Starting phenix.real_space_refine on Wed Mar 4 13:59:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm3_20385/03_2026/6pm3_20385.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm3_20385/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pm3_20385/03_2026/6pm3_20385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm3_20385/03_2026/6pm3_20385.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm3_20385/03_2026/6pm3_20385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm3_20385/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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: 2.17, per 1000 atoms: 0.15 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: 1.05 Conformation dependent library (CDL) restraints added in 648.0 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: 0.42 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: 2.56 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: 8415 16.78 - 33.56: 325 33.56 - 50.34: 25 50.34 - 67.12: 5 67.12 - 83.90: 10 Dihedral angle restraints: 8780 sinusoidal: 3680 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 8777 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: 0.06 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: 2.890 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.320 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 9.093 73.327 5440 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 covalent geometry : bond 0.00917 (14470) covalent geometry : angle 1.05914 (19630) SS BOND : bond 0.00777 ( 10) SS BOND : angle 1.77374 ( 20) hydrogen bonds : bond 0.26628 ( 600) hydrogen bonds : angle 9.83245 ( 1965) link_BETA1-4 : bond 0.00338 ( 5) link_BETA1-4 : angle 3.80928 ( 15) link_NAG-ASN : bond 0.00192 ( 5) link_NAG-ASN : angle 1.78100 ( 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 : 0.468 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: 0.6032 time to fit residues: 290.9999 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 : 0.432 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 321 ASN B 131 ASN B 321 ASN C 180 ASN C 321 ASN D 131 ASN D 321 ASN E 180 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093044 restraints weight = 18161.144| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.90 r_work: 0.2824 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2402 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= 0.142 Angle : 0.668 6.995 19680 Z= 0.350 Chirality : 0.047 0.191 2230 Planarity : 0.005 0.045 2430 Dihedral : 5.279 22.416 2095 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.39 % Allowed : 13.03 % 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: -2.59 (0.18), residues: 1705 helix: -1.94 (0.17), residues: 590 sheet: -1.13 (0.22), residues: 425 loop : -1.68 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.011 0.001 TYR A 144 PHE 0.011 0.001 PHE A 124 TRP 0.017 0.002 TRP D 110 HIS 0.003 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00319 (14470) covalent geometry : angle 0.66380 (19630) SS BOND : bond 0.00544 ( 10) SS BOND : angle 1.93772 ( 20) hydrogen bonds : bond 0.04215 ( 600) hydrogen bonds : angle 5.02848 ( 1965) link_BETA1-4 : bond 0.00153 ( 5) link_BETA1-4 : angle 1.99421 ( 15) link_NAG-ASN : bond 0.00060 ( 5) link_NAG-ASN : angle 0.66150 ( 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 303 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.536 Fit side-chains REVERT: A 32 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8506 (tttm) REVERT: A 391 MET cc_start: 0.5017 (tpp) cc_final: 0.4670 (tpt) REVERT: A 400 LYS cc_start: 0.8252 (mttm) cc_final: 0.7781 (mmmt) REVERT: A 401 ARG cc_start: 0.7619 (tpt90) cc_final: 0.6876 (tpm-80) REVERT: A 402 ILE cc_start: 0.8362 (tt) cc_final: 0.8137 (mt) REVERT: B 129 THR cc_start: 0.8134 (m) cc_final: 0.7887 (p) REVERT: B 400 LYS cc_start: 0.8109 (mttm) cc_final: 0.7688 (mmmt) REVERT: B 401 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7154 (tpm-80) REVERT: B 402 ILE cc_start: 0.8336 (tt) cc_final: 0.8066 (mt) REVERT: C 129 THR cc_start: 0.8039 (m) cc_final: 0.7831 (p) REVERT: C 279 MET cc_start: 0.9156 (tpt) cc_final: 0.8717 (tpt) REVERT: C 400 LYS cc_start: 0.8226 (mttm) cc_final: 0.7805 (mmmt) REVERT: C 401 ARG cc_start: 0.7688 (tpt90) cc_final: 0.6935 (tpm-80) REVERT: C 402 ILE cc_start: 0.8419 (tt) cc_final: 0.8111 (mt) REVERT: D 206 LYS cc_start: 0.8722 (mttt) cc_final: 0.8468 (mmmm) REVERT: D 400 LYS cc_start: 0.8183 (mttm) cc_final: 0.7729 (mmmt) REVERT: D 