Starting phenix.real_space_refine on Sat Sep 12 05:57:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm3_20385/09_2026/6pm3_20385.cif" } resolution = 3.0 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9195 2.51 5 N 2290 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s 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: 14120 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.77, per 1000 atoms: 0.20 Number of scatterers: 14120 At special positions: 0 Unit cell: (97.114, 98.76, 134.149, 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 105 16.00 O 2530 8.00 N 2290 7.00 C 9195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 486.0 milliseconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 39.7% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.012A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.628A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 108 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.551A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.566A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.522A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 425 removed outlier: 3.683A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.516A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.012A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.628A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.551A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.565A pdb=" N LEU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.522A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 425 removed outlier: 3.683A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.515A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.012A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.628A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.551A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.565A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.523A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 315 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.683A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.515A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.012A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.628A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 254 removed outlier: 3.550A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.566A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 324 removed outlier: 3.522A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 425 removed outlier: 3.684A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.515A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.012A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.628A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 254 removed outlier: 3.551A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 260 Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.566A pdb=" N LEU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 324 removed outlier: 3.522A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 315 " --> pdb=" O PHE E 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 425 removed outlier: 3.683A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.515A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.491A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.221A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.507A pdb=" N ASP A 210 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLU A 233 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS A 206 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.490A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.222A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.507A pdb=" N ASP B 210 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU B 233 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS B 206 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.490A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.223A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.507A pdb=" N ASP C 210 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU C 233 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS C 206 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.490A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.223A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.507A pdb=" N ASP D 210 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU D 233 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS D 206 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.490A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.222A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.507A pdb=" N ASP E 210 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS E 206 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 216 through 217 685 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4038 1.33 - 1.46: 3654 1.46 - 1.58: 6603 1.58 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 14470 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 ... (remaining 