Starting phenix.real_space_refine on Tue Sep 15 11:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sml_10243/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.cif" model { file = "/net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sml_10243/09_2026/6sml_10243.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 13.15, per 1000 atoms: 0.59 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: 2.06 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: 0.86 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: 4.91 Time building geometry restraints manager: 2.69 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: 0.05 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.410 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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/Z covalent geometry : bond 0.00912 / 0.39 (22650) covalent geometry : angle 1.01918 / 0.55 (30658) hydrogen bonds : bond 0.13016 / 8.78 ( 944) hydrogen bonds : angle 6.22492 / 4.39 ( 2692) Misc. bond : bond 0.00052 / 0.03 ( 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 : 0.863 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: D 430 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7865 (mtp180) 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: 0.1627 time to fit residues: 87.4802 Evaluate side-chains 242 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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... A 64 GLN ** 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 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 677 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.143110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.109364 restraints weight = 36102.227| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.84 r_work: 0.2696 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- 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 = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 : 0.003 0.035 22654 Z= 0.119 Angle : 0.593 13.424 30658 Z= 0.310 Chirality : 0.042 0.179 3254 Planarity : 0.004 0.059 4016 Dihedral : 5.234 47.563 3148 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.20 % Allowed : 13.26 % Favored : 85.54 % 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: -2.35 (0.14), residues: 2796 helix: -1.32 (0.19), residues: 564 sheet: -0.41 (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 611 TYR 0.017 0.001 TYR E 514 PHE 0.016 0.001 PHE E 868 TRP 0.013 0.001 TRP B 321 HIS 0.006 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22650) covalent geometry : angle 0.59266 / 0.31 (30658) hydrogen bonds : bond 0.03439 / 2.24 ( 944) hydrogen bonds : angle 4.97508 / 3.49 ( 2692) Misc. bond : bond 0.00013 / 0.01 ( 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 330 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 0.925 Fit side-chains REVERT: A 22 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 60 MET cc_start: 0.8895 (mmp) cc_final: 0.8575 (mmt) REVERT: B 172 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 227 GLN cc_start: 0.8260 (mt0) cc_final: 0.7982 (mt0) REVERT: B 541 MET cc_start: 0.8775 (ptp) cc_final: 0.8241 (ptt) REVERT: B 598 TYR cc_start: 0.8682 (t80) cc_final: 0.8216 (t80) REVERT: B 774 TYR cc_start: 0.8432 (p90) cc_final: 0.8112 (p90) REVERT: B 778 ASN cc_start: 0.8856 (p0) cc_final: 0.8615 (p0) REVERT: B 783 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7845 (ttt90) REVERT: B 797 MET cc_start: 0.8339 (pmm) cc_final: 0.7876 (ttt) REVERT: B 993 GLU cc_start: 0.8835 (tt0) cc_final: 0.8627 (tt0) REVERT: D 22 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7988 (pp) REVERT: D 331 TYR cc_start: 0.7681 (m-80) cc_final: 0.7278 (m-80) REVERT: D 406 LYS cc_start: 0.8858 (mttt) cc_final: 0.8479 (mmmt) REVERT: E 172 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8337 (pp) REVERT: E 279 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8080 (mm-40) REVERT: E 446 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8169 (mm-30) REVERT: E 713 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8293 (t0) REVERT: E 797 MET cc_start: 0.8235 (pmm) cc_final: 0.7785 (ttt) outliers start: 28 outliers final: 14 residues processed: 321 average time/residue: 0.1553 time to fit residues: 78.7813 Evaluate side-chains 265 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 591 SER 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: 8.9990 chunk 21 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN B 463 ASN B 638 ASN B 713 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 64 GLN D 449 ASN E 463 