401 ARG cc_start: 0.7382 (tpt-90) cc_final: 0.6607 (tpm-80) REVERT: D 402 ILE cc_start: 0.8408 (tt) cc_final: 0.8124 (mt) REVERT: E 193 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: E 398 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7214 (mtt-85) REVERT: E 400 LYS cc_start: 0.8194 (mttm) cc_final: 0.7767 (mmmt) REVERT: E 401 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7130 (tpm-80) REVERT: E 402 ILE cc_start: 0.8402 (tt) cc_final: 0.8166 (mt) outliers start: 52 outliers final: 10 residues processed: 278 average time/residue: 0.5940 time to fit residues: 180.2476 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 412 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 193 GLN 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: 6.9990 chunk 41 optimal weight: 0.0010 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN E 141 ASN E 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.087417 restraints weight = 18392.607| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.94 r_work: 0.2757 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 14490 Z= 0.193 Angle : 0.655 8.222 19680 Z= 0.340 Chirality : 0.047 0.208 2230 Planarity : 0.005 0.047 2430 Dihedral : 4.938 22.326 2095 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.28 % Allowed : 14.14 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1705 helix: -0.48 (0.21), residues: 585 sheet: -0.22 (0.24), residues: 395 loop : -1.28 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 147 TYR 0.016 0.002 TYR A 144 PHE 0.015 0.002 PHE E 175 TRP 0.012 0.002 TRP B 110 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00468 (14470) covalent geometry : angle 0.65000 (19630) SS BOND : bond 0.00697 ( 10) SS BOND : angle 1.62180 ( 20) hydrogen bonds : bond 0.03604 ( 600) hydrogen bonds : angle 4.35299 ( 1965) link_BETA1-4 : bond 0.00232 ( 5) link_BETA1-4 : angle 2.23388 ( 15) link_NAG-ASN : bond 0.00025 ( 5) link_NAG-ASN : angle 0.88202 ( 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 295 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 214 time to evaluate : 0.526 Fit side-chains REVERT: A 32 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8744 (ttpp) REVERT: A 287 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7408 (mtm180) REVERT: A 292 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7810 (mmtp) REVERT: A 391 MET cc_start: 0.5000 (tpp) cc_final: 0.4653 (tpt) REVERT: A 400 LYS cc_start: 0.8258 (mttm) cc_final: 0.7773 (mmmt) REVERT: A 402 ILE cc_start: 0.8462 (tt) cc_final: 0.8174 (mt) REVERT: B 109 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 129 THR cc_start: 0.8215 (m) cc_final: 0.7932 (p) REVERT: B 243 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9098 (mtm) REVERT: B 398 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7422 (mtt-85) REVERT: B 400 LYS cc_start: 0.8159 (mttm) cc_final: 0.7734 (mmmt) REVERT: B 401 ARG cc_start: 0.7914 (tpt90) cc_final: 0.7150 (tpm-80) REVERT: B 402 ILE cc_start: 0.8390 (tt) cc_final: 0.8104 (mt) REVERT: C 72 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8551 (mtp) REVERT: C 109 ILE cc_start: 0.8697 (mm) cc_final: 0.8441 (tt) REVERT: C 279 MET cc_start: 0.9268 (tpt) cc_final: 0.8818 (tpt) REVERT: C 400 LYS cc_start: 0.8320 (mttm) cc_final: 0.7880 (mmmt) REVERT: C 401 ARG cc_start: 0.7929 (tpt90) cc_final: 0.7086 (tpm-80) REVERT: C 402 ILE cc_start: 0.8576 (tt) cc_final: 0.8244 (mt) REVERT: D 83 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8791 (mt0) REVERT: D 109 ILE cc_start: 0.8707 (mm) cc_final: 0.8439 (tt) REVERT: D 130 ASP cc_start: 0.8159 (m-30) cc_final: 0.7930 (t0) REVERT: D 212 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8087 (ptp-170) REVERT: D 400 LYS cc_start: 0.8143 (mttm) cc_final: 0.7739 (mmmt) REVERT: D 401 ARG cc_start: 0.7536 (tpt-90) cc_final: 0.6754 (tpm-80) REVERT: D 402 ILE cc_start: 0.8475 (tt) cc_final: 0.8162 (mt) REVERT: E 72 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: E 109 ILE cc_start: 0.8681 (mm) cc_final: 0.8477 (tt) REVERT: E 193 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8582 (mp10) REVERT: E 282 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: E 398 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7329 (mtt-85) REVERT: E 400 LYS cc_start: 0.8261 (mttm) cc_final: 0.7800 (mmmt) REVERT: E 401 ARG cc_start: 0.7812 (tpt90) cc_final: 0.7054 (tpm-80) REVERT: E 402 ILE cc_start: 0.8439 (tt) cc_final: 0.8137 (mt) outliers start: 81 outliers final: 25 residues processed: 266 average time/residue: 0.5592 time to fit residues: 163.0855 Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER 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 63 SER 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 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 289 SER 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 193 GLN Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 269 VAL 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 193 GLN 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 284 SER 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: 0.