14465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 19161 2.78 - 5.56: 377 5.56 - 8.34: 77 8.34 - 11.12: 5 11.12 - 13.89: 10 Bond angle restraints: 19630 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 135.43 -13.89 1.91e+00 2.74e-01 5.29e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 135.42 -13.88 1.91e+00 2.74e-01 5.28e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 135.41 -13.87 1.91e+00 2.74e-01 5.28e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 135.40 -13.86 1.91e+00 2.74e-01 5.27e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 135.39 -13.85 1.91e+00 2.74e-01 5.26e+01 ... (remaining 19625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 8215 16.78 - 33.56: 315 33.56 - 50.34: 25 50.34 - 67.12: 5 67.12 - 83.90: 10 Dihedral angle restraints: 8570 sinusoidal: 3470 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " pdb=" CB CYS B 225 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 8567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1870 0.079 - 0.158: 329 0.158 - 0.237: 26 0.237 - 0.317: 0 0.317 - 0.396: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CG LEU A 314 " pdb=" CB LEU A 314 " pdb=" CD1 LEU A 314 " pdb=" CD2 LEU A 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CG LEU D 314 " pdb=" CB LEU D 314 " pdb=" CD1 LEU D 314 " pdb=" CD2 LEU D 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CG LEU E 314 " pdb=" CB LEU E 314 " pdb=" CD1 LEU E 314 " pdb=" CD2 LEU E 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 2227 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 128 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C THR D 128 " -0.043 2.00e-02 2.50e+03 pdb=" O THR D 128 " 0.016 2.00e-02 2.50e+03 pdb=" N THR D 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C THR B 128 " 0.043 2.00e-02 2.50e+03 pdb=" O THR B 128 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B 129 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C THR A 128 " 0.043 2.00e-02 2.50e+03 pdb=" O THR A 128 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 129 " -0.014 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4521 2.84 - 3.35: 12121 3.35 - 3.87: 23138 3.87 - 4.38: 27840 4.38 - 4.90: 47816 Nonbonded interactions: 115436 Sorted by model distance: nonbonded pdb=" NH2 ARG A 325 " pdb=" O TRP E 259 " model vdw 2.322 3.120 nonbonded pdb=" O LEU A 271 " pdb=" OG1 THR A 275 " model vdw 2.335 3.040 nonbonded pdb=" O LEU B 271 " pdb=" OG1 THR B 275 " model vdw 2.336 3.040 nonbonded pdb=" O LEU D 271 " pdb=" OG1 THR D 275 " model vdw 2.336 3.040 nonbonded pdb=" O LEU E 271 " pdb=" OG1 THR E 275 " model vdw 2.336 3.040 ... (remaining 115431 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 0.075 14490 Z= 0.374 Angle : 1.066 13.895 19680 Z= 0.549 Chirality : 0.062 0.396 2230 Planarity : 0.007 0.055 2430 Dihedral : 9.201 73.327 5230 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.15), residues: 1705 helix: -4.31 (0.10), residues: 590 sheet: -1.78 (0.20), residues: 425 loop : -2.25 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 147 TYR 0.030 0.003 TYR A 144 PHE 0.025 0.003 PHE E 115 TRP 0.031 0.004 TRP D 110 HIS 0.006 0.002 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.37 (14470) covalent geometry : angle 1.05914 / 0.55 (19630) SS BOND : bond 0.00777 / 0.48 ( 10) SS BOND : angle 1.77374 / 1.07 ( 20) hydrogen bonds : bond 0.26628 / 17.32 ( 600) hydrogen bonds : angle 9.83245 / 6.82 ( 1965) link_BETA1-4 : bond 0.00338 / 0.20 ( 5) link_BETA1-4 : angle 3.80928 / 2.20 ( 15) link_NAG-ASN : bond 0.00192 / 0.11 ( 5) link_NAG-ASN : angle 1.78100 / 0.84 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 0.472 Fit side-chains REVERT: A 49 LYS cc_start: 0.8605 (mttt) cc_final: 0.8380 (mtpt) REVERT: A 206 LYS cc_start: 0.8539 (mttt) cc_final: 0.8038 (mtmt) REVERT: A 400 LYS cc_start: 0.8348 (mttm) cc_final: 0.8001 (mmmt) REVERT: A 401 ARG cc_start: 0.7411 (tpt90) cc_final: 0.6974 (tpm-80) REVERT: A 402 ILE cc_start: 0.8635 (tt) cc_final: 0.8365 (mt) REVERT: B 400 LYS cc_start: 0.8285 (mttm) cc_final: 0.8056 (mmmt) REVERT: B 401 ARG cc_start: 0.7599 (tpt90) cc_final: 0.7093 (tpm-80) REVERT: B 402 ILE cc_start: 0.8627 (tt) cc_final: 0.8290 (mt) REVERT: C 49 LYS cc_start: 0.8622 (mttt) cc_final: 0.8422 (mtmt) REVERT: C 102 ASP cc_start: 0.8718 (t70) cc_final: 0.8431 (t70) REVERT: C 206 LYS cc_start: 0.8526 (mttt) cc_final: 0.7933 (mmmm) REVERT: C 279 MET cc_start: 0.9205 (tpt) cc_final: 0.8565 (tpt) REVERT: C 400 LYS cc_start: 0.8360 (mttm) cc_final: 0.8056 (mmmt) REVERT: C 401 ARG cc_start: 0.7510 (tpt90) cc_final: 0.7021 (tpm-80) REVERT: C 402 ILE cc_start: 0.8749 (tt) cc_final: 0.8444 (mt) REVERT: D 206 LYS cc_start: 0.8536 (mttt) cc_final: 0.7793 (mmmm) REVERT: D 400 LYS cc_start: 0.8247 (mttm) cc_final: 0.8001 (mmmt) REVERT: D 402 ILE cc_start: 0.8748 (tt) cc_final: 0.8417 (mt) REVERT: E 206 LYS cc_start: 0.8564 (mttt) cc_final: 0.8038 (mmmm) REVERT: E 400 LYS cc_start: 0.8359 (mttm) cc_final: 0.8071 (mmmt) REVERT: E 401 ARG cc_start: 0.7552 (tpt90) cc_final: 