D 421 MET cc_start: 0.6572 (tpt) cc_final: 0.6096 (tpt) REVERT: E 172 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8032 (pp) REVERT: E 283 LYS cc_start: 0.8756 (tttp) cc_final: 0.8500 (tttp) REVERT: E 541 MET cc_start: 0.8502 (ptp) cc_final: 0.8090 (ptt) REVERT: E 547 GLU cc_start: 0.8452 (tt0) cc_final: 0.8197 (tt0) REVERT: E 598 TYR cc_start: 0.8696 (t80) cc_final: 0.8421 (t80) REVERT: E 640 PHE cc_start: 0.7393 (m-10) cc_final: 0.7164 (m-10) REVERT: E 778 ASN cc_start: 0.8767 (p0) cc_final: 0.8540 (p0) REVERT: E 797 MET cc_start: 0.8209 (pmm) cc_final: 0.7953 (ttt) outliers start: 51 outliers final: 30 residues processed: 304 average time/residue: 0.1356 time to fit residues: 67.0482 Evaluate side-chains 276 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 757 VAL Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 67 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN B 343 GLN B 575 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 388 ASN E 465 ASN E 481 GLN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.105443 restraints weight = 29609.992| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.98 r_work: 0.2669 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22654 Z= 0.156 Angle : 0.590 13.655 30658 Z= 0.304 Chirality : 0.043 0.179 3254 Planarity : 0.004 0.084 4016 Dihedral : 4.913 47.976 3148 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.74 % Allowed : 18.18 % Favored : 79.08 % 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: -1.12 (0.15), residues: 2796 helix: 0.34 (0.22), residues: 566 sheet: 0.02 (0.17), residues: 852 loop : -1.74 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 973 TYR 0.017 0.001 TYR B 514 PHE 0.017 0.001 PHE E 375 TRP 0.010 0.001 TRP E 697 HIS 0.008 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00371 (22650) covalent geometry : angle 0.58988 (30658) hydrogen bonds : bond 0.03551 ( 944) hydrogen bonds : angle 4.66993 ( 2692) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 0.830 Fit side-chains REVERT: A 22 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8254 (pp) REVERT: A 60 MET cc_start: 0.8926 (mmp) cc_final: 0.8624 (mmt) REVERT: A 182 ASP cc_start: 0.8212 (t0) cc_final: 0.7851 (t0) REVERT: B 172 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8214 (pp) REVERT: B 342 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8072 (m) REVERT: B 537 LEU cc_start: 0.8349 (mp) cc_final: 0.8104 (mp) REVERT: B 598 TYR cc_start: 0.8715 (t80) cc_final: 0.8193 (t80) REVERT: B 774 TYR cc_start: 0.8325 (p90) cc_final: 0.8030 (p90) REVERT: B 783 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7971 (ttt90) REVERT: D 164 MET cc_start: 0.9004 (tpp) cc_final: 0.8712 (mmt) REVERT: D 348 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8927 (mmmm) REVERT: D 386 LEU cc_start: 0.7849 (mt) cc_final: 0.7607 (mp) REVERT: D 421 MET cc_start: 0.6511 (tpt) cc_final: 0.6147 (tpt) REVERT: E 172 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8167 (pp) REVERT: E 283 LYS cc_start: 0.8775 (tttp) cc_final: 0.8507 (tttp) REVERT: E 541 MET cc_start: 0.8632 (ptp) cc_final: 0.8206 (ptt) REVERT: E 547 GLU cc_start: 0.8554 (tt0) cc_final: 0.8298 (tt0) REVERT: E 598 TYR cc_start: 0.8757 (t80) cc_final: 0.8471 (t80) REVERT: E 640 PHE cc_start: 0.7446 (m-10) cc_final: 0.7149 (m-10) REVERT: E 778 ASN cc_start: 0.8877 (p0) cc_final: 0.8644 (p0) REVERT: E 797 MET cc_start: 0.8323 (pmm) cc_final: 0.8052 (ttt) outliers start: 64 outliers final: 47 residues processed: 283 average time/residue: 0.1417 time to fit residues: 64.7799 Evaluate side-chains 282 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 182 optimal weight: 0.0670 chunk 239 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 GLN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 465 ASN E 575 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.105956 restraints weight = 42003.958| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.84 r_work: 0.2582 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22654 Z= 0.177 Angle : 0.608 14.199 30658 Z= 0.313 Chirality : 0.044 0.178 3254 Planarity : 0.004 0.082 4016 Dihedral : 5.021 50.635 3148 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.65 % Allowed : 19.12 % Favored : 78.23 % 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: -1.11 (0.15), residues: 2796 helix: 0.35 (0.22), residues: 566 sheet: 0.00 (0.17), residues: 854 loop : -1.72 