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN D 58 ASN E 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.089832 restraints weight = 18238.256| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.90 r_work: 0.2789 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3257 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= 0.136 Angle : 0.591 7.021 19680 Z= 0.308 Chirality : 0.045 0.260 2230 Planarity : 0.004 0.043 2430 Dihedral : 4.657 22.063 2095 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.30 % Allowed : 15.44 % Favored : 80.26 % 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: -0.68 (0.20), residues: 1705 helix: 0.09 (0.22), residues: 585 sheet: 0.10 (0.25), residues: 395 loop : -1.14 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.012 0.001 TYR C 317 PHE 0.011 0.001 PHE D 417 TRP 0.010 0.001 TRP D 84 HIS 0.002 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00323 (14470) covalent geometry : angle 0.58385 (19630) SS BOND : bond 0.00440 ( 10) SS BOND : angle 2.27326 ( 20) hydrogen bonds : bond 0.03006 ( 600) hydrogen bonds : angle 4.00830 ( 1965) link_BETA1-4 : bond 0.00231 ( 5) link_BETA1-4 : angle 2.13360 ( 15) link_NAG-ASN : bond 0.00023 ( 5) link_NAG-ASN : angle 0.70900 ( 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 256 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 0.361 Fit side-chains REVERT: A 32 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8830 (ttpp) REVERT: A 287 ARG cc_start: 0.7952 (ptp-170) cc_final: 0.7488 (mtm180) REVERT: A 292 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7947 (mmtp) REVERT: A 391 MET cc_start: 0.4989 (tpp) cc_final: 0.4586 (tpt) REVERT: A 400 LYS cc_start: 0.8288 (mttm) cc_final: 0.7808 (mmmt) REVERT: A 402 ILE cc_start: 0.8480 (tt) cc_final: 0.8137 (mt) REVERT: B 109 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 129 THR cc_start: 0.8175 (m) cc_final: 0.7860 (p) REVERT: B 243 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.9104 (mtm) REVERT: B 287 ARG cc_start: 0.7912 (ptp-170) cc_final: 0.7491 (mtm180) REVERT: B 400 LYS cc_start: 0.8190 (mttm) cc_final: 0.7754 (mmmt) REVERT: B 401 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7025 (tpm170) REVERT: B 402 ILE cc_start: 0.8361 (tt) cc_final: 0.8069 (mt) REVERT: B 403 ASP cc_start: 0.8432 (t0) cc_final: 0.8167 (t0) REVERT: C 72 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8492 (mtp) REVERT: C 276 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9052 (m) REVERT: C 279 MET cc_start: 0.9219 (tpt) cc_final: 0.8897 (tpt) REVERT: C 400 LYS cc_start: 0.8366 (mttm) cc_final: 0.7912 (mmmt) REVERT: C 401 ARG cc_start: 0.7988 (tpt90) cc_final: 0.7135 (tpm-80) REVERT: C 402 ILE cc_start: 0.8598 (tt) cc_final: 0.8250 (mt) REVERT: D 83 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8759 (mt0) REVERT: D 212 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8113 (ptp-170) REVERT: D 287 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7487 (mtm180) REVERT: D 400 LYS cc_start: 0.8202 (mttm) cc_final: 0.7797 (mmmt) REVERT: D 401 ARG cc_start: 0.7547 (tpt-90) cc_final: 0.6783 (tpm-80) REVERT: D 402 ILE cc_start: 0.8491 (tt) cc_final: 0.8135 (mt) REVERT: E 72 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8839 (mmm) REVERT: E 83 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (mt0) REVERT: E 126 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: E 282 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: E 400 LYS cc_start: 0.8286 (mttm) cc_final: 0.7808 (mmmt) REVERT: E 401 ARG cc_start: 0.7798 (tpt90) cc_final: 0.6910 (tpm-80) REVERT: E 402 ILE cc_start: 0.8455 (tt) cc_final: 0.8132 (mt) outliers start: 66 outliers final: 31 residues processed: 236 average time/residue: 0.6263 time to fit residues: 160.8266 Evaluate side-chains 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 262 MET 