0.7129 (tpm-80) REVERT: E 402 ILE cc_start: 0.8760 (tt) cc_final: 0.8355 (mt) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.6277 time to fit residues: 303.6249 Evaluate side-chains 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 321 ASN B 131 ASN B 321 ASN C 131 ASN C 180 ASN C 321 ASN D 131 ASN D 321 ASN E 131 ASN E 180 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093371 restraints weight = 18156.304| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.89 r_work: 0.2879 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14490 Z= 0.141 Angle : 0.659 6.740 19680 Z= 0.344 Chirality : 0.047 0.186 2230 Planarity : 0.005 0.045 2430 Dihedral : 5.181 21.500 1885 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.45 % Allowed : 12.96 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.18), residues: 1705 helix: -1.87 (0.18), residues: 590 sheet: -1.08 (0.22), residues: 425 loop : -1.63 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 75 TYR 0.012 0.001 TYR C 317 PHE 0.010 0.001 PHE D 115 TRP 0.016 0.002 TRP D 110 HIS 0.003 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (14470) covalent geometry : angle 0.65572 / 0.34 (19630) SS BOND : bond 0.00536 / 0.32 ( 10) SS BOND : angle 1.94359 / 1.26 ( 20) hydrogen bonds : bond 0.03870 / 2.61 ( 600) hydrogen bonds : angle 4.88668 / 3.41 ( 1965) link_BETA1-4 : bond 0.00196 / 0.13 ( 5) link_BETA1-4 : angle 1.59946 / 0.96 ( 15) link_NAG-ASN : bond 0.00084 / 0.05 ( 5) link_NAG-ASN : angle 0.52323 / 0.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.588 Fit side-chains REVERT: A 32 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8575 (tttm) REVERT: A 287 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.7481 (mtm180) REVERT: A 391 MET cc_start: 0.5031 (tpp) cc_final: 0.4752 (tpt) REVERT: A 400 LYS cc_start: 0.8347 (mttm) cc_final: 0.7866 (mmmt) REVERT: A 401 ARG cc_start: 0.7665 (tpt90) cc_final: 0.7106 (tpm-80) REVERT: B 129 THR cc_start: 0.8112 (m) cc_final: 0.7881 (p) REVERT: B 400 LYS cc_start: 0.8137 (mttm) cc_final: 0.7750 (mmmt) REVERT: B 401 ARG cc_start: 0.7821 (tpt90) cc_final: 0.7235 (tpm-80) REVERT: B 402 ILE cc_start: 0.8388 (tt) cc_final: 0.8114 (mt) REVERT: C 279 MET cc_start: 0.9163 (tpt) cc_final: 0.8751 (tpt) REVERT: C 400 LYS cc_start: 0.8311 (mttm) cc_final: 0.7890 (mmmt) REVERT: C 401 ARG cc_start: 0.7773 (tpt90) cc_final: 0.7069 (tpm-80) REVERT: C 402 ILE cc_start: 0.8550 (tt) cc_final: 0.8241 (mt) REVERT: D 109 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8387 (mm) REVERT: D 206 LYS cc_start: 0.8689 (mttt) cc_final: 0.8445 (mmmm) REVERT: D 212 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8142 (ptp-170) REVERT: D 400 LYS cc_start: 0.8237 (mttm) cc_final: 0.7807 (mmmt) REVERT: D 401 ARG cc_start: 0.7451 (tpt-90) cc_final: 0.6705 (tpm-80) REVERT: D 402 ILE cc_start: 0.8480 (tt) cc_final: 0.8222 (mt) REVERT: E 398 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7363 (mtt-85) REVERT: E 400 LYS cc_start: 0.8283 (mttm) cc_final: 0.7862 (mmmt) REVERT: E 401 ARG cc_start: 0.7864 (tpt90) cc_final: 0.7236 (tpm-80) REVERT: E 402 ILE cc_start: 0.8417 (tt) cc_final: 0.8199 (mt) outliers start: 53 outliers final: 11 residues processed: 283 average time/residue: 0.6186 time to fit residues: 191.7240 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 398 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 41 optimal weight: 0.0370 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.0270 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN E 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.092510 restraints weight = 18238.485| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.90 r_work: 0.2808 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14490 Z= 0.131 Angle : 0.592 7.152 19680 Z= 0.309 Chirality : 0.045 0.208 2230 Planarity : 0.004 0.046 2430 Dihedral : 4.651 21.438 1885 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.30 % Allowed : 14.98 % Favored : 80.72 % 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: -1.13 (0.19), residues: 1705 helix: -0.33 (0.21), residues: 585 sheet: -0.25 (0.24), residues: 395 loop : -1.28 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 75 TYR 0.014 0.001 TYR C 144 PHE 0.011 0.002 PHE D 417 TRP 0.011 0.001 TRP B 110 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14470) covalent geometry : angle 0.58890 / 0.31 (19630) SS BOND : bond 0.00953 / 0.66 ( 10) SS BOND : angle 1.40364 / 0.82 ( 20) hydrogen bonds : bond 0.03294 / 2.17 ( 600) hydrogen bonds : angle 4.25422 / 2.95 ( 1965) link_BETA1-4 : bond 0.00419 / 0.23 ( 5) link_BETA1-4 : angle 1.72547 / 1.05 ( 15) link_NAG-ASN : bond 0.00071 / 0.04 ( 5) link_NAG-ASN : angle 0.69645 / 0.