Starting phenix.real_space_refine on Wed Mar 4 14:16:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2o_26317/03_2026/7u2o_26317_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2o_26317/03_2026/7u2o_26317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u2o_26317/03_2026/7u2o_26317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2o_26317/03_2026/7u2o_26317.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2o_26317/03_2026/7u2o_26317_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2o_26317/03_2026/7u2o_26317_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.220 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 100 5.16 5 C 9145 2.51 5 N 2265 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s 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: 14075 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, J, N, R, V Time building chain proxies: 2.39, per 1000 atoms: 0.17 Number of scatterers: 14075 At special positions: 0 Unit cell: (105.537, 107.199, 132.129, 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 100 16.00 O 2565 8.00 N 2265 7.00 C 9145 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=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 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 F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG J 1 " - " ASN B 54 " " NAG N 1 " - " ASN C 54 " " NAG R 1 " - " ASN D 54 " " NAG V 1 " - " ASN E 54 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 636.0 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 38.7% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.842A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.603A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 4.214A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 426 removed outlier: 4.139A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix Processing helix chain 'B' and resid 25 through 34 removed outlier: 3.843A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.602A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 4.213A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 426 removed outlier: 4.139A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.841A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.602A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.872A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 4.213A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 426 removed outlier: 4.140A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix Processing helix chain 'D' and resid 25 through 34 removed outlier: 3.842A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 4.213A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 426 removed outlier: 4.139A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix Processing helix chain 'E' and resid 25 through 34 removed outlier: 3.843A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.602A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.871A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 4.214A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 426 removed outlier: 4.138A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 7.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 4.638A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU A 233 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.112A 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 122 through 124 removed outlier: 7.205A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 removed outlier: 4.639A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU B 233 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.111A 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 122 through 124 removed outlier: 7.205A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 removed outlier: 4.638A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU C 233 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.111A 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 122 through 124 removed outlier: 7.206A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 136 removed outlier: 7.206A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 removed outlier: 4.639A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU D 233 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.111A 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 122 through 124 removed outlier: 7.205A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 132 through 136 removed outlier: 7.205A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 4.638A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU E 233 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 7.112A 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 217 750 hydrogen bonds defined for protein. 