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 173 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN 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 287 ARG Chi-restraints excluded: chain C residue 289 SER 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 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 126 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 284 SER 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: 1.9990 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.084286 restraints weight = 18344.703| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.95 r_work: 0.2700 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14490 Z= 0.223 Angle : 0.669 8.581 19680 Z= 0.345 Chirality : 0.048 0.249 2230 Planarity : 0.004 0.044 2430 Dihedral : 4.878 22.510 2095 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.50 % Allowed : 15.96 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1705 helix: 0.35 (0.22), residues: 585 sheet: 0.35 (0.26), residues: 395 loop : -1.09 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 147 TYR 0.015 0.002 TYR E 144 PHE 0.016 0.002 PHE C 115 TRP 0.008 0.002 TRP A 186 HIS 0.004 0.002 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00551 (14470) covalent geometry : angle 0.66157 (19630) SS BOND : bond 0.00749 ( 10) SS BOND : angle 2.42745 ( 20) hydrogen bonds : bond 0.03374 ( 600) hydrogen bonds : angle 4.03527 ( 1965) link_BETA1-4 : bond 0.00199 ( 5) link_BETA1-4 : angle 2.47136 ( 15) link_NAG-ASN : bond 0.00081 ( 5) link_NAG-ASN : angle 1.06622 ( 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 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 0.537 Fit side-chains REVERT: A 287 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.7511 (mtm180) REVERT: A 400 LYS cc_start: 0.8155 (mttm) cc_final: 0.7657 (mmmt) REVERT: A 402 ILE cc_start: 0.8471 (tt) cc_final: 0.8137 (mt) REVERT: B 206 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8258 (mmmm) REVERT: B 243 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9111 (mtm) REVERT: B 282 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: B 287 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7444 (mtm180) REVERT: B 400 LYS cc_start: 0.8153 (mttm) cc_final: 0.7717 (mmmt) REVERT: B 402 ILE cc_start: 0.8394 (tt) cc_final: 0.8092 (mt) REVERT: C 24 MET cc_start: 0.7407 (ttt) cc_final: 0.6955 (ttm) REVERT: C 72 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: C 279 MET cc_start: 0.9293 (tpt) cc_final: 0.8857 (tpt) REVERT: C 400 LYS cc_start: 0.8284 (mttm) cc_final: 0.7823 (mmmt) REVERT: C 402 ILE cc_start: 0.8609 (tt) cc_final: 0.8216 (mt) REVERT: D 28 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: D 83 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8873 (mt0) REVERT: D 212 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8087 (ptp-170) REVERT: D 287 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7480 (mtm180) REVERT: D 400 LYS cc_start: 0.8153 (mttm) cc_final: 0.7767 (mmmt) REVERT: D 401 ARG cc_start: 0.7546 (tpt-90) cc_final: 0.6763 (tpm-80) REVERT: D 402 ILE cc_start: 0.8479 (tt) cc_final: 0.8099 (mt) REVERT: E 72 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8904 (mmm) REVERT: E 83 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8951 (mt0) REVERT: E 126 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: E 282 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: E 400 LYS cc_start: 0.8229 (mttm) cc_final: 0.7739 (mmmt) REVERT: E 401 ARG cc_start: 0.7840 (tpt90) cc_final: 0.6935 (tpm-80) REVERT: E 402 ILE cc_start: 0.8433 (tt) cc_final: 0.8089 (mt) outliers start: 69 outliers final: 36 residues processed: 225 average time/residue: 0.6386 time to fit residues: 156.5499 Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 262 MET 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 173 GLU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 243 MET 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 98 SER 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 28 GLU 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 34 MET 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 126 GLU Chi-restraints excluded: chain E residue 204 ILE 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 303 MET 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: 0.8980 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087759 restraints weight = 18156.953| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.95 