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 0.660 Fit side-chains REVERT: A 32 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8804 (ttpp) REVERT: A 204 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8666 (mm) REVERT: A 287 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7430 (mtm180) REVERT: A 391 MET cc_start: 0.4991 (tpp) cc_final: 0.4656 (tpt) REVERT: A 400 LYS cc_start: 0.8229 (mttm) cc_final: 0.7776 (mmmt) REVERT: A 401 ARG cc_start: 0.7708 (tpt90) cc_final: 0.6999 (tpm-80) REVERT: B 109 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (tt) REVERT: B 129 THR cc_start: 0.8169 (m) cc_final: 0.7874 (p) REVERT: B 243 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9074 (mtm) REVERT: B 287 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7415 (mtm180) REVERT: B 398 ARG cc_start: 0.7627 (tpp-160) cc_final: 0.7407 (mtt-85) REVERT: B 400 LYS cc_start: 0.8151 (mttm) cc_final: 0.7729 (mmmt) REVERT: B 401 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7152 (tpm-80) REVERT: B 402 ILE cc_start: 0.8334 (tt) cc_final: 0.8050 (mt) REVERT: B 403 ASP cc_start: 0.8443 (t0) cc_final: 0.8240 (t0) REVERT: C 279 MET cc_start: 0.9180 (tpt) cc_final: 0.8838 (tpt) REVERT: C 400 LYS cc_start: 0.8352 (mttm) cc_final: 0.7921 (mmmt) REVERT: C 401 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7117 (tpm-80) REVERT: C 402 ILE cc_start: 0.8454 (tt) cc_final: 0.8164 (mt) REVERT: D 83 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8756 (mt0) REVERT: D 109 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (tt) REVERT: D 212 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8105 (ptp-170) REVERT: D 287 ARG cc_start: 0.7841 (ptp-170) cc_final: 0.7477 (mtm180) REVERT: D 400 LYS cc_start: 0.8133 (mttm) cc_final: 0.7750 (mmmt) REVERT: D 401 ARG cc_start: 0.7463 (tpt-90) cc_final: 0.6688 (tpm-80) REVERT: D 402 ILE cc_start: 0.8450 (tt) cc_final: 0.8147 (mt) REVERT: E 72 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8568 (mtp) REVERT: E 282 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: E 398 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7341 (mtt-85) REVERT: E 400 LYS cc_start: 0.8271 (mttm) cc_final: 0.7816 (mmmt) REVERT: E 401 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7041 (tpm-80) REVERT: E 402 ILE cc_start: 0.8421 (tt) cc_final: 0.8123 (mt) outliers start: 66 outliers final: 22 residues processed: 252 average time/residue: 0.5863 time to fit residues: 162.6603 Evaluate side-chains 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 398 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 202 GLN C 58 ASN D 58 ASN E 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.084932 restraints weight = 18358.897| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.92 r_work: 0.2706 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14490 Z= 0.241 Angle : 0.704 8.739 19680 Z= 0.362 Chirality : 0.049 0.271 2230 Planarity : 0.005 0.043 2430 Dihedral : 4.885 22.277 1885 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.89 % Allowed : 15.11 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1705 helix: 0.08 (0.22), residues: 585 sheet: 0.09 (0.25), residues: 395 loop : -1.19 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 147 TYR 0.017 0.002 TYR A 144 PHE 0.018 0.002 PHE B 175 TRP 0.010 0.002 TRP D 110 HIS 0.005 0.002 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (14470) covalent geometry : angle 0.69695 / 0.36 (19630) SS BOND : bond 0.00793 / 0.48 ( 10) SS BOND : angle 2.56468 / 1.78 ( 20) hydrogen bonds : bond 0.03531 / 2.30 ( 600) hydrogen bonds : angle 4.15328 / 2.90 ( 1965) link_BETA1-4 : bond 0.00247 / 0.15 ( 5) link_BETA1-4 : angle 2.10889 / 1.27 ( 15) link_NAG-ASN : bond 0.00038 / 0.02 ( 5) link_NAG-ASN : angle 1.13990 / 0.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 182 time to evaluate : 0.549 Fit side-chains REVERT: A 32 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8755 (ttpp) REVERT: A 198 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 287 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.7495 (mtm180) REVERT: A 400 LYS cc_start: 0.8086 (mttm) cc_final: 0.7652 (mmmt) REVERT: B 109 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 129 THR cc_start: 0.8241 (m) cc_final: 0.7911 (p) REVERT: B 243 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9129 (mtm) REVERT: B 282 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: B 400 LYS cc_start: 0.8143 (mttm) cc_final: 0.7710 (mmmt) REVERT: B 402 ILE cc_start: 0.8405 (tt) cc_final: 0.8112 (mt) REVERT: B 403 ASP cc_start: 0.8510 (t0) cc_final: 0.8276 (t0) REVERT: C 72 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: C 279 MET cc_start: 0.9294 (tpt) cc_final: 0.8887 (tpt) REVERT: C 400 LYS cc_start: 0.8276 (mttm) cc_final: 0.7830 (mmmt) REVERT: C 401 ARG cc_start: 0.7947 (tpt90) cc_final: 0.7081 (tpm-80) REVERT: C 402 ILE cc_start: 0.8625 (tt) cc_final: 0.8243 (mt) REVERT: D 83 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8856 (mt0) REVERT: D 212 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8072 (ptp-170) REVERT: D 287 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7440 (mtm180) REVERT: D 400 LYS cc_start: 0.8150 (mttm) cc_final: 0.7734 (mmmt) REVERT: D 401 ARG cc_start: 0.7475 (tpt-90) cc_final: 0.6731 (tpm-80) REVERT: D 402 ILE cc_start: 0.8517 (tt) cc_final: 0.8143 (mt) REVERT: E 