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.140010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.106242 restraints weight = 29260.698| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.12 r_work: 0.2706 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22654 Z= 0.146 Angle : 0.601 14.482 30658 Z= 0.313 Chirality : 0.043 0.180 3254 Planarity : 0.004 0.064 4016 Dihedral : 5.119 51.073 3148 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.27 % Allowed : 14.29 % Favored : 83.45 % 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: -1.81 (0.15), residues: 2796 helix: -0.45 (0.21), residues: 566 sheet: -0.29 (0.17), residues: 866 loop : -2.18 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 715 TYR 0.018 0.001 TYR E 514 PHE 0.017 0.001 PHE E 990 TRP 0.014 0.001 TRP E 874 HIS 0.006 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (22650) covalent geometry : angle 0.60126 / 0.31 (30658) hydrogen bonds : bond 0.03756 / 2.45 ( 944) hydrogen bonds : angle 4.79754 / 3.37 ( 2692) Misc. bond : bond 0.00025 / 0.01 ( 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 305 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 60 MET cc_start: 0.8882 (mmp) cc_final: 0.8571 (mmt) REVERT: A 166 ARG cc_start: 0.8772 (tpm170) cc_final: 0.8511 (tpm170) REVERT: A 313 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7843 (tptt) REVERT: B 172 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8130 (pp) REVERT: B 227 GLN cc_start: 0.8244 (mt0) cc_final: 0.7975 (mt0) REVERT: B 541 MET cc_start: 0.8530 (ptp) cc_final: 0.8048 (ptt) REVERT: B 774 TYR cc_start: 0.8329 (p90) cc_final: 0.8062 (p90) REVERT: B 778 ASN cc_start: 0.8890 (p0) cc_final: 0.8607 (p0) REVERT: B 783 ARG cc_start: 0.8261 (ptm160) cc_final: 0.7939 (ttt90) REVERT: D 22 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8190 (pp) REVERT: D 406 LYS cc_start: 0.8892 (mttt) cc_final: 0.8557 (mmmt) REVERT: D 421 MET cc_start: 0.6547 (tpt) cc_final: 0.6049 (tpt) REVERT: D 449 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8581 (t0) REVERT: E 142 LEU cc_start: 0.8579 (mp) cc_final: 0.8357 (mt) REVERT: E 172 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8254 (pp) REVERT: E 283 LYS cc_start: 0.8718 (tttp) cc_final: 0.8468 (tttp) REVERT: E 446 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8122 (mm-30) REVERT: E 547 GLU cc_start: 0.8591 (tt0) cc_final: 0.8332 (tt0) REVERT: E 753 LYS cc_start: 0.8597 (pttp) cc_final: 0.8391 (ptmt) REVERT: E 797 MET cc_start: 0.8292 (pmm) cc_final: 0.7949 (ttt) REVERT: E 894 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8751 (t160) REVERT: E 930 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8575 (mm) outliers start: 53 outliers final: 29 residues processed: 287 average time/residue: 0.1483 time to fit residues: 69.1528 Evaluate side-chains 266 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 158 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 124 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 449 ASN 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 233 MET Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 591 SER 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 759 LEU 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 930 LEU 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: 10.0000 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 220 optimal weight: 0.4980 chunk 176 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN B 575 ASN B 582 HIS B 638 ASN B 713 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 318 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.139242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.106902 restraints weight = 36140.293| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.56 r_work: 0.2640 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22654 Z= 0.152 Angle : 0.583 13.636 30658 Z= 0.302 Chirality : 0.043 0.179 3254 Planarity : 0.004 0.090 4016 Dihedral : 5.026 48.731 3148 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.61 % Allowed : 15.27 % Favored : 82.12 % 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: -1.50 (0.15), residues: 2796 helix: -0.05 (0.22), residues: 566 sheet: -0.23 (0.17), residues: 880 loop : -1.97 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 490 TYR 0.018 0.001 TYR E 514 PHE 0.015 0.001 PHE E 990 TRP 0.016 0.001 TRP E 874 HIS 0.006 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (22650) covalent geometry : angle 0.58301 / 0.30 (30658) hydrogen bonds : bond 0.03556 / 2.32 ( 944) hydrogen bonds : angle 4.74879 / 3.33 ( 