r_work: 0.2748 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3598 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= 0.119 Angle : 0.566 6.827 19680 Z= 0.294 Chirality : 0.044 0.263 2230 Planarity : 0.004 0.039 2430 Dihedral : 4.584 22.301 2095 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.26 % Allowed : 17.79 % Favored : 78.96 % 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: -0.19 (0.21), residues: 1705 helix: 0.67 (0.22), residues: 585 sheet: 0.45 (0.26), residues: 395 loop : -1.07 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 401 TYR 0.013 0.001 TYR B 317 PHE 0.009 0.001 PHE D 417 TRP 0.012 0.001 TRP E 422 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00279 (14470) covalent geometry : angle 0.56006 (19630) SS BOND : bond 0.00375 ( 10) SS BOND : angle 1.68702 ( 20) hydrogen bonds : bond 0.02756 ( 600) hydrogen bonds : angle 3.83229 ( 1965) link_BETA1-4 : bond 0.00176 ( 5) link_BETA1-4 : angle 2.20525 ( 15) link_NAG-ASN : bond 0.00018 ( 5) link_NAG-ASN : angle 0.66703 ( 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 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.553 Fit side-chains REVERT: A 212 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8040 (ptp-170) REVERT: A 287 ARG cc_start: 0.7927 (ptp-170) cc_final: 0.7452 (mtm180) REVERT: A 292 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8020 (mmtp) REVERT: A 400 LYS cc_start: 0.8176 (mttm) cc_final: 0.7663 (mmmt) REVERT: A 402 ILE cc_start: 0.8437 (tt) cc_final: 0.8064 (mt) REVERT: B 243 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.9098 (mtm) REVERT: B 287 ARG cc_start: 0.7926 (ptp-170) cc_final: 0.7416 (mtm180) REVERT: B 400 LYS cc_start: 0.8169 (mttm) cc_final: 0.7713 (mmmt) REVERT: B 401 ARG cc_start: 0.7568 (tpt-90) cc_final: 0.6838 (tpm-80) REVERT: B 402 ILE cc_start: 0.8384 (tt) cc_final: 0.8090 (mt) REVERT: C 400 LYS cc_start: 0.8270 (mttm) cc_final: 0.7858 (mmmt) REVERT: C 402 ILE cc_start: 0.8618 (tt) cc_final: 0.8238 (mt) REVERT: C 418 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8975 (m-40) REVERT: D 212 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8098 (ptp-170) REVERT: D 287 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7443 (mtm180) REVERT: D 400 LYS cc_start: 0.8184 (mttm) cc_final: 0.7747 (mmmt) REVERT: D 401 ARG cc_start: 0.7570 (tpt-90) cc_final: 0.6773 (tpm-80) REVERT: D 402 ILE cc_start: 0.8475 (tt) cc_final: 0.8070 (mt) REVERT: E 72 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8926 (mmm) REVERT: E 282 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: E 400 LYS cc_start: 0.8228 (mttm) cc_final: 0.7741 (mmmt) REVERT: E 401 ARG cc_start: 0.7845 (tpt90) cc_final: 0.6920 (tpm-80) REVERT: E 402 ILE cc_start: 0.8419 (tt) cc_final: 0.8063 (mt) outliers start: 50 outliers final: 21 residues processed: 206 average time/residue: 0.6708 time to fit residues: 149.7650 Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN 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 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 193 GLN Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 261 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.088606 restraints weight = 18177.826| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.93 r_work: 0.2788 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14490 Z= 0.104 Angle : 0.545 6.637 19680 Z= 0.283 Chirality : 0.044 0.285 2230 Planarity : 0.004 0.038 2430 Dihedral : 4.384 22.337 2095 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.21 % Allowed : 18.50 % Favored : 79.28 % 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: 0.04 (0.21), residues: 1705 helix: 1.01 (0.22), residues: 580 sheet: 0.54 (0.26), residues: 395 loop : -1.06 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 401 TYR 0.013 0.001 TYR A 317 PHE 0.009 0.001 PHE D 417 TRP 0.010 0.001 TRP D 84 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00239 (14470) covalent geometry : angle 0.54095 (19630) SS BOND : bond 0.00346 ( 10) SS BOND : angle 1.44611 ( 20) hydrogen bonds : bond 0.02592 ( 600) hydrogen bonds : angle 3.66955 ( 1965) link_BETA1-4 : bond 0.00210 ( 5) link_BETA1-4 : angle 2.04984 ( 15) link_NAG-ASN : bond 0.00036 ( 5) link_NAG-ASN : angle 0.61909 ( 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 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.590 Fit side-chains REVERT: A 212 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8028 (ptp-170) REVERT: A 287 ARG cc_start: 