2190 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: 2.30 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4340 1.34 - 1.47: 3687 1.47 - 1.60: 6223 1.60 - 1.72: 0 1.72 - 1.85: 165 Bond restraints: 14415 Sorted by residual: bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 BMA V 3 " pdb=" C2 BMA V 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 14410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 19057 2.22 - 4.44: 451 4.44 - 6.66: 62 6.66 - 8.88: 10 8.88 - 11.10: 5 Bond angle restraints: 19585 Sorted by residual: angle pdb=" O04 L2L C 600 " pdb=" S03 L2L C 600 " pdb=" O05 L2L C 600 " ideal model delta sigma weight residual 112.97 101.87 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O04 L2L A 600 " pdb=" S03 L2L A 600 " pdb=" O05 L2L A 600 " ideal model delta sigma weight residual 112.97 101.89 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L B 600 " pdb=" S03 L2L B 600 " pdb=" O05 L2L B 600 " ideal model delta sigma weight residual 112.97 101.89 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L D 600 " pdb=" S03 L2L D 600 " pdb=" O05 L2L D 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L E 600 " pdb=" S03 L2L E 600 " pdb=" O05 L2L E 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 ... (remaining 19580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 8540 22.49 - 44.98: 200 44.98 - 67.47: 10 67.47 - 89.97: 40 89.97 - 112.46: 20 Dihedral angle restraints: 8810 sinusoidal: 3695 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.18 50.82 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.19 50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.20 50.80 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1853 0.054 - 0.107: 345 0.107 - 0.161: 52 0.161 - 0.215: 0 0.215 - 0.269: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2257 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 151 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL B 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 151 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C VAL A 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 151 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C VAL D 151 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL D 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 152 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 287 2.66 - 3.22: 14540 3.22 - 3.78: 21205 3.78 - 4.34: 30758 4.34 - 4.90: 47876 Nonbonded interactions: 114666 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.102 3.040 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.102 3.040 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.102 3.040 ... (remaining 114661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } 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: 2.830 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.007 0.043 14440 Z= 0.300 Angle : 0.845 11.097 19650 Z= 0.457 Chirality : 0.048 0.269 2260 Planarity : 0.005 0.051 2425 Dihedral : 13.058 112.457 5460 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 37.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.16), residues: 1710 helix: -3.68 (0.14), residues: 585 sheet: -3.06 (0.18), residues: 390 loop : -2.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 407 TYR 0.017 0.003 TYR C 144 PHE 0.017 0.002 PHE C 309 TRP 0.016 0.002 TRP B 422 HIS 0.003 0.002 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00653 (14415) covalent geometry : angle 0.83702 (19585) SS BOND : bond 0.00636 ( 10) SS BOND : angle 2.71096 ( 20) hydrogen bonds : bond 0.30265 ( 655) hydrogen bonds : angle 10.48375 ( 2190) link_BETA1-4 : bond 0.00181 ( 10) link_BETA1-4 : angle 1.77754 ( 30) link_NAG-ASN : bond 0.00183 ( 5) link_NAG-ASN : angle 1.94028 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9032 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: A 104 SER cc_start: 0.8212 (p) cc_final: 0.7601 (t) REVERT: A 127 VAL cc_start: 0.9007 (t) cc_final: 0.8648 (p) REVERT: A 206 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8281 (mttp) REVERT: A 295 TYR cc_start: 0.8847 (p90) cc_final: 0.8646 (p90) REVERT: B 105 MET cc_start: 0.6200 (mmp) cc_final: 0.5754 (mmp) REVERT: B 127 VAL cc_start: 0.9003 (t) cc_final: 0.8655 (p) REVERT: B 206 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8231 (mttp) REVERT: B 239 TYR cc_start: 0.8761 (m-80) cc_final: 0.8139 (m-80) REVERT: B 295 TYR cc_start: 0.8867 (p90) cc_final: 0.8567 (p90) REVERT: C 43 