2692) Misc. bond : bond 0.00025 / 0.01 ( 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 313 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 0.698 Fit side-chains REVERT: A 22 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 60 MET cc_start: 0.8958 (mmp) cc_final: 0.8641 (mmt) REVERT: B 172 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8132 (pp) REVERT: B 598 TYR cc_start: 0.8748 (t80) cc_final: 0.8206 (t80) REVERT: B 774 TYR cc_start: 0.8415 (p90) cc_final: 0.8114 (p90) REVERT: B 778 ASN cc_start: 0.8904 (p0) cc_final: 0.8618 (p0) REVERT: B 783 ARG cc_start: 0.8330 (ptm160) cc_final: 0.7996 (ttt90) REVERT: D 22 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8350 (pp) REVERT: D 99 ASP cc_start: 0.7646 (m-30) cc_final: 0.7370 (m-30) REVERT: D 212 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7812 (mmp-170) REVERT: D 331 TYR cc_start: 0.7516 (m-80) cc_final: 0.7059 (m-80) REVERT: D 406 LYS cc_start: 0.8978 (mttt) cc_final: 0.8720 (mmmt) REVERT: D 421 MET cc_start: 0.6636 (tpt) cc_final: 0.6113 (tpt) REVERT: E 142 LEU cc_start: 0.8702 (mp) cc_final: 0.8436 (mt) REVERT: E 172 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8179 (pp) REVERT: E 283 LYS cc_start: 0.8772 (tttp) cc_final: 0.8542 (tttp) REVERT: E 446 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8216 (mm-30) REVERT: E 547 GLU cc_start: 0.8706 (tt0) cc_final: 0.8466 (tt0) REVERT: E 774 TYR cc_start: 0.8403 (p90) cc_final: 0.8084 (p90) REVERT: E 778 ASN cc_start: 0.8909 (p0) cc_final: 0.8675 (p0) REVERT: E 797 MET cc_start: 0.8353 (pmm) cc_final: 0.8095 (ttt) REVERT: E 930 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8653 (mm) outliers start: 61 outliers final: 39 residues processed: 297 average time/residue: 0.1403 time to fit residues: 68.1439 Evaluate side-chains 276 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 158 LEU 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 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 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 158 LEU 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 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 730 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 23 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN B 465 ASN B 481 GLN B 575 ASN B 638 ASN B 713 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 198 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.135255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.102291 restraints weight = 38645.557| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.96 r_work: 0.2522 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 22654 Z= 0.285 Angle : 0.699 16.799 30658 Z= 0.360 Chirality : 0.047 0.180 3254 Planarity : 0.005 0.101 4016 Dihedral : 5.741 62.681 3148 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 2.82 % Allowed : 16.60 % Favored : 80.58 % 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: -1.64 (0.15), residues: 2796 helix: -0.15 (0.22), residues: 566 sheet: -0.35 (0.17), residues: 878 loop : -2.03 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.023 0.002 TYR E1003 PHE 0.022 0.002 PHE B1017 TRP 0.018 0.001 TRP E 874 HIS 0.006 0.002 HIS E 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 (22650) covalent geometry : angle 0.69901 / 0.36 (30658) hydrogen bonds : bond 0.04609 / 3.01 ( 944) hydrogen bonds : angle 5.03692 / 3.53 ( 2692) Misc. bond : bond 0.00034 / 0.02 ( 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 294 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 0.821 Fit side-chains REVERT: A 22 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 313 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7794 (tptt) REVERT: B 172 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8307 (pp) REVERT: B 282 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8654 (tp-100) REVERT: B 342 SER cc_start: 0.8536 (m) cc_final: 0.8268 (m) REVERT: B 774 TYR cc_start: 0.8445 (p90) cc_final: 0.8136 (p90) REVERT: B 783 ARG cc_start: 0.8484 (ptm160) cc_final: 0.7983 (ttt90) REVERT: D 22 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8327 (pp) REVERT: D 348 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8892 (mmmm) REVERT: D 352 TYR cc_start: 0.7658 (m-80) cc_final: 0.7359 (m-80) REVERT: D 421 MET cc_start: 0.6420 (tpt) cc_final: 0.5985 (tpt) REVERT: E 172 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8159 (pp) REVERT: E 283 LYS cc_start: 0.8824 (tttp) cc_final: 0.8623 (tttp) REVERT: E 342 SER cc_start: 0.8466 (m) cc_final: 0.8199 (m) REVERT: E 575 ASN cc_start: 0.8780 (t0) cc_final: 