0.7909 (ptp-170) cc_final: 0.7434 (mtm180) REVERT: A 292 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8031 (mmtp) REVERT: A 400 LYS cc_start: 0.8262 (mttm) cc_final: 0.7725 (mmmt) REVERT: A 402 ILE cc_start: 0.8466 (tt) cc_final: 0.8066 (mt) REVERT: B 129 THR cc_start: 0.8032 (m) cc_final: 0.7708 (p) REVERT: B 243 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9016 (mtm) REVERT: B 282 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: B 287 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7447 (mtm180) REVERT: B 400 LYS cc_start: 0.8210 (mttm) cc_final: 0.7747 (mmmt) REVERT: B 401 ARG cc_start: 0.7587 (tpt-90) cc_final: 0.6817 (tpm-80) REVERT: B 402 ILE cc_start: 0.8360 (tt) cc_final: 0.8038 (mt) REVERT: B 403 ASP cc_start: 0.8465 (t0) cc_final: 0.8136 (t0) REVERT: C 400 LYS cc_start: 0.8341 (mttm) cc_final: 0.7917 (mmmt) REVERT: C 402 ILE cc_start: 0.8630 (tt) cc_final: 0.8250 (mt) REVERT: D 212 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8126 (ptp-170) REVERT: D 287 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7446 (mtm180) REVERT: D 400 LYS cc_start: 0.8251 (mttm) cc_final: 0.7807 (mmmt) REVERT: D 402 ILE cc_start: 0.8512 (tt) cc_final: 0.8059 (mt) REVERT: E 72 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8953 (mmm) REVERT: E 126 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: E 282 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: E 400 LYS cc_start: 0.8256 (mttm) cc_final: 0.7846 (mmmt) REVERT: E 401 ARG cc_start: 0.7812 (tpt90) cc_final: 0.6887 (tpm-80) REVERT: E 402 ILE cc_start: 0.8434 (tt) cc_final: 0.8053 (mt) outliers start: 34 outliers final: 20 residues processed: 201 average time/residue: 0.6971 time to fit residues: 151.8389 Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 212 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 63 SER 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 63 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 63 SER 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 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 261 ASN Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 412 LEU 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: 2.9990 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.090186 restraints weight = 18084.329| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.89 r_work: 0.2763 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14490 Z= 0.120 Angle : 0.560 7.030 19680 Z= 0.290 Chirality : 0.045 0.297 2230 Planarity : 0.004 0.035 2430 Dihedral : 4.357 22.724 2095 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.67 % Allowed : 18.57 % Favored : 78.76 % 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: 0.18 (0.21), residues: 1705 helix: 1.18 (0.22), residues: 580 sheet: 0.63 (0.27), residues: 395 loop : -1.03 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 401 TYR 0.013 0.001 TYR E 317 PHE 0.010 0.001 PHE C 115 TRP 0.009 0.001 TRP D 84 HIS 0.003 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00287 (14470) covalent geometry : angle 0.55501 (19630) SS BOND : bond 0.00397 ( 10) SS BOND : angle 1.54710 ( 20) hydrogen bonds : bond 0.02624 ( 600) hydrogen bonds : angle 3.66213 ( 1965) link_BETA1-4 : bond 0.00244 ( 5) link_BETA1-4 : angle 2.10441 ( 15) link_NAG-ASN : bond 0.00029 ( 5) link_NAG-ASN : angle 0.69151 ( 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 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.471 Fit side-chains REVERT: A 212 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8007 (ptp-170) REVERT: A 287 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.7445 (mtm180) REVERT: A 292 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8024 (mmtp) REVERT: A 400 LYS cc_start: 0.8309 (mttm) cc_final: 0.7784 (mmmt) REVERT: A 402 ILE cc_start: 0.8452 (tt) cc_final: 0.8024 (mt) REVERT: B 129 THR cc_start: 0.8044 (m) cc_final: 0.7718 (p) REVERT: B 243 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9026 (mtm) REVERT: B 282 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: B 287 ARG cc_start: 0.7910 (ptp-170) cc_final: 0.7407 (mtm180) REVERT: B 400 LYS cc_start: 0.8219 (mttm) cc_final: 0.7739 (mmmt) REVERT: B 402 ILE cc_start: 0.8369 (tt) cc_final: 0.8052 (mt) REVERT: B 403 ASP cc_start: 0.8465 (t0) cc_final: 0.8138 (t0) REVERT: C 400 LYS cc_start: 0.8356 (mttm) cc_final: 0.7928 (mmmt) REVERT: C 402 ILE cc_start: 0.8625 (tt) cc_final: 0.8225 (mt) REVERT: C 418 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8956 (m-40) REVERT: D 212 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8122 (ptp-170) REVERT: D 287 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7431 (mtm180) REVERT: D 400 LYS cc_start: 0.8235 (mttm) cc_final: 0.7798 (mmmt) REVERT: D 402 ILE cc_start: 0.8510 (tt) cc_final: 0.8027 (mt) REVERT: E 72 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8980 (mmm) REVERT: E 126 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: E 282 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: E 400 LYS cc_start: 0.8261 (mttm) cc_final: 0.7847 (mmmt) REVERT: E 401 ARG cc_start: 0.7828 (tpt90) cc_final: 0.6886 (tpm-80) REVERT: E 402 ILE cc_start: 0.8441 (tt) cc_final: 0.8034 (mt) outliers start: 41 outliers final: 24 residues processed: 202 average time/residue: 0.6788 time to fit residues: 148.4610 Evaluate side-chains 201 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 212 ARG Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 243 MET 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 63 SER 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 56 THR 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 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 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 282 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 ARG Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.088974 restraints weight = 18251.634| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.96 r_work: 0.2790 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3817 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= 0.105 Angle : 0.540 6.547 19680 Z= 0.280 Chirality : 0.044 0.286 2230 Planarity : 0.003 0.035 2430 Dihedral : 4.272 22.691 2095 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.41 % Allowed : 19.09 % Favored : 78.50 % 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: 0.34 (0.21), residues: 1705 helix: 1.40 (0.22), residues: 580 sheet: 0.67 (0.27), residues: 395 loop : -0.99 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 401 TYR 0.013 0.001 TYR D 317 PHE 0.009 0.001 PHE D 417 TRP 0.009 0.001 TRP D 84 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00246 (14470) covalent geometry : angle 0.53547 (19630) SS BOND : bond 0.00325 ( 10) SS BOND : angle 1.41155 ( 20) hydrogen bonds : bond 0.02505 ( 600) hydrogen bonds : angle 3.59883 ( 1965) link_BETA1-4 : bond 0.00233 ( 5) link_BETA1-4 : angle 2.03240 ( 15) link_NAG-ASN : bond 0.00048 ( 5) link_NAG-ASN : angle 0.62428 ( 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 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.482 Fit side-chains REVERT: A 212 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8058 (ptp-170) REVERT: A 287 ARG cc_start: 0.7916 (ptp-170) cc_final: 0.7448 (mtm180) REVERT: A 292 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8050 (mmtp) REVERT: A 400 LYS cc_start: 0.8322 (mttm) cc_final: 0.7787 (mmmt) REVERT: A 402 ILE cc_start: 0.8448 (tt) cc_final: 0.7977 (mt) REVERT: B 129 THR cc_start: 0.8032 (m) cc_final: 0.7701 (p) REVERT: B 282 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: B 287 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7427 (mtm180) REVERT: B 400 LYS cc_start: 0.8248 (mttm) cc_final: 0.7770 (mmmt) REVERT: B 402 ILE cc_start: 0.8371 (tt) cc_final: 0.8032 (mt) REVERT: B 403 ASP cc_start: 0.8442 (t0) cc_final: 0.8145 (t0) REVERT: C 400 LYS cc_start: 0.8377 (mttm) cc_final: 0.7941 (mmmt) REVERT: C 402 ILE cc_start: 0.8620 (tt) cc_final: 0.8213 (mt) REVERT: C 418 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8940 (m-40) REVERT: D 212 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8148 (ptp-170) REVERT: D 287 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7482 (mtm180) REVERT: D 400 LYS cc_start: 0.8251 (mttm) cc_final: 0.7810 (mmmt) REVERT: D 402 ILE cc_start: 0.8527 (tt) cc_final: 0.8008 (mt) REVERT: E 72 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8951 (mmm) REVERT: E 126 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: E 400 LYS cc_start: 0.8289 (mttm) cc_final: 0.7877 (mmmt) REVERT: E 401 ARG cc_start: 0.7839 (tpt90) cc_final: 0.6904 (tpm-80) REVERT: E 402 ILE cc_start: 0.8426 (tt) cc_final: 0.8006 (mt) outliers start: 37 outliers final: 24 residues processed: 202 average time/residue: 0.6955 time to fit residues: 151.8742 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 282 GLN 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 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 