72 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8895 (mmm) REVERT: E 83 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (mt0) REVERT: E 282 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: E 398 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7322 (mtt-85) REVERT: E 400 LYS cc_start: 0.8204 (mttm) cc_final: 0.7731 (mmmt) REVERT: E 401 ARG cc_start: 0.7808 (tpt90) cc_final: 0.6902 (tpm-80) REVERT: E 402 ILE cc_start: 0.8412 (tt) cc_final: 0.8064 (mt) outliers start: 75 outliers final: 30 residues processed: 236 average time/residue: 0.6178 time to fit residues: 159.5929 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN E 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.087320 restraints weight = 18229.248| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.97 r_work: 0.2753 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14490 Z= 0.121 Angle : 0.570 6.797 19680 Z= 0.296 Chirality : 0.044 0.211 2230 Planarity : 0.004 0.041 2430 Dihedral : 4.602 22.111 1885 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.19 % Allowed : 17.07 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1705 helix: 0.57 (0.22), residues: 580 sheet: 0.31 (0.25), residues: 395 loop : -1.11 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 401 TYR 0.013 0.001 TYR B 317 PHE 0.010 0.001 PHE D 417 TRP 0.010 0.001 TRP D 84 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (14470) covalent geometry : angle 0.56449 / 0.29 (19630) SS BOND : bond 0.00456 / 0.27 ( 10) SS BOND : angle 1.92824 / 1.37 ( 20) hydrogen bonds : bond 0.02821 / 1.86 ( 600) hydrogen bonds : angle 3.89823 / 2.72 ( 1965) link_BETA1-4 : bond 0.00292 / 0.17 ( 5) link_BETA1-4 : angle 1.83561 / 1.13 ( 15) link_NAG-ASN : bond 0.00051 / 0.03 ( 5) link_NAG-ASN : angle 0.71790 / 0.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.568 Fit side-chains REVERT: A 198 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 287 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7452 (mtm180) REVERT: A 400 LYS cc_start: 0.8171 (mttm) cc_final: 0.7728 (mmmt) REVERT: B 206 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.7988 (mmmm) REVERT: B 243 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9090 (mtm) REVERT: B 287 ARG cc_start: 0.7945 (ptp-170) cc_final: 0.7498 (mtm180) REVERT: B 400 LYS cc_start: 0.8176 (mttm) cc_final: 0.7720 (mmmt) REVERT: B 401 ARG cc_start: 0.7627 (tpt-90) cc_final: 0.6727 (tpm-80) REVERT: B 402 ILE cc_start: 0.8386 (tt) cc_final: 0.8067 (mt) REVERT: B 403 ASP cc_start: 0.8496 (t0) cc_final: 0.8247 (t0) REVERT: C 279 MET cc_start: 0.9233 (tpt) cc_final: 0.8863 (tpt) REVERT: C 400 LYS cc_start: 0.8270 (mttm) cc_final: 0.7863 (mmmt) REVERT: C 401 ARG cc_start: 0.8024 (tpt90) cc_final: 0.7122 (tpm-80) REVERT: C 402 ILE cc_start: 0.8582 (tt) cc_final: 0.8211 (mt) REVERT: D 83 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8836 (mt0) REVERT: D 212 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8095 (ptp-170) REVERT: D 287 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7436 (mtm180) REVERT: D 400 LYS cc_start: 0.8170 (mttm) cc_final: 0.7766 (mmmt) REVERT: D 401 ARG cc_start: 0.7527 (tpt-90) cc_final: 0.6737 (tpm-80) REVERT: D 402 ILE cc_start: 0.8534 (tt) cc_final: 0.8125 (mt) REVERT: E 72 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8922 (mmm) REVERT: E 126 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: E 198 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7880 (mp) REVERT: E 282 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: E 400 LYS cc_start: 0.8205 (mttm) cc_final: 0.7724 (mmmt) REVERT: E 401 ARG cc_start: 0.7745 (tpt90) cc_final: 0.6861 (tpm-80) REVERT: E 402 ILE cc_start: 0.8420 (tt) cc_final: 0.8071 (mt) outliers start: 49 outliers final: 20 residues processed: 208 average time/residue: 0.6608 time to fit residues: 149.7138 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 16 optimal weight: 0.0030 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 150 optimal weight: 0.1980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 ASN C 131 ASN E 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.091092 restraints weight = 18115.779| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.00 r_work: 0.2797 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14490 Z= 0.092 Angle : 0.531 6.430 19680 Z= 0.276 Chirality : 0.044 0.276 2230 Planarity : 0.003 0.039 2430 Dihedral : 4.268 22.021 1885 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.08 % Allowed : 18.50 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1705 helix: 1.00 (0.22), residues: 580 sheet: 0.44 (0.26), residues: 395 loop : -1.09 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.012 0.001 TYR C 317 PHE 0.010 0.001 PHE D 417 TRP 0.011 0.001 TRP B 84 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (14470) covalent geometry : angle 0.52785 / 0.27 (19630) SS BOND : bond 0.00285 / 0.17 ( 10) SS BOND : angle 1.46845 / 1.02 ( 20) hydrogen bonds : bond 0.02474 / 1.64 ( 600) hydrogen bonds : angle 3.61398 / 2.51 ( 1965) link_BETA1-4 : bond 0.00235 / 0.13 ( 5) link_BETA1-4 : angle 1.52303 / 0.93 ( 15) link_NAG-ASN : bond 0.00109 / 0.06 ( 5) link_NAG-ASN : angle 0.48196 / 0.25 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.574 Fit side-chains REVERT: A 287 ARG cc_start: 0.7839 (ptp-170) cc_final: 0.7360 (mtm180) REVERT: A 400 LYS cc_start: 0.8077 (mttm) cc_final: 0.7602 (mmmt) REVERT: B 129 THR cc_start: 0.8021 (m) cc_final: 0.7641 (p) REVERT: B 243 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9066 (mtm) REVERT: B 287 ARG cc_start: 0.7839 (ptp-170) cc_final: 0.7430 (mtm180) REVERT: B 400 LYS cc_start: 0.8094 (mttm) cc_final: 0.7621 (mmmt) REVERT: B 401 ARG cc_start: 0.7451 (tpt-90) cc_final: 0.6682 (tpm-80) REVERT: B 402 ILE cc_start: 0.8208 (tt) cc_final: 0.7890 (mt) REVERT: B 403 ASP cc_start: 0.8332 (t0) cc_final: 0.8112 (t0) REVERT: C 400 LYS cc_start: 0.8203 (mttm) cc_final: 0.7771 (mmmt) REVERT: C 401 ARG cc_start: 0.7865 (tpt90) cc_final: 0.6944 (tpm-80) REVERT: C 402 ILE cc_start: 0.8432 (tt) cc_final: 0.8063 (mt) REVERT: D 83 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8860 (mt0) REVERT: D 287 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7437 (mtm180) REVERT: D 400 LYS cc_start: 0.8111 (mttm) cc_final: 0.7645 (mmmt) REVERT: D 402 ILE cc_start: 0.8434 (tt) cc_final: 0.7955 (mt) REVERT: E 72 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8887 (mmm) REVERT: E 126 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: E 400 LYS cc_start: 0.8093 (mttm) cc_final: 0.7661 (mmmt) REVERT: E 401 ARG cc_start: 0.7638 (tpt90) cc_final: 0.6738 (tpm-80) REVERT: E 402 ILE cc_start: 0.8288 (tt) cc_final: 0.7910 (mt) outliers start: 32 outliers final: 12 residues processed: 195 average time/residue: 0.6913 time to fit residues: 146.2338 Evaluate side-chains 183 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN E 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.113180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089353 restraints weight = 18248.012| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.92 r_work: 0.2792 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14490 Z= 0.116 Angle : 0.552 7.748 19680 Z= 0.284 Chirality : 0.044 0.236 2230 Planarity : 0.003 0.037 2430 Dihedral : 4.266 22.480 1885 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.48 % Allowed : 18.44 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1705 helix: 1.22 (0.22), residues: 580 sheet: 0.56 (0.26), residues: 395 loop : -1.04 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.012 0.001 TYR B 317 PHE 0.010 0.001 PHE A 115 TRP 0.012 0.001 TRP E 422 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14470) covalent geometry : angle 0.54833 / 0.28 (19630) SS BOND : bond 0.00371 / 0.22 ( 10) SS BOND : angle 1.61174 / 1.11 ( 20) hydrogen bonds : bond 0.02575 / 1.69 ( 600) hydrogen bonds : angle 3.59606 / 2.50 ( 1965) link_BETA1-4 : bond 0.00265 / 0.15 ( 5) link_BETA1-4 : angle 1.62662 / 0.99 ( 15) link_NAG-ASN : bond 0.00064 / 0.04 ( 5) link_NAG-ASN : angle 0.69156 / 0.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.602 Fit side-chains REVERT: A 287 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.7453 (mtm180) REVERT: A 400 LYS cc_start: 0.8216 (mttm) cc_final: 0.7754 (mmmt) REVERT: B 129 THR cc_start: 0.8100 (m) cc_final: 0.7767 (p) REVERT: B 243 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.9074 (mtm) REVERT: B 287 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7468 (mtm180) REVERT: B 400 LYS cc_start: 0.8215 (mttm) cc_final: 0.7756 (mmmt) REVERT: B 401 ARG cc_start: 0.7579 (tpt-90) cc_final: 0.6813 (tpm-80) REVERT: B 402 ILE cc_start: 0.8301 (tt) cc_final: 0.7974 (mt) REVERT: B 403 ASP cc_start: 0.8376 (t0) cc_final: 0.8163 (t0) REVERT: C 279 MET cc_start: 0.9342 (tpt) cc_final: 0.8711 (tpt) REVERT: C 282 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: C 400 LYS cc_start: 0.8317 (mttm) cc_final: 0.7902 (mmmt) REVERT: C 402 ILE cc_start: 0.8565 (tt) cc_final: 0.8136 (mt) REVERT: D 287 ARG cc_start: 0.7978 (ptp-170) cc_final: 0.7454 (mtm180) REVERT: D 400 LYS cc_start: 0.8226 (mttm) cc_final: 0.7792 (mmmt) REVERT: D 402 ILE cc_start: 0.8531 (tt) cc_final: 0.8020 (mt) REVERT: E 72 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8953 (mmm) REVERT: E 126 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: E 400 LYS cc_start: 0.8220 (mttm) cc_final: 0.7803 (mmmt) REVERT: E 401 ARG cc_start: 0.7729 (tpt90) cc_final: 0.6851 (tpm-80) REVERT: E 402 ILE cc_start: 0.8398 (tt) cc_final: 0.7995 (mt) outliers start: 38 outliers final: 23 residues processed: 200 average time/residue: 0.6796 time to fit residues: 148.0968 Evaluate side-chains 194 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.089621 restraints weight = 18133.364| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.88 r_work: 0.2748 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14490 Z= 0.142 Angle : 0.579 7.499 19680 Z= 0.299 Chirality : 0.045 0.314 2230 Planarity : 0.004 0.036 2430 Dihedral : 4.352 22.689 1885 