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8525 (mtm-85) REVERT: C 104 SER cc_start: 0.8295 (p) cc_final: 0.7557 (p) REVERT: C 105 MET cc_start: 0.6121 (mmp) cc_final: 0.5865 (mmp) REVERT: C 127 VAL cc_start: 0.9038 (t) cc_final: 0.8621 (p) REVERT: C 137 SER cc_start: 0.9171 (m) cc_final: 0.8472 (p) REVERT: C 206 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8395 (mttm) REVERT: C 210 ASP cc_start: 0.8513 (m-30) cc_final: 0.8156 (m-30) REVERT: C 239 TYR cc_start: 0.8718 (m-80) cc_final: 0.8508 (m-80) REVERT: D 43 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8758 (mtm-85) REVERT: D 104 SER cc_start: 0.8210 (p) cc_final: 0.7547 (t) REVERT: D 105 MET cc_start: 0.6113 (mmp) cc_final: 0.5834 (mmp) REVERT: D 127 VAL cc_start: 0.9005 (t) cc_final: 0.8629 (p) REVERT: D 206 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8359 (mttm) REVERT: D 299 ILE cc_start: 0.9091 (tp) cc_final: 0.8874 (tp) REVERT: E 43 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: E 104 SER cc_start: 0.8121 (p) cc_final: 0.7090 (p) REVERT: E 127 VAL cc_start: 0.8846 (t) cc_final: 0.8524 (p) REVERT: E 130 ASP cc_start: 0.8342 (m-30) cc_final: 0.8110 (m-30) REVERT: E 206 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8368 (mttp) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.1265 time to fit residues: 100.1361 Evaluate side-chains 386 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 82 GLN B 77 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN D 77 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN E 77 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127183 restraints weight = 20490.048| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.17 r_work: 0.3316 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14440 Z= 0.186 Angle : 0.800 7.175 19650 Z= 0.412 Chirality : 0.050 0.277 2260 Planarity : 0.005 0.046 2425 Dihedral : 11.364 72.079 2195 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.78 % Allowed : 11.39 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.18), residues: 1710 helix: -1.43 (0.19), residues: 595 sheet: -1.96 (0.21), residues: 390 loop : -2.03 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 43 TYR 0.021 0.002 TYR A 421 PHE 0.024 0.002 PHE D 322 TRP 0.010 0.001 TRP D 422 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00410 (14415) covalent geometry : angle 0.78369 (19585) SS BOND : bond 0.00799 ( 10) SS BOND : angle 2.24587 ( 20) hydrogen bonds : bond 0.05983 ( 655) hydrogen bonds : angle 6.04700 ( 2190) link_BETA1-4 : bond 0.00633 ( 10) link_BETA1-4 : angle 3.05469 ( 30) link_NAG-ASN : bond 0.00366 ( 5) link_NAG-ASN : angle 3.19025 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 477 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7804 (tptt) REVERT: A 43 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8664 (mtm-85) REVERT: A 96 ASP cc_start: 0.8309 (m-30) cc_final: 0.8080 (m-30) REVERT: A 133 LEU cc_start: 0.8733 (tp) cc_final: 0.8435 (tt) REVERT: A 159 LYS cc_start: 0.8664 (mttt) cc_final: 0.8392 (mtmt) REVERT: A 206 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8342 (mttp) REVERT: A 227 GLU cc_start: 0.8737 (pt0) cc_final: 0.8491 (pt0) REVERT: B 32 LYS cc_start: 0.8589 (pttp) cc_final: 0.7920 (tptt) REVERT: B 104 SER cc_start: 0.8586 (p) cc_final: 0.8127 (t) REVERT: B 105 MET cc_start: 0.7194 (mmp) cc_final: 0.6838 (mmp) REVERT: B 133 LEU cc_start: 0.8715 (tp) cc_final: 0.8401 (tt) REVERT: B 206 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8424 (mttp) REVERT: B 208 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 239 TYR cc_start: 0.8683 (m-80) cc_final: 0.8429 (m-80) REVERT: C 32 LYS cc_start: 0.8446 (pttp) cc_final: 0.7711 (tptt) REVERT: C 105 MET cc_start: 0.6985 (mmp) cc_final: 0.6612 (mmp) REVERT: C 133 LEU cc_start: 0.8779 (tp) cc_final: 0.8425 (tt) REVERT: C 137 SER cc_start: 0.9002 (m) cc_final: 0.8155 (p) REVERT: C 206 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8426 (mttp) REVERT: C 210 ASP cc_start: 0.8704 (m-30) cc_final: 0.8481 (m-30) REVERT: C 282 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8435 (mm-40) REVERT: D 43 ARG cc_start: 0.9184 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: D 69 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: D 105 MET cc_start: 0.7143 (mmp) cc_final: 0.6751 (mmp) REVERT: D 133 LEU cc_start: 0.8736 (tp) cc_final: 0.8422 (tt) REVERT: D 159 LYS cc_start: 0.8721 (mttt) cc_final: 0.8484 (mtpt) REVERT: D 165 VAL cc_start: 0.9324 (t) cc_final: 0.9122 (p) REVERT: D 206 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8533 (mttp) REVERT: E 32 LYS