0.8577 (t0) REVERT: E 640 PHE cc_start: 0.7509 (m-10) cc_final: 0.7264 (m-10) REVERT: E 797 MET cc_start: 0.8506 (pmm) cc_final: 0.8118 (ttt) REVERT: E 930 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8677 (mm) outliers start: 66 outliers final: 43 residues processed: 279 average time/residue: 0.1504 time to fit residues: 68.1452 Evaluate side-chains 269 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 158 LEU Chi-restraints excluded: chain A residue 165 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 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 165 ASP 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 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 757 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 26 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 HIS B 575 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 543 HIS ** 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 = 0.3418 r_free = 0.3418 target = 0.137432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.102900 restraints weight = 27863.464| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.03 r_work: 0.2675 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2978 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= 0.177 Angle : 0.606 14.612 30658 Z= 0.313 Chirality : 0.044 0.180 3254 Planarity : 0.004 0.087 4016 Dihedral : 5.256 50.635 3148 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 2.65 % Allowed : 17.41 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.15), residues: 2796 helix: 0.07 (0.22), residues: 566 sheet: -0.29 (0.17), residues: 880 loop : -1.90 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 973 TYR 0.018 0.001 TYR E 514 PHE 0.013 0.001 PHE E 868 TRP 0.011 0.001 TRP B 321 HIS 0.003 0.001 HIS B 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (22650) covalent geometry : angle 0.60584 / 0.31 (30658) hydrogen bonds : bond 0.03780 / 2.47 ( 944) hydrogen bonds : angle 4.84662 / 3.39 ( 2692) Misc. bond : bond 0.00035 / 0.02 ( 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 297 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 0.887 Fit side-chains REVERT: A 22 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8271 (pp) REVERT: A 182 ASP cc_start: 0.8186 (t0) cc_final: 0.7854 (t0) REVERT: A 313 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7807 (tptt) REVERT: B 172 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 282 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8641 (tp-100) REVERT: B 342 SER cc_start: 0.8352 (m) cc_final: 0.8079 (m) REVERT: B 774 TYR cc_start: 0.8283 (p90) cc_final: 0.7973 (p90) REVERT: B 778 ASN cc_start: 0.8908 (p0) cc_final: 0.8611 (p0) REVERT: B 783 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7918 (ttt90) REVERT: D 22 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8347 (pp) REVERT: D 348 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8964 (mmmm) REVERT: D 421 MET cc_start: 0.6539 (tpt) cc_final: 0.5960 (tpt) REVERT: E 172 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8164 (pp) REVERT: E 279 GLN cc_start: 0.8562 (mm110) cc_final: 0.8154 (mm-40) REVERT: E 547 GLU cc_start: 0.8589 (tt0) cc_final: 0.8333 (tt0) REVERT: E 575 ASN cc_start: 0.8612 (t0) cc_final: 0.8391 (t0) REVERT: E 640 PHE cc_start: 0.7462 (m-10) cc_final: 0.7153 (m-10) REVERT: E 778 ASN cc_start: 0.8896 (p0) cc_final: 0.8666 (p0) REVERT: E 797 MET cc_start: 0.8296 (pmm) cc_final: 0.8020 (ttt) REVERT: E 930 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8570 (mm) outliers start: 62 outliers final: 47 residues processed: 283 average time/residue: 0.1471 time to fit residues: 68.0668 Evaluate side-chains 279 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 158 LEU 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 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 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 64 GLN 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 67 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 263 optimal weight: 0.0570 chunk 275 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 575 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.136179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.102115 restraints weight = 29983.911| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.24 r_work: 0.2621 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22654 Z= 0.236 Angle : 0.659 15.981 30658 Z= 0.339 Chirality : 0.045 0.178 3254 Planarity : 0.004 0.099 4016 Dihedral : 5.473 56.782 3148 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.49 % Rotamer: Outliers : 2.91 % Allowed : 17.88 % Favored : 79.21 % 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: -1.48 (0.15), residues: 2796 helix: 0.06 (0.22), residues: 566 sheet: -0.31 (0.17), residues: 878 loop : -1.93 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 973 TYR 0.020 0.002 TYR B1003 PHE 0.017 0.001 PHE B1017 TRP 0.013 0.001 TRP E 697 HIS 0.008 0.001 HIS B 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (22650) covalent geometry : angle 0.65909 / 0.34 (30658) hydrogen bonds : bond 0.04230 / 2.77 ( 944) hydrogen bonds : angle 4.93734 / 3.45 ( 2692) Misc. bond : bond 0.00025 / 0.01 ( 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 296 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.849 Fit side-chains REVERT: A 22 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8303 (pp) REVERT: A 182 ASP cc_start: 0.8230 (t0) cc_final: 0.7923 (t0) REVERT: B 172 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8177 (pp) REVERT: B 282 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8659 (tp-100) REVERT: B 342 SER cc_start: 0.8527 (m) cc_final: 0.8261 (m) REVERT: B 778 ASN cc_start: 0.8990 (p0) cc_final: 0.8674 (p0) REVERT: B 783 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7909 (ttt90) REVERT: D 22 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (pp) REVERT: D 164 MET cc_start: 0.8982 (tpp) cc_final: 0.8680 (mmt) REVERT: D 348 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8981 (mmmm) REVERT: E 172 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8115 (pp) REVERT: E 279 GLN cc_start: 0.8615 (mm110) cc_final: 0.8041 (mm-40) REVERT: E 283 LYS cc_start: 0.8763 (tttp) cc_final: 0.8462 (tttp) REVERT: E 547 GLU cc_start: 0.8666 (tt0) cc_final: 0.8409 (tt0) REVERT: E 640 PHE cc_start: 0.7563 (m-10) cc_final: 0.7337 (m-10) REVERT: E 778 ASN cc_start: 0.8971 (p0) cc_final: 0.8724 (p0) REVERT: E 797 MET cc_start: 0.8392 (pmm) cc_final: 0.8074 (ttt) REVERT: E 930 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8576 (mm) outliers start: 68 outliers final: 55 residues processed: 279 average time/residue: 0.1487 time to fit residues: 67.4679 Evaluate side-chains 287 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 158 LEU 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 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 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 124 VAL Chi-restraints excluded: chain D residue 188 LEU 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 322 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 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 251 LEU 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 757 VAL 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: 0.0970 chunk 239 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 264 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN B 575 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 156 GLN D 465 ASN E 388 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 = 0.3445 r_free = 0.3445 target = 0.139312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.108924 restraints weight = 41676.989| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.66 r_work: 0.2607 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22654 Z= 0.118 Angle : 0.563 12.511 30658 Z= 0.292 Chirality : 0.042 0.178 3254 Planarity : 0.004 0.065 4016 Dihedral : 4.869 47.537 3148 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.69 % Allowed : 18.48 % Favored : 78.83 % 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: -1.17 (0.15), residues: 2796 helix: 0.23 (0.22), residues: 578 sheet: -0.05 (0.17), residues: 850 loop : -1.72 (0.16), residues: 1368 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 0.012 0.001 PHE E 990 TRP 0.012 0.001 TRP B 321 HIS 0.005 0.001 HIS E 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (22650) covalent geometry : angle 0.56319 / 0.29 (30658) hydrogen bonds : bond 0.03214 / 2.09 ( 944) hydrogen bonds : angle 4.67468 / 3.27 ( 2692) Misc. bond : bond 0.00013 / 0.01 ( 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 319 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 0.888 Fit side-chains REVERT: A 22 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8409 (pp) REVERT: A 30 ASP cc_start: 0.9065 (t0) cc_final: 0.8848 (t0) REVERT: A 60 MET cc_start: 0.9001 (mmp) cc_final: 0.8680 (mmt) REVERT: A 182 ASP cc_start: 0.8199 (t0) cc_final: 0.7834 (t0) REVERT: B 172 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 436 MET cc_start: 0.8842 (mmt) cc_final: 0.8178 (mmt) REVERT: B 537 LEU