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 973 TYR 0.017 0.001 TYR B 514 PHE 0.017 0.001 PHE E 375 TRP 0.013 0.001 TRP E 697 HIS 0.009 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00422 (22650) covalent geometry : angle 0.60765 (30658) hydrogen bonds : bond 0.03694 ( 944) hydrogen bonds : angle 4.71310 ( 2692) Misc. bond : bond 0.00016 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 0.602 Fit side-chains REVERT: A 22 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8350 (pp) REVERT: A 182 ASP cc_start: 0.8240 (t0) cc_final: 0.7873 (t0) REVERT: B 172 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8207 (pp) REVERT: B 342 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8035 (m) REVERT: B 598 TYR cc_start: 0.8800 (t80) cc_final: 0.8259 (t80) REVERT: B 774 TYR cc_start: 0.8428 (p90) cc_final: 0.8128 (p90) REVERT: B 783 ARG cc_start: 0.8416 (ptm160) cc_final: 0.7976 (ttt90) REVERT: D 132 GLN cc_start: 0.7866 (tp40) cc_final: 0.7616 (tt0) REVERT: D 348 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8914 (mmmm) REVERT: D 386 LEU cc_start: 0.7947 (mt) cc_final: 0.7732 (mp) REVERT: D 421 MET cc_start: 0.6655 (tpt) cc_final: 0.6195 (tpt) REVERT: E 172 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8178 (pp) REVERT: E 283 LYS cc_start: 0.8769 (tttp) cc_final: 0.8518 (tttp) REVERT: E 547 GLU cc_start: 0.8792 (tt0) cc_final: 0.8550 (tt0) REVERT: E 598 TYR cc_start: 0.8815 (t80) cc_final: 0.8494 (t80) REVERT: E 640 PHE cc_start: 0.7598 (m-10) cc_final: 0.7248 (m-10) REVERT: E 778 ASN cc_start: 0.8959 (p0) cc_final: 0.8733 (p0) REVERT: E 797 MET cc_start: 0.8473 (pmm) cc_final: 0.8113 (ttt) outliers start: 62 outliers final: 53 residues processed: 277 average time/residue: 0.1399 time to fit residues: 63.5314 Evaluate side-chains 287 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 894 ASN Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 164 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN B 282 GLN B 343 GLN B 575 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 575 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.136684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.104927 restraints weight = 40830.673| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.84 r_work: 0.2566 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22654 Z= 0.212 Angle : 0.637 14.876 30658 Z= 0.328 Chirality : 0.045 0.178 3254 Planarity : 0.004 0.089 4016 Dihedral : 5.183 53.112 3148 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.87 % Allowed : 19.08 % Favored : 78.06 % 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: -1.16 (0.15), residues: 2796 helix: 0.30 (0.22), residues: 566 sheet: -0.02 (0.17), residues: 852 loop : -1.74 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 973 TYR 0.019 0.002 TYR B1003 PHE 0.017 0.001 PHE E 375 TRP 0.012 0.001 TRP E 697 HIS 0.010 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00509 (22650) covalent geometry : angle 0.63746 (30658) hydrogen bonds : bond 0.03970 ( 944) hydrogen bonds : angle 4.79340 ( 2692) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 0.841 Fit side-chains REVERT: A 22 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8356 (pp) REVERT: A 182 ASP cc_start: 0.8260 (t0) cc_final: 0.7889 (t0) REVERT: B 172 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8391 (pp) REVERT: B 282 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8697 (tp-100) REVERT: B 436 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8516 (mtt) REVERT: B 598 TYR cc_start: 0.8801 (t80) cc_final: 0.8217 (t80) REVERT: B 783 ARG cc_start: 0.8440 (ptm160) cc_final: 0.7977 (ttt90) REVERT: D 188 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 348 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8924 (mmmm) REVERT: D 352 TYR cc_start: 0.7650 (m-80) cc_final: 0.7363 (m-80) REVERT: D 421 MET cc_start: 0.6693 (tpt) cc_final: 0.6275 (tpt) REVERT: E 172 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8216 (pp) REVERT: E 283 LYS cc_start: 0.8813 (tttp) cc_final: 0.8566 (tttp) REVERT: E 547 GLU cc_start: 0.8793 (tt0) cc_final: 0.8547 (tt0) REVERT: E 640 PHE cc_start: 0.7591 (m-10) cc_final: 0.7304 (m-10) REVERT: E 778 ASN cc_start: 0.9003 (p0) cc_final: 0.8784 (p0) REVERT: E 797 MET cc_start: 0.8500 (pmm) cc_final: 0.8132 (ttt) outliers start: 67 outliers final: 56 residues processed: 275 average time/residue: 0.1453 time to fit residues: 65.1268 