cc_start: 0.8486 (pttp) cc_final: 0.7730 (tptt) REVERT: E 43 ARG cc_start: 0.9196 (mtm-85) cc_final: 0.8769 (mtm-85) REVERT: E 96 ASP cc_start: 0.8487 (m-30) cc_final: 0.8247 (m-30) REVERT: E 105 MET cc_start: 0.6863 (mmp) cc_final: 0.6657 (mmp) REVERT: E 133 LEU cc_start: 0.8550 (tp) cc_final: 0.8214 (tt) REVERT: E 159 LYS cc_start: 0.8682 (mttt) cc_final: 0.8442 (mtpt) REVERT: E 206 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8600 (mttp) REVERT: E 248 LEU cc_start: 0.8529 (tt) cc_final: 0.8326 (tp) outliers start: 42 outliers final: 30 residues processed: 488 average time/residue: 0.1074 time to fit residues: 77.5371 Evaluate side-chains 441 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 409 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 85 ASN B 85 ASN B 231 HIS C 47 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 231 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124240 restraints weight = 20837.577| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.19 r_work: 0.3278 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14440 Z= 0.228 Angle : 0.790 15.003 19650 Z= 0.401 Chirality : 0.051 0.484 2260 Planarity : 0.005 0.046 2425 Dihedral : 9.046 53.063 2195 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.30 % Allowed : 12.25 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.19), residues: 1710 helix: -0.41 (0.20), residues: 595 sheet: -1.11 (0.24), residues: 345 loop : -1.90 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 229 TYR 0.020 0.002 TYR A 421 PHE 0.024 0.002 PHE A 322 TRP 0.010 0.002 TRP D 422 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00523 (14415) covalent geometry : angle 0.76550 (19585) SS BOND : bond 0.01243 ( 10) SS BOND : angle 2.30504 ( 20) hydrogen bonds : bond 0.04989 ( 655) hydrogen bonds : angle 5.46134 ( 2190) link_BETA1-4 : bond 0.00433 ( 10) link_BETA1-4 : angle 3.29154 ( 30) link_NAG-ASN : bond 0.01289 ( 5) link_NAG-ASN : angle 4.86892 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 398 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7845 (tptt) REVERT: A 43 ARG cc_start: 0.9149 (mtm-85) cc_final: 0.8655 (mtm-85) REVERT: A 133 LEU cc_start: 0.8783 (tp) cc_final: 0.8480 (tt) REVERT: A 159 LYS cc_start: 0.8706 (mttt) cc_final: 0.8503 (mtpt) REVERT: A 206 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8333 (mttp) REVERT: A 227 GLU cc_start: 0.8711 (pt0) cc_final: 0.8510 (pt0) REVERT: A 240 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 32 LYS cc_start: 0.8618 (pttp) cc_final: 0.7917 (tptt) REVERT: B 133 LEU cc_start: 0.8767 (tp) cc_final: 0.8512 (tt) REVERT: B 206 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8435 (mttp) REVERT: B 227 GLU cc_start: 0.8805 (pt0) cc_final: 0.8512 (pt0) REVERT: B 239 TYR cc_start: 0.8770 (m-80) cc_final: 0.8348 (m-80) REVERT: B 295 TYR cc_start: 0.8998 (p90) cc_final: 0.8760 (p90) REVERT: C 32 LYS cc_start: 0.8499 (pttp) cc_final: 0.7763 (tptt) REVERT: C 107 ASP cc_start: 0.8627 (t0) cc_final: 0.8400 (m-30) REVERT: C 133 LEU cc_start: 0.8932 (tp) cc_final: 0.8682 (tt) REVERT: C 159 LYS cc_start: 0.8706 (mttt) cc_final: 0.8503 (mtpt) REVERT: C 210 ASP cc_start: 0.8742 (m-30) cc_final: 0.8525 (m-30) REVERT: D 54 ASN cc_start: 0.8305 (m-40) cc_final: 0.7715 (p0) REVERT: D 159 LYS cc_start: 0.8797 (mttt) cc_final: 0.8540 (mtpt) REVERT: D 206 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8611 (mttm) REVERT: D 282 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8393 (mm-40) REVERT: E 43 ARG cc_start: 0.9180 (mtm-85) cc_final: 0.8926 (mtm-85) REVERT: E 105 MET cc_start: 0.7089 (mmp) cc_final: 0.6737 (mmp) REVERT: E 159 LYS cc_start: 0.8738 (mttt) cc_final: 0.8497 (mtpt) outliers start: 80 outliers final: 63 residues processed: 422 average time/residue: 0.1035 time to fit residues: 66.3619 Evaluate side-chains 434 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 369 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122258 restraints weight = 21062.536| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.24 r_work: 0.3261 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14440 Z= 0.238 Angle : 0.823 18.046 19650 Z= 0.415 Chirality : 0.057 0.786 2260 Planarity : 0.005 0.045 2425 Dihedral : 7.600 46.724 2195 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.89 % Allowed : 13.38 % Favored : 80.73 % 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: -1.40 (0.19), residues: 1710 helix: 0.14 (0.21), residues: 595 sheet: -0.65 (0.26), residues: 335 loop : -1.90 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.019 0.002 TYR A 421 PHE 0.025 0.002 PHE A 322 