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 126 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.087164 restraints weight = 18267.947| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.92 r_work: 0.2739 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14490 Z= 0.157 Angle : 0.592 7.431 19680 Z= 0.306 Chirality : 0.045 0.277 2230 Planarity : 0.004 0.036 2430 Dihedral : 4.422 22.792 2095 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.15 % Allowed : 19.22 % 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: 0.37 (0.21), residues: 1705 helix: 1.38 (0.22), residues: 580 sheet: 0.73 (0.27), residues: 395 loop : -0.96 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 401 TYR 0.013 0.001 TYR E 317 PHE 0.013 0.001 PHE C 115 TRP 0.007 0.001 TRP D 84 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00382 (14470) covalent geometry : angle 0.58598 (19630) SS BOND : bond 0.00498 ( 10) SS BOND : angle 1.72488 ( 20) hydrogen bonds : bond 0.02783 ( 600) hydrogen bonds : angle 3.71785 ( 1965) link_BETA1-4 : bond 0.00223 ( 5) link_BETA1-4 : angle 2.24683 ( 15) link_NAG-ASN : bond 0.00047 ( 5) link_NAG-ASN : angle 0.84623 ( 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 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.530 Fit side-chains REVERT: A 212 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8019 (ptp-170) REVERT: A 287 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7411 (mtm180) REVERT: A 292 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8049 (mmtp) REVERT: A 400 LYS cc_start: 0.8227 (mttm) cc_final: 0.7682 (mmmt) REVERT: A 402 ILE cc_start: 0.8410 (tt) cc_final: 0.7964 (mt) REVERT: B 129 THR cc_start: 0.8113 (m) cc_final: 0.7771 (p) REVERT: B 243 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.9092 (mtm) REVERT: B 282 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: B 287 ARG cc_start: 0.7935 (ptp-170) cc_final: 0.7456 (mtm180) REVERT: B 400 LYS cc_start: 0.8202 (mttm) cc_final: 0.7729 (mmmt) REVERT: B 402 ILE cc_start: 0.8360 (tt) cc_final: 0.8029 (mt) REVERT: C 400 LYS cc_start: 0.8334 (mttm) cc_final: 0.7895 (mmmt) REVERT: C 402 ILE cc_start: 0.8630 (tt) cc_final: 0.8202 (mt) REVERT: C 418 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8979 (m-40) REVERT: D 212 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8119 (ptp-170) REVERT: D 287 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7470 (mtm180) REVERT: D 400 LYS cc_start: 0.8196 (mttm) cc_final: 0.7741 (mmmt) REVERT: D 402 ILE cc_start: 0.8476 (tt) cc_final: 0.7962 (mt) REVERT: E 72 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8961 (mmm) REVERT: E 400 LYS cc_start: 0.8241 (mttm) cc_final: 0.7820 (mmmt) REVERT: E 401 ARG cc_start: 0.7847 (tpt90) cc_final: 0.6872 (tpm-80) REVERT: E 402 ILE cc_start: 0.8446 (tt) cc_final: 0.8008 (mt) outliers start: 33 outliers final: 26 residues processed: 200 average time/residue: 0.6714 time to fit residues: 145.6774 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 282 GLN 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 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 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 134 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.087175 restraints weight = 18268.904| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.90 r_work: 0.2747 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3844 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= 0.142 Angle : 0.577 7.410 19680 Z= 0.299 Chirality : 0.045 0.271 2230 Planarity : 0.004 0.034 2430 Dihedral : 4.421 22.642 2095 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.21 % Allowed : 19.54 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.21), residues: 1705 helix: 1.41 (0.22), residues: 580 sheet: 0.73 (0.27), residues: 395 loop : -0.91 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 401 TYR 0.013 0.001 TYR E 317 PHE 0.011 0.001 PHE C 115 TRP 0.008 0.001 TRP C 84 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00342 (14470) covalent geometry : angle 0.57165 (19630) SS BOND : bond 0.00436 ( 10) SS BOND : angle 1.63562 ( 20) hydrogen bonds : bond 0.02713 ( 600) hydrogen bonds : angle 3.71172 ( 1965) link_BETA1-4 : bond 0.00222 ( 5) link_BETA1-4 : angle 2.25256 ( 15) link_NAG-ASN : bond 0.00027 ( 5) link_NAG-ASN : angle 0.76287 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4641.61 seconds wall clock time: 79 minutes 42.86 seconds (4782.86 seconds total)