Evaluate side-chains 290 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 932 GLN Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 271 optimal weight: 0.0870 chunk 223 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 163 optimal weight: 10.0000 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN B 343 GLN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 638 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.142224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.109440 restraints weight = 34115.363| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.42 r_work: 0.2704 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22654 Z= 0.092 Angle : 0.535 10.196 30658 Z= 0.279 Chirality : 0.041 0.177 3254 Planarity : 0.004 0.056 4016 Dihedral : 4.573 47.478 3148 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.97 % Allowed : 20.19 % Favored : 77.84 % 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: -0.85 (0.16), residues: 2796 helix: 0.48 (0.22), residues: 578 sheet: 0.15 (0.17), residues: 838 loop : -1.49 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 973 TYR 0.013 0.001 TYR A 109 PHE 0.014 0.001 PHE E 375 TRP 0.013 0.001 TRP D 161 HIS 0.005 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00199 (22650) covalent geometry : angle 0.53532 (30658) hydrogen bonds : bond 0.02785 ( 944) hydrogen bonds : angle 4.51849 ( 2692) Misc. bond : bond 0.00005 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 0.843 Fit side-chains REVERT: A 22 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (pp) REVERT: A 30 ASP cc_start: 0.8898 (t0) cc_final: 0.8692 (t0) REVERT: A 182 ASP cc_start: 0.8295 (t0) cc_final: 0.7941 (t0) REVERT: B 185 MET cc_start: 0.9113 (ptm) cc_final: 0.8718 (ptt) REVERT: B 342 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8454 (m) REVERT: B 537 LEU cc_start: 0.8381 (mp) cc_final: 0.8173 (mp) REVERT: B 598 TYR cc_start: 0.8713 (t80) cc_final: 0.8251 (t80) REVERT: B 774 TYR cc_start: 0.8378 (p90) cc_final: 0.8090 (p90) REVERT: B 783 ARG cc_start: 0.8372 (ptm160) cc_final: 0.7944 (ttt90) REVERT: D 30 ASP cc_start: 0.8911 (t0) cc_final: 0.8702 (t0) REVERT: D 352 TYR cc_start: 0.7610 (m-80) cc_final: 0.7374 (m-80) REVERT: D 386 LEU cc_start: 0.8026 (mt) cc_final: 0.7780 (mp) REVERT: E 172 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8065 (pp) REVERT: E 282 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8096 (pt0) REVERT: E 283 LYS cc_start: 0.8663 (tttp) cc_final: 0.8392 (ttmm) REVERT: E 541 MET cc_start: 0.8610 (ptp) cc_final: 0.8246 (ptt) REVERT: E 547 GLU cc_start: 0.8628 (tt0) cc_final: 0.8374 (tt0) REVERT: E 598 TYR cc_start: 0.8748 (t80) cc_final: 0.8448 (t80) REVERT: E 640 PHE cc_start: 0.7538 (m-10) cc_final: 0.7238 (m-10) REVERT: E 774 TYR cc_start: 0.8403 (p90) cc_final: 0.8102 (p90) REVERT: E 797 MET cc_start: 0.8464 (pmm) cc_final: 0.8107 (ttt) outliers start: 46 outliers final: 32 residues processed: 297 average time/residue: 0.1505 time to fit residues: 72.1689 Evaluate side-chains 288 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 51 optimal weight: 0.1980 chunk 201 optimal weight: 0.0570 chunk 194 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN B 343 GLN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 258 ASN E 575 ASN E 638 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.140522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.108981 restraints weight = 40551.819| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.66 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22654 Z= 0.116 Angle : 0.557 11.478 30658 Z= 0.287 Chirality : 0.042 0.177 3254 Planarity : 0.004 0.059 4016 Dihedral : 4.564 46.721 3148 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.67 % Allowed : 20.40 % Favored : 77.93 % 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 (0.16), residues: 2796 helix: 0.66 (0.22), residues: 570 sheet: 0.19 (0.17), residues: 842 loop : -1.47 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 973 TYR 0.015 0.001 TYR B 514 PHE 0.015 0.001 PHE E 375 TRP 0.011 0.001 TRP D 161 HIS 0.006 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00269 (22650) covalent geometry : angle 0.55677 (30658) hydrogen bonds : bond 0.03045 ( 944) hydrogen bonds : angle 4.48772 ( 2692) Misc. bond : bond 0.00005 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.58 seconds wall clock time: 87 minutes 29.56 seconds (5249.56 seconds total)