TRP 0.010 0.001 TRP E 186 HIS 0.005 0.002 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00549 (14415) covalent geometry : angle 0.77076 (19585) SS BOND : bond 0.00956 ( 10) SS BOND : angle 2.64061 ( 20) hydrogen bonds : bond 0.04797 ( 655) hydrogen bonds : angle 5.22002 ( 2190) link_BETA1-4 : bond 0.00357 ( 10) link_BETA1-4 : angle 3.61592 ( 30) link_NAG-ASN : bond 0.00991 ( 5) link_NAG-ASN : angle 8.71118 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 385 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8771 (tp) cc_final: 0.8523 (tt) REVERT: A 206 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8342 (mttp) REVERT: A 240 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8788 (mp) REVERT: A 282 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8527 (mm-40) REVERT: B 32 LYS cc_start: 0.8618 (pttp) cc_final: 0.7906 (tptt) REVERT: B 133 LEU cc_start: 0.8767 (tp) cc_final: 0.8520 (tt) REVERT: B 206 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8557 (mttm) REVERT: B 239 TYR cc_start: 0.8768 (m-80) cc_final: 0.8334 (m-80) REVERT: B 240 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8773 (mp) REVERT: B 243 MET cc_start: 0.8875 (mtt) cc_final: 0.8647 (mtt) REVERT: C 133 LEU cc_start: 0.8839 (tp) cc_final: 0.8608 (tt) REVERT: C 159 LYS cc_start: 0.8737 (mttt) cc_final: 0.8500 (mtpt) REVERT: D 159 LYS cc_start: 0.8803 (mttt) cc_final: 0.8539 (mtpt) REVERT: D 179 MET cc_start: 0.8754 (mmm) cc_final: 0.8545 (mmm) REVERT: D 206 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8669 (mttm) REVERT: D 240 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8842 (mp) REVERT: D 248 LEU cc_start: 0.8439 (tt) cc_final: 0.8212 (tp) REVERT: E 159 LYS cc_start: 0.8757 (mttt) cc_final: 0.8495 (mtpt) REVERT: E 282 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8469 (mm-40) outliers start: 89 outliers final: 74 residues processed: 415 average time/residue: 0.1011 time to fit residues: 64.4751 Evaluate side-chains 445 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 368 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN C 231 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122268 restraints weight = 20964.575| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.23 r_work: 0.3263 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14440 Z= 0.222 Angle : 0.789 10.715 19650 Z= 0.401 Chirality : 0.051 0.356 2260 Planarity : 0.005 0.048 2425 Dihedral : 6.936 56.563 2195 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.03 % Allowed : 15.36 % Favored : 78.61 % 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: -1.02 (0.20), residues: 1710 helix: 0.55 (0.22), residues: 595 sheet: -0.63 (0.24), residues: 390 loop : -1.71 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.019 0.002 TYR A 421 PHE 0.027 0.002 PHE A 322 TRP 0.011 0.001 TRP E 186 HIS 0.004 0.002 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00512 (14415) covalent geometry : angle 0.74618 (19585) SS BOND : bond 0.00735 ( 10) SS BOND : angle 3.37958 ( 20) hydrogen bonds : bond 0.04526 ( 655) hydrogen bonds : angle 5.08223 ( 2190) link_BETA1-4 : bond 0.00641 ( 10) link_BETA1-4 : angle 2.64860 ( 30) link_NAG-ASN : bond 0.01134 ( 5) link_NAG-ASN : angle 7.63657 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 385 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8765 (tp) cc_final: 0.8464 (tt) REVERT: A 206 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8357 (mttp) REVERT: A 240 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8775 (mp) REVERT: B 133 LEU cc_start: 0.8756 (tp) cc_final: 0.8549 (tt) REVERT: B 206 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8566 (mttm) REVERT: B 239 TYR cc_start: 0.8742 (m-80) cc_final: 0.8303 (m-80) REVERT: B 240 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8755 (mp) REVERT: B 243 MET cc_start: 0.8919 (mtt) cc_final: 0.8707 (mtt) REVERT: B 282 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8461 (mm-40) REVERT: C 133 LEU cc_start: 0.8842 (tp) cc_final: 0.8621 (tt) REVERT: C 159 LYS cc_start: 0.8767 (mttt) cc_final: 0.8491 (mtpt) REVERT: C 282 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8606 (mm-40) REVERT: D 133 LEU cc_start: 0.8828 (tp) cc_final: 0.8574 (tt) REVERT: D 159 LYS cc_start: 0.8794 (mttt) cc_final: 0.8512 (mtpt) REVERT: D 206 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8646 (mttm) REVERT: D 248 LEU cc_start: 0.8417 (tt) cc_final: 0.8196 (tp) REVERT: E 159 LYS cc_start: 0.8777 (mttt) cc_final: 0.8502 (mtpt) REVERT: E 240 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8749 (mp) outliers start: 91 outliers