Starting phenix.real_space_refine on Tue Sep 15 12:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sm3_10241/09_2026/6sm3_10241.map" } resolution = 3.3 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= 0.020 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 21772 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 13982 2.51 5 N 3700 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.02s 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: 22040 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: 7064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 7056 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 871} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 903, 7056 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 871} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 7210 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 79 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, '5PL:plan-2': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: D, E, F Time building chain proxies: 10.90, per 1000 atoms: 0.49 Number of scatterers: 22040 At special positions: 0 Unit cell: (161.57, 101.65, 134.82, 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 4276 8.00 N 3700 7.00 C 13982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 34 sheets defined 21.7% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.831A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 105 through 134 removed outlier: 3.604A pdb=" N TYR A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 3.527A pdb=" N ILE A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 4.282A 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 removed outlier: 3.622A pdb=" N LYS A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.675A pdb=" N VAL A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.521A pdb=" N LYS A 338 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 339' Processing helix chain 'A' and resid 380 through 395 removed outlier: 4.065A pdb=" N VAL A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.802A pdb=" N TYR A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.746A pdb=" N TYR A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.531A pdb=" N ASP B 140 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.695A 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 218 through 221 Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.203A pdb=" N ASN B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 280 through 288 removed outlier: 3.996A pdb=" N MET B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.693A pdb=" N TYR B 299 " --> pdb=" O TYR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.571A pdb=" N MET B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 567 through 571 removed outlier: 4.122A pdb=" N GLY B 571 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 741 Processing helix chain 'B' and resid 895 through 898 Processing helix chain 'B' and resid 959 through 963 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.831A pdb=" N THR D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 81 through 86 Processing helix chain 'D' and resid 105 through 134 removed outlier: 3.604A pdb=" N TYR D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 168 removed outlier: 3.527A pdb=" N ILE D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 168 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 218 removed outlier: 4.282A 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 removed outlier: 3.622A pdb=" N LYS D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.675A pdb=" N VAL D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.521A pdb=" N LYS D 338 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D 339 " --> pdb=" O PHE D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 339' Processing helix chain 'D' and resid 380 through 395 removed outlier: 4.065A pdb=" N VAL D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.802A pdb=" N TYR D 404 " --> pdb=" O THR D 400 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 477 through 481 removed outlier: 3.746A pdb=" N TYR D 480 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.531A pdb=" N ASP E 140 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.695A 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 218 through 221 Processing helix chain 'E' and resid 253 through 258 removed outlier: 4.203A pdb=" N ASN E 258 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 272 Processing helix chain 'E' and resid 280 through 288 removed outlier: 3.996A pdb=" N MET E 287 " --> pdb=" O LYS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 299 removed outlier: 3.693A pdb=" N TYR E 299 " --> pdb=" O TYR E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.571A pdb=" N MET E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 452 Processing helix chain 'E' and resid 567 through 571 removed outlier: 4.122A pdb=" N GLY E 571 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 741 Processing helix chain 'E' and resid 895 through 898 Processing helix chain 'E' and resid 959 through 963 Processing sheet with id=1, first strand: chain 'A' and resid 30 through 31 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 99 Processing sheet with id=4, first strand: chain 'A' and resid 289 through 290 removed outlier: 6.543A pdb=" N PHE A 289 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=6, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=7, first strand: chain 'A' and resid 342 through 346 removed outlier: 5.610A pdb=" N LYS A 344 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 353 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.540A pdb=" N SER B 202 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 223 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=10, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.911A pdb=" N TYR B 628 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY B 660 " --> pdb=" O TRP B 626 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N TRP B 626 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 541 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY B 507 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 457 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG B 396 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 465 " --> pdb=" O ASN B 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 352 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B1012 " --> pdb=" O TYR B 975 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 974 " --> pdb=" O TYR B 956 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 978 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.901A pdb=" N ALA B 718 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 758 " --> pdb=" O ASP B 721 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 775 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 864 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 951 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 884 " --> pdb=" O LEU B 949 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU B 949 " --> pdb=" O ALA B 884 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE B 886 " --> pdb=" O LEU B 947 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU B 947 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 433 through 434 Processing sheet with id=13, first strand: chain 'B' and resid 731 through 735 Processing sheet with id=14, first strand: chain 'B' and resid 751 through 753 removed outlier: 6.048A pdb=" N SER B 751 " --> pdb=" O THR B 787 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 795 through 797 removed outlier: 3.915A pdb=" N PHE B 813 " --> pdb=" O ILE B 856 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 818 through 821 removed outlier: 6.917A pdb=" N LEU B 829 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL B 843 " --> pdb=" O VAL B 832 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 941 through 943 removed outlier: 7.940A pdb=" N GLY B 999 " --> pdb=" O TRP B 890 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE B 892 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=19, first strand: chain 'D' and resid 71 through 73 Processing sheet with id=20, first strand: chain 'D' and resid 97 through 99 Processing sheet with id=21, first strand: chain 'D' and resid 289 through 290 removed outlier: 6.543A pdb=" N PHE D 289 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=23, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=24, first strand: chain 'D' and resid 342 through 346 removed outlier: 5.610A pdb=" N LYS D 344 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU D 353 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.540A pdb=" N SER E 202 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 223 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 185 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 149 through 152 Processing sheet with id=27, first strand: chain 'E' and resid 726 through 728 removed outlier: 3.911A pdb=" N TYR E 628 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY E 660 " --> pdb=" O TRP E 626 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N TRP E 626 " --> pdb=" O GLY E 660 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET E 541 " --> pdb=" O ALA E 525 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY E 507 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER E 457 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG E 396 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 465 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY E 352 " --> pdb=" O SER E 370 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E1012 " --> pdb=" O TYR E 975 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 974 " --> pdb=" O TYR E 956 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 978 " --> pdb=" O LEU E 952 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 726 through 728 removed outlier: 3.901A pdb=" N ALA E 718 " --> pdb=" O ALA E 709 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP E 758 " --> pdb=" O ASP E 721 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 775 " --> pdb=" O GLY E 763 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 864 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 951 " --> pdb=" O ASP E 882 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA E 884 " --> pdb=" O LEU E 949 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU E 949 " --> pdb=" O ALA E 884 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE E 886 " --> pdb=" O LEU E 947 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU E 947 " --> pdb=" O ILE E 886 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 433 through 434 Processing sheet with id=30, first strand: chain 'E' and resid 731 through 735 Processing sheet with id=31, first strand: chain 'E' and resid 751 through 753 removed outlier: 6.048A pdb=" N SER E 751 " --> pdb=" O THR E 787 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'E' and resid 795 through 797 removed outlier: 3.915A pdb=" N PHE E 813 " --> pdb=" O ILE E 856 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'E' and resid 818 through 821 removed outlier: 6.917A pdb=" N LEU E 829 " --> pdb=" O ALA E 819 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 843 " --> pdb=" O VAL E 832 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 941 through 943 removed outlier: 7.940A pdb=" N GLY E 999 " --> pdb=" O TRP E 890 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE E 892 " --> pdb=" O GLY E 999 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2638 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: 4.64 Time building geometry restraints manager: 2.09 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: 3726 1.30 - 1.42: 6106 1.42 - 1.55: 12510 1.55 - 1.68: 38 1.68 - 1.80: 158 Bond restraints: 22538 Sorted by residual: bond pdb=" CBU 5PL A 601 " pdb=" OCK 5PL A 601 " ideal model delta sigma weight residual 1.328 1.412 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CBU 5PL D 601 " pdb=" OCK 5PL D 601 " ideal model delta sigma weight residual 1.328 1.412 -0.084 2.00e-02 2.50e+03 1.78e+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 1.52e+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 1.52e+01 bond pdb=" CA TYR B 405 " pdb=" CB TYR B 405 " ideal model delta sigma weight residual 1.526 1.473 0.053 1.76e-02 3.23e+03 9.07e+00 ... (remaining 22533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 29532 2.32 - 4.64: 848 