cc_start: 0.8380 (mp) cc_final: 0.8137 (mp) REVERT: B 598 TYR cc_start: 0.8718 (t80) cc_final: 0.8261 (t80) REVERT: B 640 PHE cc_start: 0.7417 (m-10) cc_final: 0.7151 (m-10) REVERT: B 774 TYR cc_start: 0.8431 (p90) cc_final: 0.8122 (p90) REVERT: B 783 ARG cc_start: 0.8421 (ptm160) cc_final: 0.7921 (ttt90) REVERT: D 30 ASP cc_start: 0.9041 (t0) cc_final: 0.8816 (t0) REVERT: D 164 MET cc_start: 0.8991 (tpp) cc_final: 0.8756 (mmt) REVERT: D 348 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8893 (mmmm) REVERT: D 421 MET cc_start: 0.6580 (tpt) cc_final: 0.6080 (tpt) REVERT: E 172 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8102 (pp) REVERT: E 201 GLU cc_start: 0.8684 (tt0) cc_final: 0.8460 (tp30) REVERT: E 541 MET cc_start: 0.8773 (ptp) cc_final: 0.8344 (ptt) REVERT: E 547 GLU cc_start: 0.8742 (tt0) cc_final: 0.8508 (tt0) REVERT: E 598 TYR cc_start: 0.8757 (t80) cc_final: 0.8519 (t80) REVERT: E 640 PHE cc_start: 0.7624 (m-10) cc_final: 0.7284 (m-10) REVERT: E 778 ASN cc_start: 0.8908 (p0) cc_final: 0.8704 (p0) REVERT: E 797 MET cc_start: 0.8428 (pmm) cc_final: 0.8069 (ttt) REVERT: E 930 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8287 (mm) outliers start: 63 outliers final: 48 residues processed: 303 average time/residue: 0.1421 time to fit residues: 71.0170 Evaluate side-chains 294 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 158 LEU 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 281 VAL 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 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 124 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 322 VAL 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 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 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 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: 8.9990 chunk 20 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 GLN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.107260 restraints weight = 40528.192| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.85 r_work: 0.2601 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22654 Z= 0.135 Angle : 0.577 12.908 30658 Z= 0.298 Chirality : 0.043 0.178 3254 Planarity : 0.004 0.079 4016 Dihedral : 4.857 47.373 3148 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.61 % Allowed : 18.99 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2796 helix: 0.44 (0.22), residues: 566 sheet: 0.03 (0.17), residues: 850 loop : -1.68 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 973 TYR 0.016 0.001 TYR B 514 PHE 0.012 0.001 PHE B 779 TRP 0.012 0.001 TRP E 697 HIS 0.005 0.001 HIS E 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (22650) covalent geometry : angle 0.57708 / 0.30 (30658) hydrogen bonds : bond 0.03349 / 2.18 ( 944) hydrogen bonds : angle 4.64529 / 3.26 ( 2692) Misc. bond : bond 0.00008 / 0.00 ( 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 303 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 0.865 Fit side-chains REVERT: A 22 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8378 (pp) REVERT: A 60 MET cc_start: 0.8982 (mmp) cc_final: 0.8683 (mmt) REVERT: A 182 ASP cc_start: 0.8197 (t0) cc_final: 0.7858 (t0) REVERT: B 172 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8148 (pp) REVERT: B 436 MET cc_start: 0.8847 (mmt) cc_final: 0.8206 (mmt) REVERT: B 537 LEU cc_start: 0.8350 (mp) cc_final: 0.8108 (mp) REVERT: B 598 TYR cc_start: 0.8693 (t80) cc_final: 0.8272 (t80) REVERT: B 774 TYR cc_start: 0.8424 (p90) cc_final: 0.8111 (p90) REVERT: B 783 ARG cc_start: 0.8420 (ptm160) cc_final: 0.7891 (ttt90) REVERT: D 348 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8915 (mmmm) REVERT: D 385 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: D 421 MET cc_start: 0.6583 (tpt) cc_final: 0.6175 (tpt) REVERT: E 172 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8051 (pp) REVERT: E 201 GLU cc_start: 0.8680 (tt0) cc_final: 0.8447 (tp30) REVERT: E 541 MET cc_start: 0.8773 (ptp) cc_final: 0.8345 (ptt) REVERT: E 547 GLU cc_start: 0.8743 (tt0) cc_final: 0.8500 (tt0) REVERT: E 598 TYR cc_start: 0.8735 (t80) cc_final: 0.8502 (t80) REVERT: E 640 PHE cc_start: 0.7589 (m-10) cc_final: 0.7304 (m-10) REVERT: E 778 ASN cc_start: 0.8923 (p0) cc_final: 0.8710 (p0) REVERT: E 797 MET cc_start: 0.8481 (pmm) cc_final: 0.8098 (ttt) outliers start: 61 outliers final: 51 residues processed: 290 average time/residue: 0.1410 time to fit residues: 67.1451 Evaluate side-chains 294 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 158 LEU 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 