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.54 % Allowed : 18.63 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1705 helix: 1.34 (0.22), residues: 580 sheet: 0.66 (0.26), residues: 395 loop : -1.00 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 212 TYR 0.012 0.001 TYR E 317 PHE 0.012 0.001 PHE C 115 TRP 0.007 0.001 TRP D 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (14470) covalent geometry : angle 0.57441 / 0.30 (19630) SS BOND : bond 0.00450 / 0.27 ( 10) SS BOND : angle 1.76401 / 1.20 ( 20) hydrogen bonds : bond 0.02734 / 1.78 ( 600) hydrogen bonds : angle 3.68242 / 2.56 ( 1965) link_BETA1-4 : bond 0.00264 / 0.16 ( 5) link_BETA1-4 : angle 1.78541 / 1.08 ( 15) link_NAG-ASN : bond 0.00045 / 0.03 ( 5) link_NAG-ASN : angle 0.81494 / 0.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.585 Fit side-chains REVERT: A 212 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8025 (ptp-170) REVERT: A 287 ARG cc_start: 0.7912 (ptp-170) cc_final: 0.7439 (mtm180) REVERT: A 400 LYS cc_start: 0.8190 (mttm) cc_final: 0.7726 (mmmt) REVERT: B 129 THR cc_start: 0.8103 (m) cc_final: 0.7751 (p) REVERT: B 243 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9093 (mtm) REVERT: B 287 ARG cc_start: 0.7939 (ptp-170) cc_final: 0.7416 (mtm180) REVERT: B 400 LYS cc_start: 0.8187 (mttm) cc_final: 0.7717 (mmmt) REVERT: B 402 ILE cc_start: 0.8325 (tt) cc_final: 0.7989 (mt) REVERT: B 403 ASP cc_start: 0.8395 (t0) cc_final: 0.8169 (t0) REVERT: C 282 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: C 400 LYS cc_start: 0.8307 (mttm) cc_final: 0.7890 (mmmt) REVERT: C 402 ILE cc_start: 0.8600 (tt) cc_final: 0.8151 (mt) REVERT: C 418 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8975 (m-40) REVERT: D 72 MET cc_start: 0.9210 (mmm) cc_final: 0.8788 (mmm) REVERT: D 287 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.7432 (mtm180) REVERT: D 400 LYS cc_start: 0.8200 (mttm) cc_final: 0.7764 (mmmt) REVERT: D 402 ILE cc_start: 0.8542 (tt) cc_final: 0.8025 (mt) REVERT: E 72 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8941 (mmm) REVERT: E 126 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: E 198 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7995 (mp) REVERT: E 400 LYS cc_start: 0.8200 (mttm) cc_final: 0.7791 (mmmt) REVERT: E 401 ARG cc_start: 0.7799 (tpt90) cc_final: 0.6840 (tpm-80) REVERT: E 402 ILE cc_start: 0.8386 (tt) cc_final: 0.7964 (mt) outliers start: 39 outliers final: 24 residues processed: 192 average time/residue: 0.6959 time to fit residues: 145.1978 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 GLN D 131 ASN E 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090823 restraints weight = 18223.443| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.90 r_work: 0.2779 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14490 Z= 0.103 Angle : 0.545 9.002 19680 Z= 0.282 Chirality : 0.044 0.294 2230 Planarity : 0.003 0.037 2430 Dihedral : 4.238 22.341 1885 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 18.89 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1705 helix: 1.53 (0.22), residues: 580 sheet: 0.67 (0.26), residues: 395 loop : -0.94 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 401 TYR 0.013 0.001 TYR C 317 PHE 0.009 0.001 PHE D 417 TRP 0.009 0.001 TRP D 84 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (14470) covalent geometry : angle 0.54108 / 0.28 (19630) SS BOND : bond 0.00300 / 0.18 ( 10) SS BOND : angle 1.50504 / 1.05 ( 20) hydrogen bonds : bond 0.02485 / 1.63 ( 600) hydrogen bonds : angle 3.59198 / 2.50 ( 1965) link_BETA1-4 : bond 0.00266 / 0.15 ( 5) link_BETA1-4 : angle 1.63355 / 1.00 ( 15) link_NAG-ASN : bond 0.00087 / 0.05 ( 5) link_NAG-ASN : angle 0.59660 / 0.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.552 Fit side-chains REVERT: A 212 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8018 (ptp-170) REVERT: A 287 ARG cc_start: 0.7888 (ptp-170) cc_final: 0.7412 (mtm180) REVERT: A 400 LYS cc_start: 0.8186 (mttm) cc_final: 0.7719 (mmmt) REVERT: B 129 THR cc_start: 0.8031 (m) cc_final: 0.7660 (p) REVERT: B 287 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7451 (mtm180) REVERT: B 400 LYS cc_start: 0.8189 (mttm) cc_final: 0.7711 (mmmt) REVERT: B 401 ARG cc_start: 0.7607 (tpt-90) cc_final: 0.6767 (tpm170) REVERT: B 402 ILE cc_start: 0.8287 (tt) cc_final: 0.7944 (mt) REVERT: B 403 ASP cc_start: 0.8374 (t0) cc_final: 0.8129 (t0) REVERT: C 282 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: C 400 LYS cc_start: 0.8332 (mttm) cc_final: 0.7899 (mmmt) REVERT: C 402 ILE cc_start: 0.8570 (tt) cc_final: 0.8130 (mt) REVERT: C 418 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8952 (m-40) REVERT: D 72 MET cc_start: 0.9195 (mmm) cc_final: 0.8794 (mmm) REVERT: D 212 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8107 (ptp-170) REVERT: D 287 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7487 (mtm180) REVERT: D 400 LYS cc_start: 0.8205 (mttm) cc_final: 0.7760 (mmmt) REVERT: D 402 ILE cc_start: 0.8517 (tt) cc_final: 0.7970 (mt) REVERT: E 72 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: E 126 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: E 400 LYS cc_start: 0.8223 (mttm) cc_final: 0.7807 (mmmt) REVERT: E 401 ARG cc_start: 0.7747 (tpt90) cc_final: 0.6810 (tpm-80) REVERT: E 402 ILE cc_start: 0.8369 (tt) cc_final: 0.7926 (mt) outliers start: 31 outliers final: 17 residues processed: 191 average time/residue: 0.7011 time to fit residues: 145.0562 Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 0.0270 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 119 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.089865 restraints weight = 18216.164| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.90 r_work: 0.2782 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14490 Z= 0.117 Angle : 0.553 6.759 19680 Z= 0.286 Chirality : 0.044 0.286 2230 Planarity : 0.003 0.034 2430 Dihedral : 4.232 22.485 1885 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.76 % Allowed : 19.54 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1705 helix: 1.60 (0.22), residues: 580 sheet: 0.71 (0.27), residues: 395 loop : -0.93 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 401 TYR 0.013 0.001 TYR C 317 PHE 0.010 0.001 PHE C 115 TRP 0.008 0.001 TRP D 84 HIS 0.002 0.001 HIS D 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14470) covalent geometry : angle 0.54881 / 0.29 (19630) SS BOND : bond 0.00383 / 0.23 ( 10) SS BOND : angle 1.58738 / 1.08 ( 20) hydrogen bonds : bond 0.02543 / 1.67 ( 600) hydrogen bonds : angle 3.59259 / 2.50 ( 1965) link_BETA1-4 : bond 0.00220 / 0.14 ( 5) link_BETA1-4 : angle 1.66808 / 1.01 ( 15) link_NAG-ASN : bond 0.00052 / 0.03 ( 5) link_NAG-ASN : angle 0.70147 / 0.35 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.564 Fit side-chains REVERT: A 126 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: A 212 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8028 (ptp-170) REVERT: A 287 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.7451 (mtm180) REVERT: A 292 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7979 (mmtp) REVERT: A 400 LYS cc_start: 0.8244 (mttm) cc_final: 0.7768 (mmmt) REVERT: B 129 THR cc_start: 0.8069 (m) cc_final: 0.7719 (p) REVERT: B 243 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9095 (mtm) REVERT: B 287 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7482 (mtm180) REVERT: B 400 LYS cc_start: 0.8213 (mttm) cc_final: 0.7737 (mmmt) REVERT: B 402 ILE cc_start: 0.8349 (tt) cc_final: 0.7998 (mt) REVERT: B 403 ASP cc_start: 0.8386 (t0) cc_final: 0.8138 (t0) REVERT: C 282 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: C 400 LYS cc_start: 0.8358 (mttm) cc_final: 0.7928 (mmmt) REVERT: C 402 ILE cc_start: 0.8597 (tt) cc_final: 0.8146 (mt) REVERT: C 418 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8954 (m-40) REVERT: D 72 MET cc_start: 0.9204 (mmm) cc_final: 0.8813 (mmm) REVERT: D 212 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8117 (ptp-170) REVERT: D 287 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7496 (mtm180) REVERT: D 400 LYS cc_start: 0.8233 (mttm) cc_final: 0.7797 (mmmt) REVERT: D 402 ILE cc_start: 0.8549 (tt) cc_final: 0.7984 (mt) REVERT: E 72 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8955 (mmm) REVERT: E 126 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: E 400 LYS cc_start: 0.8262 (mttm) cc_final: 0.7850 (mmmt) REVERT: E 401 ARG cc_start: 0.7806 (tpt90) cc_final: 0.6863 (tpm-80) REVERT: E 402 ILE cc_start: 0.8402 (tt) cc_final: 0.7947 (mt) outliers start: 27 outliers final: 20 residues processed: 187 average time/residue: 0.7141 time to fit residues: 144.8355 Evaluate side-chains 194 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 113 optimal weight: 0.0270 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088440 restraints weight = 18326.574| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.93 r_work: 0.2763 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14490 Z= 0.115 Angle : 0.548 6.737 19680 Z= 0.284 Chirality : 0.044 0.282 2230 Planarity : 0.003 0.036 2430 Dihedral : 4.222 22.533 1885 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.95 % Allowed : 19.41 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1705 helix: 1.66 (0.22), residues: 580 sheet: 0.73 (0.27), residues: 395 loop : -0.89 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 401 TYR 0.013 0.001 TYR E 317 PHE 0.010 0.001 PHE C 115 TRP 0.008 0.001 TRP B 84 HIS 0.002 0.001 HIS D 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14470) covalent geometry : angle 0.54365 / 0.28 (19630) SS BOND : bond 0.00364 / 0.22 ( 10) SS BOND : angle 1.59096 / 1.10 ( 20) hydrogen bonds : bond 0.02528 / 1.66 ( 600) hydrogen bonds : angle 3.58676 / 2.50 ( 1965) link_BETA1-4 : bond 0.00246 / 0.14 ( 5) link_BETA1-4 : angle 1.66619 / 1.02 ( 15) link_NAG-ASN : bond 0.00057 / 0.04 ( 5) link_NAG-ASN : angle 0.68221 / 0.34 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.91 seconds wall clock time: 80 minutes 25.65 seconds (4825.65 seconds total)