4.64 - 6.96: 84 6.96 - 9.28: 26 9.28 - 11.60: 24 Bond angle restraints: 30514 Sorted by residual: angle pdb=" N GLU D 422 " pdb=" CA GLU D 422 " pdb=" C GLU D 422 " ideal model delta sigma weight residual 114.04 107.41 6.63 1.24e+00 6.50e-01 2.86e+01 angle pdb=" N GLU A 422 " pdb=" CA GLU A 422 " pdb=" C GLU A 422 " ideal model delta sigma weight residual 114.04 107.41 6.63 1.24e+00 6.50e-01 2.86e+01 angle pdb=" C PHE E 712 " pdb=" N ASN E 713 " pdb=" CA ASN E 713 " ideal model delta sigma weight residual 121.54 131.57 -10.03 1.91e+00 2.74e-01 2.76e+01 angle pdb=" C PHE B 712 " pdb=" N ASN B 713 " pdb=" CA ASN B 713 " ideal model delta sigma weight residual 121.54 131.57 -10.03 1.91e+00 2.74e-01 2.76e+01 angle pdb=" C LYS A 347 " pdb=" N LYS A 348 " pdb=" CA LYS A 348 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 ... (remaining 30509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11972 17.79 - 35.58: 1174 35.58 - 53.37: 190 53.37 - 71.16: 22 71.16 - 88.95: 8 Dihedral angle restraints: 13366 sinusoidal: 5266 harmonic: 8100 Sorted by residual: dihedral pdb=" CA ASN E 713 " pdb=" C ASN E 713 " pdb=" N ASN E 714 " pdb=" CA ASN E 714 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ASN B 713 " pdb=" C ASN B 713 " pdb=" N ASN B 714 " pdb=" CA ASN B 714 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ALA B 292 " pdb=" C ALA B 292 " pdb=" N GLU B 293 " pdb=" CA GLU B 293 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 13363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2456 0.062 - 0.125: 664 0.125 - 0.187: 102 0.187 - 0.250: 14 0.250 - 0.312: 8 Chirality restraints: 3244 Sorted by residual: chirality pdb=" CA PHE B 790 " pdb=" N PHE B 790 " pdb=" C PHE B 790 " pdb=" CB PHE B 790 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PHE E 790 " pdb=" N PHE E 790 " pdb=" C PHE E 790 " pdb=" CB PHE E 790 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CG LEU B 506 " pdb=" CB LEU B 506 " pdb=" CD1 LEU B 506 " pdb=" CD2 LEU B 506 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3241 not shown) Planarity restraints: 3996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 82 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO D 83 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 83 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 83 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 82 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 83 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 254 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO E 255 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 255 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 255 " -0.039 5.00e-02 4.00e+02 ... (remaining 3993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2728 2.74 - 3.28: 18075 3.28 - 3.82: 34692 3.82 - 4.36: 42002 4.36 - 4.90: 78776 Nonbonded interactions: 176273 Sorted by model distance: nonbonded pdb=" OG SER B 377 " pdb=" OH TYR E 347 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR B 347 " pdb=" OG SER E 377 " model vdw 2.206 3.040 nonbonded pdb=" O SER A 437 " pdb=" OG SER A 437 " model vdw 2.294 3.040 nonbonded pdb=" O SER D 437 " pdb=" OG SER D 437 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR E 405 " pdb=" OD1 ASP E 895 " model vdw 2.298 3.040 ... (remaining 176268 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.490 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 0.084 22542 Z= 0.398 Angle : 0.961 11.601 30514 Z= 0.519 Chirality : 0.059 0.312 3244 Planarity : 0.006 0.071 3996 Dihedral : 13.969 88.945 8222 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.26 % Allowed : 9.12 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.64 (0.13), residues: 2786 helix: -2.81 (0.15), residues: 580 sheet: -1.45 (0.17), residues: 836 loop : -2.86 (0.13), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 617 TYR 0.019 0.003 TYR E 587 PHE 0.034 0.003 PHE E1017 TRP 0.019 0.002 TRP B 874 HIS 0.009 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00932 / 0.39 (22538) covalent geometry : angle 0.96146 / 0.52 (30514) hydrogen bonds : bond 0.16036 / 10.48 ( 940) hydrogen bonds : angle 6.94015 / 4.97 ( 2638) Misc. bond : bond 0.05183 / 2.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 331 time to evaluate : 0.942 Fit side-chains REVERT: A 22 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8038 (pp) REVERT: A 164 MET cc_start: 0.8088 (mmm) cc_final: 0.7718 (mmm) REVERT: A 181 LYS cc_start: 0.8903 (tttt) cc_final: 0.8606 (tttm) REVERT: A 251 LYS cc_start: 0.8392 (mttt) cc_final: 0.7902 (mtmm) REVERT: A 255 ASP cc_start: 0.7678 (m-30) cc_final: 0.7298 (m-30) REVERT: A 410 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8724 (ttpt) REVERT: A 494 GLN cc_start: 0.8690 (tt0) cc_final: 0.8488 (tt0) REVERT: B 271 LYS cc_start: 0.8346 (mttp) cc_final: 0.8042 (mtmt) REVERT: B 353 TYR cc_start: 0.8260 (p90) cc_final: 0.6813 (p90) REVERT: B 564 LYS cc_start: 0.8572 (mptt) cc_final: 0.8343 (mmmt) REVERT: B 604 MET cc_start: 0.8225 (ttt) cc_final: 0.8025 (ttp) REVERT: B 822 ASP cc_start: 0.7992 (t0) cc_final: 0.7665 (t0) REVERT: D 22 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8091 (pp) REVERT: D 100 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6827 (mt-10) REVERT: D 137 LYS cc_start: 0.8499 (mmtt) cc_final: 0.7975 (mtpt) REVERT: D 223 ASN cc_start: 0.8907 (m-40) cc_final: 0.8641 (m-40) REVERT: D 251 LYS cc_start: 0.8149 (mttt) cc_final: 0.7541 (mttm) REVERT: D 255 ASP cc_start: 0.7768 (m-30) cc_final: 0.7452 (m-30) REVERT: D 410 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8657 (ttpt) REVERT: E 308 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8286 (ttpp) REVERT: E 353 TYR cc_start: 0.8003 (p90) cc_final: 0.7387 (p90) REVERT: E 404 LYS cc_start: 0.8361 (mppt) cc_final: 0.8062 (mptt) REVERT: E 564 LYS cc_start: 0.8099 (mptt) cc_final: 0.7804 (mmtt) REVERT: E 890 TRP cc_start: 0.8760 (m100) cc_final: 0.8480 (m100) outliers start: 6 outliers final: 3 residues processed: 335 average time/residue: 0.1525 time to fit residues: 80.0410 Evaluate side-chains 265 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 260 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain E residue 659 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 133 