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 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 B residue 962 LEU Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 385 TYR 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 161 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 471 THR 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 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: 3.9990 chunk 139 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 575 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105200 restraints weight = 34399.947| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.41 r_work: 0.2631 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22654 Z= 0.178 Angle : 0.615 14.242 30658 Z= 0.317 Chirality : 0.044 0.178 3254 Planarity : 0.004 0.086 4016 Dihedral : 5.043 50.871 3148 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.61 % Allowed : 19.12 % Favored : 78.27 % 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: -1.10 (0.15), residues: 2796 helix: 0.40 (0.22), residues: 568 sheet: -0.01 (0.17), residues: 854 loop : -1.71 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 973 TYR 0.018 0.001 TYR B 514 PHE 0.013 0.001 PHE B 779 TRP 0.013 0.001 TRP E 697 HIS 0.006 0.001 HIS E 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (22650) covalent geometry : angle 0.61521 / 0.32 (30658) hydrogen bonds : bond 0.03712 / 2.43 ( 944) hydrogen bonds : angle 4.73257 / 3.32 ( 2692) Misc. bond : bond 0.00009 / 0.00 ( 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 295 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 0.861 Fit side-chains REVERT: A 22 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 182 ASP cc_start: 0.8167 (t0) cc_final: 0.7834 (t0) REVERT: B 172 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8164 (pp) REVERT: B 342 SER cc_start: 0.8452 (m) cc_final: 0.8220 (m) REVERT: B 598 TYR cc_start: 0.8655 (t80) cc_final: 0.8262 (t80) REVERT: B 774 TYR cc_start: 0.8343 (p90) cc_final: 0.8035 (p90) REVERT: B 783 ARG cc_start: 0.8357 (ptm160) cc_final: 0.7963 (ttt90) REVERT: D 188 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (mm) REVERT: D 348 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8963 (mmmm) REVERT: E 172 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8012 (pp) REVERT: E 201 GLU cc_start: 0.8625 (tt0) cc_final: 0.8402 (tp30) REVERT: E 547 GLU cc_start: 0.8651 (tt0) cc_final: 0.8397 (tt0) REVERT: E 774 TYR cc_start: 0.8381 (p90) cc_final: 0.8084 (p90) REVERT: E 778 ASN cc_start: 0.8928 (p0) cc_final: 0.8703 (p0) REVERT: E 797 MET cc_start: 0.8417 (pmm) cc_final: 0.8093 (ttt) outliers start: 61 outliers final: 51 residues processed: 280 average time/residue: 0.1444 time to fit residues: 66.2720 Evaluate side-chains 287 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 158 LEU 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 248 SER Chi-restraints excluded: chain B residue 281 VAL 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 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 B residue 962 LEU Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 322 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 161 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 471 THR 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 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 106 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 638 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.136963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105109 restraints weight = 40850.548| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.84 r_work: 0.2571 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22654 Z= 0.198 Angle : 0.632 14.796 30658 Z= 0.325 Chirality : 0.044 0.177 3254 Planarity : 0.004 0.090 4016 Dihedral : 5.163 52.909 3148 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.78 % Allowed : 19.03 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 2796 helix: 0.36 (0.22), residues: 568 sheet: -0.04 (0.17), residues: 854 loop : -1.74 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 973 TYR 0.018 0.002 TYR B 514 PHE 0.014 0.001 PHE B1017 TRP 0.014 0.001 TRP E 697 HIS 0.006 0.001 HIS E 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (22650) covalent geometry : angle 0.63231 / 0.33 (30658) hydrogen bonds : bond 0.03885 / 2.54 ( 944) hydrogen bonds : angle 4.79512 / 3.36 ( 2692) Misc. bond : bond 0.00015 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5395.90 seconds wall clock time: 93 minutes 10.50 seconds (5590.50 seconds total)