ASN A 449 ASN B 137 ASN B 196 ASN B 252 ASN B 278 ASN B 279 GLN B 298 ASN B 316 ASN B 374 ASN B 427 ASN B 748 ASN B 847 GLN D 118 GLN D 133 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN E 196 ASN E 252 ASN E 278 ASN E 279 GLN E 298 ASN E 316 ASN E 374 ASN E 427 ASN E 748 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.118086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.096407 restraints weight = 35350.092| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.12 r_work: 0.2726 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 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: 0.8820 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22542 Z= 0.106 Angle : 0.552 8.276 30514 Z= 0.294 Chirality : 0.043 0.173 3244 Planarity : 0.004 0.046 3996 Dihedral : 5.973 82.900 3139 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.85 % Allowed : 10.46 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2786 helix: -0.77 (0.21), residues: 558 sheet: -0.80 (0.18), residues: 812 loop : -2.24 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 489 TYR 0.013 0.001 TYR B 514 PHE 0.011 0.001 PHE B 791 TRP 0.016 0.001 TRP D 161 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (22538) covalent geometry : angle 0.55197 / 0.29 (30514) hydrogen bonds : bond 0.03337 / 2.19 ( 940) hydrogen bonds : angle 4.96582 / 3.57 ( 2638) Misc. bond : bond 0.00011 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 0.846 Fit side-chains REVERT: A 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8504 (pp) REVERT: A 23 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8223 (p0) REVERT: A 79 ASN cc_start: 0.9274 (t0) cc_final: 0.8638 (t0) REVERT: A 251 LYS cc_start: 0.8260 (mttt) cc_final: 0.7732 (mtmm) REVERT: A 255 ASP cc_start: 0.8085 (m-30) cc_final: 0.7752 (m-30) REVERT: A 273 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 410 LYS cc_start: 0.8994 (ttpp) cc_final: 0.8668 (ttpt) REVERT: B 267 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8175 (t70) REVERT: B 271 LYS cc_start: 0.8366 (mttp) cc_final: 0.7975 (mtmt) REVERT: B 353 TYR cc_start: 0.8802 (p90) cc_final: 0.7472 (p90) REVERT: B 375 PHE cc_start: 0.8842 (t80) cc_final: 0.8567 (t80) REVERT: B 441 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8215 (mtp180) REVERT: B 549 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7869 (tt0) REVERT: B 551 ASP cc_start: 0.8208 (t70) cc_final: 0.7842 (t70) REVERT: B 564 LYS cc_start: 0.8789 (mptt) cc_final: 0.8248 (mtmt) REVERT: D 22 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8668 (pp) REVERT: D 71 TYR cc_start: 0.9177 (m-80) cc_final: 0.8878 (m-80) REVERT: D 251 LYS cc_start: 0.8124 (mttt) cc_final: 0.7673 (mttm) REVERT: D 255 ASP cc_start: 0.8171 (m-30) cc_final: 0.7886 (m-30) REVERT: D 335 ASP cc_start: 0.8149 (t0) cc_final: 0.7810 (t70) REVERT: D 410 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8725 (ttpt) REVERT: E 152 MET cc_start: 0.8986 (mtp) cc_final: 0.8682 (tpp) REVERT: E 165 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 289 LEU cc_start: 0.8818 (pt) cc_final: 0.8491 (pp) REVERT: E 308 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8191 (ttpp) REVERT: E 353 TYR cc_start: 0.8613 (p90) cc_final: 0.7642 (p90) REVERT: E 404 LYS cc_start: 0.8609 (mppt) cc_final: 0.8317 (mptt) REVERT: E 429 ASP cc_start: 0.8360 (m-30) cc_final: 0.8098 (m-30) REVERT: E 549 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: E 564 LYS cc_start: 0.8616 (mptt) cc_final: 0.8173 (mmmt) REVERT: E 621 ASN cc_start: 0.8933 (m-40) cc_final: 0.8605 (p0) REVERT: E 715 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7367 (mtp-110) outliers start: 43 outliers final: 25 residues processed: 354 average time/residue: 0.1611 time to fit residues: 89.6397 Evaluate side-chains 317 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 287 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 847 GLN Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 252 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 133 ASN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 221 ASN B 252 ASN B 427 ASN B 778 ASN B 847 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 221 ASN E 778 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.112205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.091954 restraints weight = 28363.839| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.59 r_work: 0.2687 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22542 Z= 0.224 Angle : 0.639 10.964 30514 Z= 0.337 Chirality : 0.046 0.218 3244 Planarity : 0.004 0.047 3996 Dihedral : 6.218 81.399 3139 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.97 % Allowed : 12.69 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.15), residues: 2786 helix: -0.24 (0.22), residues: 560 sheet: -0.74 (0.18), residues: 824 loop : -2.12 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 490 TYR 0.025 0.002 TYR E1003 PHE 0.019 0.002 PHE B 990 TRP 0.011 0.001 TRP D 161 HIS 0.004 0.001 HIS E 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (22538) covalent geometry : angle 0.63884 / 0.34 (30514) hydrogen bonds : bond 0.04398 / 2.87 ( 940) hydrogen bonds : angle 4.93855 / 3.56 ( 2638) Misc. bond : bond 0.00013 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.881 Fit side-chains REVERT: A 22 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8288 (pp) REVERT: A 251 LYS cc_start: 0.8318 (mttt) cc_final: 0.7991 (mttm) REVERT: A 255 ASP cc_start: 0.8147 (m-30) cc_final: 0.7944 (m-30) REVERT: A 410 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8761 (ttpt) REVERT: B 271 LYS cc_start: 0.8360 (mttp) cc_final: 0.8080 (mtmt) REVERT: B 549 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7856 (tt0) REVERT: B 551 ASP cc_start: 0.7856 (t70) cc_final: 0.7476 (t70) REVERT: B 564 LYS cc_start: 0.8793 (mptt) cc_final: 0.8361 (mmmt) REVERT: B 568 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8794 (mp) REVERT: B 847 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8645 (tm-30) REVERT: D 22 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8390 (pp) REVERT: D 192 ASN cc_start: 0.8420 (t0) cc_final: 0.8176 (p0) REVERT: D 251 LYS cc_start: 0.8204 (mttt) cc_final: 0.7893 (mttm) REVERT: D 410 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8672 (ttpt) REVERT: D 494 GLN cc_start: 0.8762 (tt0) cc_final: 0.8535 (tt0) REVERT: E 132 GLU cc_start: 0.6245 (pt0) cc_final: 0.5858 (pt0) REVERT: E 308 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8376 (ttpp) REVERT: E 353 TYR cc_start: 0.8878 (p90) cc_final: 0.7558 (p90) REVERT: E 429 ASP cc_start: 0.8243 (m-30) cc_final: 0.7942 (m-30) REVERT: E 564 LYS cc_start: 0.8694 (mptt) cc_final: 0.8275 (mmmt) REVERT: E 568 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8802 (mp) REVERT: E 752 MET cc_start: 0.9271 (ttp) cc_final: 0.8995 (ttm) REVERT: E 930 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8131 (mm) outliers start: 69 outliers final: 50 residues processed: 334 average time/residue: 0.1527 time to fit residues: 81.4793 Evaluate side-chains 337 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 847 GLN Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 891 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 523 ASN B 754 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN E 754 ASN E 778 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.110231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.088762 restraints weight = 37752.604| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.18 r_work: 0.2591 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 22542 Z= 0.301 Angle : 0.691 11.692 30514 Z= 0.364 Chirality : 0.048 0.197 3244 Planarity : 0.004 0.052 3996 Dihedral : 6.459 81.528 3139 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.49 % Allowed : 14.37 % Favored : 82.14 % 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: -1.90 (0.15), residues: 2786 helix: -0.20 (0.22), residues: 560 sheet: -0.67 (0.18), residues: 792 loop : -2.09 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 490 TYR 0.027 0.002 TYR B1003 PHE 0.019 0.002 PHE E1017 TRP 0.009 0.001 TRP E 697 HIS 0.005 0.001 HIS E 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.30 (22538) covalent geometry : angle 0.69075 / 0.36 (30514) hydrogen bonds : bond 0.04745 / 3.09 ( 940) hydrogen bonds : angle 5.03404 / 3.64 ( 2638) Misc. bond : bond 0.00024 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 278 time to evaluate : 0.822 Fit side-chains REVERT: A 22 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8376 (pp) REVERT: A 251 LYS cc_start: 0.8389 (mttt) cc_final: 0.7844 (mtpt) REVERT: A 410 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8767 (ttpt) REVERT: B 215 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 271 LYS cc_start: 0.8403 (mttp) cc_final: 0.8053 (mtmt) REVERT: B 353 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.7644 (p90) REVERT: B 543 HIS cc_start: 0.9110 (OUTLIER) cc_final: 0.8529 (t-90) REVERT: B 549 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8113 (tt0) REVERT: B 551 ASP cc_start: 0.8074 (t70) cc_final: 0.7778 (t70) REVERT: B 564 LYS cc_start: 0.8821 (mptt) cc_final: 0.8228 (mtmt) REVERT: B 568 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8784 (mp) REVERT: D 22 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8425 (pp) REVERT: D 212 ARG cc_start: 0.8533 (mmp-170) cc_final: 0.8320 (mmp-170) REVERT: D 251 LYS cc_start: 0.8355 (mttt) cc_final: 0.7893 (mtpt) REVERT: D 410 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8726 (ttpt) REVERT: D 494 GLN cc_start: 0.8830 (tt0) cc_final: 0.8604 (tt0) REVERT: E 132 GLU cc_start: 0.6492 (pt0) cc_final: 0.6150 (pt0) REVERT: E 308 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8456 (ttpp) REVERT: E 353 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.7645 (p90) REVERT: E 376 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: E 429 ASP cc_start: 0.8418 (m-30) cc_final: 0.8141 (m-30) REVERT: E 543 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8505 (t-90) REVERT: E 564 LYS cc_start: 0.8822 (mptt) cc_final: 0.8391 (mmmt) REVERT: E 568 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8783 (mp) REVERT: E 752 MET cc_start: 0.9342 (ttp) cc_final: 0.9083 (ttm) outliers start: 81 outliers final: 62 residues processed: 327 average time/residue: 0.1539 time to fit residues: 80.4014 Evaluate side-chains 343 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 271 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 891 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 205 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN D 133 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.091887 restraints weight = 43037.599| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.52 r_work: 0.2610 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22542 Z= 0.154 Angle : 0.572 11.695 30514 Z= 0.302 Chirality : 0.044 0.175 3244 Planarity : 0.003 0.044 3996 Dihedral : 6.026 83.328 3139 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.23 % Allowed : 15.45 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.15), residues: 2786 helix: 0.14 (0.23), residues: 562 sheet: -0.54 (0.18), residues: 808 loop : -1.93 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 490 TYR 0.015 0.001 TYR B1003 PHE 0.012 0.001 PHE B 990 TRP 0.014 0.001 TRP D 161 HIS 0.004 0.001 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (22538) covalent geometry : angle 0.57197 / 0.30 (30514) hydrogen bonds : bond 0.03622 / 2.36 ( 940) hydrogen bonds : angle 4.75851 / 3.43 ( 2638) Misc. bond : bond 0.00014 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 0.868 Fit side-chains REVERT: A 22 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8322 (pp) REVERT: A 162 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8909 (tpp-160) REVERT: A 251 LYS cc_start: 0.8247 (mttt) cc_final: 0.7973 (mttm) REVERT: A 410 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8769 (ttpt) REVERT: B 271 LYS cc_start: 0.8327 (mttp) cc_final: 0.8006 (mtmt) REVERT: B 353 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.7442 (p90) REVERT: B 376 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8124 (tp30) REVERT: B 543 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8369 (t-90) REVERT: B 551 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7319 (t70) REVERT: B 564 LYS cc_start: 0.8736 (mptt) cc_final: 0.8341 (mmmt) REVERT: B 568 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 715 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7247 (mtp-110) REVERT: D 22 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8305 (pp) REVERT: D 162 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8988 (tpp-160) REVERT: D 212 ARG cc_start: 0.8410 (mmp-170) cc_final: 0.8181 (mmp-170) REVERT: D 251 LYS cc_start: 0.8310 (mttt) cc_final: 0.7786 (mtpt) REVERT: D 410 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8698 (ttpt) REVERT: E 149 MET cc_start: 0.9037 (ttp) cc_final: 0.8757 (ttt) REVERT: E 203 MET cc_start: 0.8959 (ttm) cc_final: 0.8749 (ttm) REVERT: E 308 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8481 (ttpp) REVERT: E 353 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7485 (p90) REVERT: E 376 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: E 429 ASP cc_start: 0.8304 (m-30) cc_final: 0.8042 (m-30) REVERT: E 543 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8344 (t-90) REVERT: E 564 LYS cc_start: 0.8762 (mptt) cc_final: 0.8342 (mmmt) REVERT: E 752 MET cc_start: 0.9164 (ttp) cc_final: 0.8821 (ttm) outliers start: 75 outliers final: 53 residues processed: 337 average time/residue: 0.1581 time to fit residues: 84.6847 Evaluate side-chains 347 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 282 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 778 ASN D 40 GLN D 133 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.111817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.090237 restraints weight = 38642.809| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.24 r_work: 0.2616 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22542 Z= 0.225 Angle : 0.624 11.937 30514 Z= 0.330 Chirality : 0.046 0.180 3244 Planarity : 0.004 0.051 3996 Dihedral : 6.154 82.327 3139 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.57 % Allowed : 15.28 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 2786 helix: 0.24 (0.23), residues: 550 sheet: -0.55 (0.18), residues: 818 loop : -1.90 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 490 TYR 0.020 0.002 TYR E1003 PHE 0.014 0.002 PHE B 990 TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 (22538) covalent geometry : angle 0.62368 / 0.33 (30514) hydrogen bonds : bond 0.04134 / 2.69 ( 940) hydrogen bonds : angle 4.82768 / 3.48 ( 2638) Misc. bond : bond 0.00019 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 0.853 Fit side-chains REVERT: A 22 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8445 (pp) REVERT: A 251 LYS cc_start: 0.8262 (mttt) cc_final: 0.8056 (mttm) REVERT: A 410 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8791 (ttpt) REVERT: B 152 MET cc_start: 0.9203 (tpp) cc_final: 0.9000 (tpp) REVERT: B 271 LYS cc_start: 0.8379 (mttp) cc_final: 0.8034 (mtmt) REVERT: B 353 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.7616 (p90) REVERT: B 543 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8468 (t-90) REVERT: B 551 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7628 (t70) REVERT: B 564 LYS cc_start: 0.8796 (mptt) cc_final: 0.8363 (mmmt) REVERT: B 568 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8771 (mp) REVERT: B 715 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.7243 (mtp-110) REVERT: D 22 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8450 (pp) REVERT: D 212 ARG cc_start: 0.8474 (mmp-170) cc_final: 0.8245 (mmp-170) REVERT: D 251 LYS cc_start: 0.8333 (mttt) cc_final: 0.7815 (mtpt) REVERT: D 410 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8746 (ttpt) REVERT: E 165 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8309 (mt-10) REVERT: E 203 MET cc_start: 0.9057 (ttm) cc_final: 0.8839 (ttm) REVERT: E 308 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8445 (ttpp) REVERT: E 353 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.7589 (p90) REVERT: E 376 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: E 429 ASP cc_start: 0.8456 (m-30) cc_final: 0.8188 (m-30) REVERT: E 543 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8451 (t-90) REVERT: E 564 LYS cc_start: 0.8790 (mptt) cc_final: 0.8356 (mmmt) REVERT: E 568 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8776 (mp) REVERT: E 752 MET cc_start: 0.9270 (ttp) cc_final: 0.8940 (ttm) outliers start: 83 outliers final: 63 residues processed: 327 average time/residue: 0.1549 time to fit residues: 80.9076 Evaluate side-chains 351 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 87 optimal weight: 4.9990 chunk 267 optimal weight: 0.0370 chunk 48 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN E 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.092352 restraints weight = 38515.860| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.31 r_work: 0.2654 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22542 Z= 0.145 Angle : 0.560 12.050 30514 Z= 0.296 Chirality : 0.044 0.167 3244 Planarity : 0.003 0.043 3996 Dihedral : 5.907 83.283 3139 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.92 % Allowed : 15.28 % Favored : 80.81 % 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: -1.39 (0.15), residues: 2786 helix: 0.44 (0.23), residues: 550 sheet: -0.42 (0.18), residues: 806 loop : -1.81 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 490 TYR 0.014 0.001 TYR E 215 PHE 0.011 0.001 PHE B 990 TRP 0.013 0.001 TRP D 161 HIS 0.004 0.001 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22538) covalent geometry : angle 0.55972 / 0.30 (30514) hydrogen bonds : bond 0.03460 / 2.25 ( 940) hydrogen bonds : angle 4.67090 / 3.36 ( 2638) Misc. bond : bond 0.00014 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 296 time to evaluate : 0.945 Fit side-chains REVERT: A 22 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8437 (pp) REVERT: A 162 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8848 (tpp-160) REVERT: A 410 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8772 (ttpt) REVERT: B 152 MET cc_start: 0.9223 (tpp) cc_final: 0.9022 (tpp) REVERT: B 271 LYS cc_start: 0.8350 (mttp) cc_final: 0.8016 (mtmt) REVERT: B 353 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.7553 (p90) REVERT: B 543 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8438 (t-90) REVERT: B 551 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7669 (t70) REVERT: B 564 LYS cc_start: 0.8817 (mptt) cc_final: 0.8207 (mtmt) REVERT: B 715 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.6996 (mtp-110) REVERT: D 22 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8413 (pp) REVERT: D 162 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8898 (tpp-160) REVERT: D 212 ARG cc_start: 0.8408 (mmp-170) cc_final: 0.8173 (mmp-170) REVERT: D 251 LYS cc_start: 0.8272 (mttt) cc_final: 0.7806 (mtpt) REVERT: D 410 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8718 (ttpt) REVERT: E 165 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8397 (mt-10) REVERT: E 203 MET cc_start: 0.9006 (ttm) cc_final: 0.8793 (ttm) REVERT: E 308 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8520 (ttpp) REVERT: E 353 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.7602 (p90) REVERT: E 376 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: E 543 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8414 (t-90) REVERT: E 564 LYS cc_start: 0.8789 (mptt) cc_final: 0.8350 (mmmt) REVERT: E 568 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8750 (mp) REVERT: E 752 MET cc_start: 0.9247 (ttp) cc_final: 0.9024 (ttm) outliers start: 91 outliers final: 69 residues processed: 347 average time/residue: 0.1533 time to fit residues: 84.8814 Evaluate side-chains 366 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 286 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 911 ASP Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 939 HIS Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 214 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 778 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN E 778 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.115463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.093296 restraints weight = 35200.473| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.13 r_work: 0.2677 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22542 Z= 0.127 Angle : 0.543 11.738 30514 Z= 0.287 Chirality : 0.043 0.164 3244 Planarity : 0.003 0.043 3996 Dihedral : 5.723 83.658 3139 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.49 % Allowed : 15.92 % Favored : 80.59 % 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: -1.32 (0.15), residues: 2786 helix: 0.48 (0.23), residues: 562 sheet: -0.39 (0.18), residues: 814 loop : -1.76 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 490 TYR 0.014 0.001 TYR E 215 PHE 0.011 0.001 PHE E 990 TRP 0.013 0.001 TRP D 161 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (22538) covalent geometry : angle 0.54255 / 0.29 (30514) hydrogen bonds : bond 0.03227 / 2.10 ( 940) hydrogen bonds : angle 4.55435 / 3.28 ( 2638) Misc. bond : bond 0.00013 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 295 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8458 (pp) REVERT: A 410 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8778 (ttpt) REVERT: B 152 MET cc_start: 0.9231 (tpp) cc_final: 0.9024 (tpp) REVERT: B 271 LYS cc_start: 0.8356 (mttp) cc_final: 0.8029 (mtmt) REVERT: B 353 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.7490 (p90) REVERT: B 389 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8955 (pt) REVERT: B 551 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7583 (t70) REVERT: B 564 LYS cc_start: 0.8778 (mptt) cc_final: 0.8142 (mtmt) REVERT: B 568 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8756 (mp) REVERT: D 22 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8459 (pp) REVERT: D 162 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8892 (tpp-160) REVERT: D 212 ARG cc_start: 0.8374 (mmp-170) cc_final: 0.8138 (mmp-170) REVERT: D 251 LYS cc_start: 0.8223 (mttt) cc_final: 0.7442 (mtpt) REVERT: D 255 ASP cc_start: 0.8118 (m-30) cc_final: 0.7659 (m-30) REVERT: D 410 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8670 (ttpt) REVERT: E 165 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8348 (mt-10) REVERT: E 203 MET cc_start: 0.9033 (ttm) cc_final: 0.8805 (ttm) REVERT: E 308 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8501 (ttpp) REVERT: E 353 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7476 (p90) REVERT: E 376 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: E 543 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8443 (t-90) REVERT: E 564 LYS cc_start: 0.8776 (mptt) cc_final: 0.8346 (mmmt) REVERT: E 568 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8752 (mp) REVERT: E 886 ILE cc_start: 0.8868 (mt) cc_final: 0.8654 (mt) outliers start: 81 outliers final: 57 residues processed: 340 average time/residue: 0.1506 time to fit residues: 82.2950 Evaluate side-chains 357 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 289 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 911 ASP Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 212 optimal weight: 7.9990 chunk 7 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.093437 restraints weight = 36778.328| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.27 r_work: 0.2679 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22542 Z= 0.132 Angle : 0.547 12.092 30514 Z= 0.289 Chirality : 0.043 0.163 3244 Planarity : 0.003 0.043 3996 Dihedral : 5.691 83.630 3139 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.40 % Allowed : 16.14 % Favored : 80.46 % 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: -1.24 (0.15), residues: 2786 helix: 0.54 (0.23), residues: 562 sheet: -0.35 (0.18), residues: 814 loop : -1.71 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 490 TYR 0.015 0.001 TYR E 215 PHE 0.012 0.001 PHE B 640 TRP 0.013 0.001 TRP A 161 HIS 0.006 0.001 HIS E 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (22538) covalent geometry : angle 0.54678 / 0.29 (30514) hydrogen bonds : bond 0.03261 / 2.12 ( 940) hydrogen bonds : angle 4.53776 / 3.26 ( 2638) Misc. bond : bond 0.00015 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 291 time to evaluate : 0.894 Fit side-chains REVERT: A 22 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8443 (pp) REVERT: A 162 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8848 (tpp-160) REVERT: A 255 ASP cc_start: 0.8133 (m-30) cc_final: 0.7834 (m-30) REVERT: A 410 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8786 (ttpt) REVERT: B 152 MET cc_start: 0.9222 (tpp) cc_final: 0.8998 (tpp) REVERT: B 287 MET cc_start: 0.7380 (mmt) cc_final: 0.6936 (mmt) REVERT: B 353 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.7527 (p90) REVERT: B 389 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8953 (pt) REVERT: B 543 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8412 (t-90) REVERT: B 551 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7568 (t70) REVERT: B 564 LYS cc_start: 0.8827 (mptt) cc_final: 0.8212 (mtmt) REVERT: B 568 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8781 (mp) REVERT: D 22 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8438 (pp) REVERT: D 162 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8932 (tpp-160) REVERT: D 195 TYR cc_start: 0.8102 (t80) cc_final: 0.7694 (t80) REVERT: D 212 ARG cc_start: 0.8384 (mmp-170) cc_final: 0.8149 (mmp-170) REVERT: D 410 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8696 (ttpt) REVERT: E 165 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8316 (mt-10) REVERT: E 203 MET cc_start: 0.9040 (ttm) cc_final: 0.8804 (ttm) REVERT: E 308 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8524 (ttpp) REVERT: E 353 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7475 (p90) REVERT: E 376 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (tp30) REVERT: E 543 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8465 (t-90) REVERT: E 564 LYS cc_start: 0.8803 (mptt) cc_final: 0.8360 (mmmt) REVERT: E 568 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8761 (mp) outliers start: 79 outliers final: 63 residues processed: 338 average time/residue: 0.1502 time to fit residues: 81.5521 Evaluate side-chains 362 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 286 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 911 ASP Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 16 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 267 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN E 901 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.112201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.091242 restraints weight = 43180.224| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.47 r_work: 0.2593 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22542 Z= 0.221 Angle : 0.620 12.546 30514 Z= 0.327 Chirality : 0.046 0.173 3244 Planarity : 0.004 0.050 3996 Dihedral : 6.032 82.364 3139 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.57 % Allowed : 16.22 % Favored : 80.21 % 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: -1.38 (0.15), residues: 2786 helix: 0.34 (0.23), residues: 562 sheet: -0.43 (0.18), residues: 818 loop : -1.75 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 490 TYR 0.020 0.002 TYR B1003 PHE 0.015 0.002 PHE E 990 TRP 0.008 0.001 TRP A 161 HIS 0.006 0.001 HIS E 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (22538) covalent geometry : angle 0.62011 / 0.33 (30514) hydrogen bonds : bond 0.04060 / 2.64 ( 940) hydrogen bonds : angle 4.75047 / 3.42 ( 2638) Misc. bond : bond 0.00019 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 0.856 Fit side-chains REVERT: A 22 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8393 (pp) REVERT: A 162 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8838 (tpp-160) REVERT: A 410 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8711 (ttpt) REVERT: B 152 MET cc_start: 0.9119 (tpp) cc_final: 0.8861 (tpp) REVERT: B 271 LYS cc_start: 0.8375 (mttp) cc_final: 0.7884 (mtmt) REVERT: B 353 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.7549 (p90) REVERT: B 543 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8405 (t-90) REVERT: B 551 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7327 (t70) REVERT: B 564 LYS cc_start: 0.8634 (mptt) cc_final: 0.8217 (mtmt) REVERT: B 568 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8766 (mp) REVERT: D 22 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8378 (pp) REVERT: D 162 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8945 (tpp-160) REVERT: D 212 ARG cc_start: 0.8379 (mmp-170) cc_final: 0.8145 (mmp-170) REVERT: D 255 ASP cc_start: 0.8006 (m-30) cc_final: 0.7576 (m-30) REVERT: D 410 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8674 (ttpt) REVERT: E 165 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8158 (mt-10) REVERT: E 203 MET cc_start: 0.8957 (ttm) cc_final: 0.8752 (ttm) REVERT: E 308 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8451 (ttpp) REVERT: E 353 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7505 (p90) REVERT: E 376 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: E 543 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8379 (t-90) REVERT: E 564 LYS cc_start: 0.8768 (mptt) cc_final: 0.8351 (mmmt) REVERT: E 568 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8774 (mp) outliers start: 83 outliers final: 63 residues processed: 333 average time/residue: 0.1499 time to fit residues: 80.3821 Evaluate side-chains 355 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 573 THR Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 901 ASN Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 984 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN E 901 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.112550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.090297 restraints weight = 38570.278| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.35 r_work: 0.2597 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 22542 Z= 0.209 Angle : 0.770 59.196 30514 Z= 0.435 Chirality : 0.046 0.545 3244 Planarity : 0.004 0.050 3996 Dihedral : 6.040 82.349 3139 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.36 % Allowed : 16.57 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2786 helix: 0.34 (0.23), residues: 562 sheet: -0.44 (0.18), residues: 818 loop : -1.76 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 490 TYR 0.018 0.002 TYR B1003 PHE 0.014 0.001 PHE E 990 TRP 0.009 0.001 TRP A 161 HIS 0.005 0.001 HIS E 939 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (22538) covalent geometry : angle 0.77012 / 0.44 (30514) hydrogen bonds : bond 0.03946 / 2.56 ( 940) hydrogen bonds : angle 4.75032 / 3.42 ( 2638) Misc. bond : bond 0.00017 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5586.68 seconds wall clock time: 96 minutes 24.03 seconds (5784.03 seconds total)