final: 76 residues processed: 419 average time/residue: 0.0990 time to fit residues: 64.6269 Evaluate side-chains 450 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 371 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 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 171 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126537 restraints weight = 20710.890| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.23 r_work: 0.3294 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14440 Z= 0.154 Angle : 0.775 14.580 19650 Z= 0.388 Chirality : 0.050 0.381 2260 Planarity : 0.004 0.042 2425 Dihedral : 6.806 54.075 2195 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.23 % Allowed : 17.35 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.79 (0.20), residues: 1710 helix: 0.76 (0.22), residues: 595 sheet: -0.25 (0.26), residues: 340 loop : -1.69 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 229 TYR 0.018 0.002 TYR A 421 PHE 0.027 0.001 PHE A 322 TRP 0.011 0.001 TRP C 186 HIS 0.002 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00345 (14415) covalent geometry : angle 0.72258 (19585) SS BOND : bond 0.00524 ( 10) SS BOND : angle 3.76890 ( 20) hydrogen bonds : bond 0.04285 ( 655) hydrogen bonds : angle 4.89388 ( 2190) link_BETA1-4 : bond 0.00897 ( 10) link_BETA1-4 : angle 2.66780 ( 30) link_NAG-ASN : bond 0.01255 ( 5) link_NAG-ASN : angle 8.42893 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8705 (tp) cc_final: 0.8416 (tt) REVERT: A 206 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8485 (mtpp) REVERT: A 240 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 282 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8535 (mm-40) REVERT: B 107 ASP cc_start: 0.8485 (t0) cc_final: 0.8282 (m-30) REVERT: B 133 LEU cc_start: 0.8712 (tp) cc_final: 0.8498 (tt) REVERT: B 206 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8543 (mttm) REVERT: B 239 TYR cc_start: 0.8602 (m-80) cc_final: 0.8019 (m-80) REVERT: B 240 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8678 (mp) REVERT: B 243 MET cc_start: 0.8899 (mtt) cc_final: 0.8685 (mtt) REVERT: B 282 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8480 (mm-40) REVERT: C 133 LEU cc_start: 0.8790 (tp) cc_final: 0.8584 (tt) REVERT: C 159 LYS cc_start: 0.8754 (mttt) cc_final: 0.8485 (mtpt) REVERT: C 163 MET cc_start: 0.8982 (mtm) cc_final: 0.8757 (mtm) REVERT: C 236 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6460 (tpp) REVERT: C 240 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8585 (mp) REVERT: C 282 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8575 (mm-40) REVERT: D 133 LEU cc_start: 0.8762 (tp) cc_final: 0.8509 (tt) REVERT: D 159 LYS cc_start: 0.8786 (mttt) cc_final: 0.8506 (mtpt) REVERT: D 206 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8646 (mttm) REVERT: D 248 LEU cc_start: 0.8433 (tt) cc_final: 0.8229 (tp) REVERT: D 282 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8429 (mm-40) REVERT: E 28 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6412 (mp0) REVERT: E 107 ASP cc_start: 0.8566 (t0) cc_final: 0.8281 (m-30) REVERT: E 159 LYS cc_start: 0.8773 (mttt) cc_final: 0.8494 (mtpt) REVERT: E 240 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8706 (mp) REVERT: E 250 ILE cc_start: 0.8476 (mm) cc_final: 0.8163 (mt) REVERT: E 282 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8542 (mm-40) outliers start: 79 outliers final: 64 residues processed: 418 average time/residue: 0.0957 time to fit residues: 62.1569 Evaluate side-chains 442 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 373 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 153 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126331 restraints weight = 20865.088| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.17 r_work: 0.3186 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14440 Z= 0.158 Angle : 0.761 13.406 19650 Z= 0.381 Chirality : 0.049 0.371 2260 Planarity : 0.004 0.038 2425 Dihedral : 6.606 56.063 2195 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.17 % Allowed : 17.88 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.66 (0.20), residues: 1710 helix: 0.88 (0.23), residues: 595 sheet: -0.22 (0.26), residues: 345 loop : -1.61 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.017 0.002 TYR A 421 PHE 0.029 0.001 PHE D 414 TRP 0.013 0.001 TRP D 186 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00361 (14415) covalent geometry : angle 0.71542 (19585) SS BOND : bond 0.00553 ( 10) SS BOND : angle 3.43331 ( 20) hydrogen bonds : bond 0.04202 ( 655) hydrogen bonds : angle 4.79290 ( 2190) link_BETA1-4 : bond 0.00734 ( 10) link_BETA1-4 : angle 2.16551 ( 30) link_NAG-ASN : bond 0.01055 ( 5) link_NAG-ASN : angle 8.01836 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 383 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8651 (ppp) cc_final: 0.7650 (ptt) REVERT: A 107 ASP cc_start: 0.8852 (m-30) cc_final: 0.8634 (t0) REVERT: A 133 LEU cc_start: 0.8639 (tp) cc_final: 0.8320 (tt) REVERT: A 206 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8397 (mtpp) REVERT: A 240 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8649 (mp) REVERT: A 282 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8561 (mm-40) REVERT: B 24 MET cc_start: 0.6626 (pmm) cc_final: 0.6397 (pmm) REVERT: B 133 LEU cc_start: 0.8628 (tp) cc_final: 0.8395 (tt) REVERT: B 206 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8311 (mttp) REVERT: B 239 TYR cc_start: 0.8615 (m-80) cc_final: 0.8070 (m-80) REVERT: B 240 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 243 MET cc_start: 0.8995 (mtt) cc_final: 0.8781 (mtt) REVERT: B 282 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8529 (mm-40) REVERT: C 133 LEU cc_start: 0.8648 (tp) cc_final: 0.8426 (tt) REVERT: C 159 LYS cc_start: 0.8683 (mttt) cc_final: 0.8411 (mtpt) REVERT: C 163 MET cc_start: 0.9015 (mtm) cc_final: 0.8765 (mtm) REVERT: C 236 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6260 (tpp) REVERT: C 240 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8545 (mp) REVERT: D 105 MET cc_start: 0.8548 (ppp) cc_final: 0.7490 (ptt) REVERT: D 133 LEU cc_start: 0.8668 (tp) cc_final: 0.8406 (tt) REVERT: D 159 LYS cc_start: 0.8716 (mttt) cc_final: 0.8412 (mtpt) REVERT: D 206 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8573 (mttm) REVERT: E 105 MET cc_start: 0.8548 (ppp) cc_final: 0.7645 (ptm) REVERT: E 159 LYS cc_start: 0.8713 (mttt) cc_final: 0.8404 (mtpt) REVERT: E 240 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8626 (mp) REVERT: E 250 ILE cc_start: 0.8287 (mm) cc_final: 0.7973 (mt) REVERT: E 282 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8519 (mm-40) outliers start: 78 outliers final: 59 residues processed: 413 average time/residue: 0.0893 time to fit residues: 58.1174 Evaluate side-chains 437 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 149 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN E 171 GLN E 235 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126615 restraints weight = 20986.817| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.23 r_work: 0.3194 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14440 Z= 0.152 Angle : 0.763 12.271 19650 Z= 0.381 Chirality : 0.049 0.364 2260 Planarity : 0.004 0.035 2425 Dihedral : 6.461 57.812 2195 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.77 % Allowed : 19.01 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.64 (0.20), residues: 1710 helix: 0.86 (0.22), residues: 595 sheet: -0.15 (0.26), residues: 345 loop : -1.60 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 45 TYR 0.025 0.002 TYR C 244 PHE 0.034 0.001 PHE D 414 TRP 0.014 0.001 TRP D 186 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00348 (14415) covalent geometry : angle 0.72219 (19585) SS BOND : bond 0.00516 ( 10) SS BOND : angle 3.05683 ( 20) hydrogen bonds : bond 0.04111 ( 655) hydrogen bonds : angle 4.76117 ( 2190) link_BETA1-4 : bond 0.00758 ( 10) link_BETA1-4 : angle 1.97719 ( 30) link_NAG-ASN : bond 0.00934 ( 5) link_NAG-ASN : angle 7.77139 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8528 (ppp) cc_final: 0.7569 (ptt) REVERT: A 107 ASP cc_start: 0.8810 (m-30) cc_final: 0.8594 (t0) REVERT: A 133 LEU cc_start: 0.8632 (tp) cc_final: 0.8325 (tt) REVERT: A 206 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8174 (mttp) REVERT: A 240 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 133 LEU cc_start: 0.8599 (tp) cc_final: 0.8376 (tt) REVERT: B 206 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8272 (mttp) REVERT: B 239 TYR cc_start: 0.8539 (m-80) cc_final: 0.7996 (m-80) REVERT: B 240 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 243 MET cc_start: 0.9010 (mtt) cc_final: 0.8789 (mtt) REVERT: B 282 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 105 MET cc_start: 0.8720 (ppp) cc_final: 0.7866 (ptm) REVERT: C 133 LEU cc_start: 0.8606 (tp) cc_final: 0.8403 (tt) REVERT: C 159 LYS cc_start: 0.8681 (mttt) cc_final: 0.8413 (mtpt) REVERT: C 163 MET cc_start: 0.8967 (mtm) cc_final: 0.8732 (mtm) REVERT: C 236 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6097 (tpp) REVERT: C 240 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8492 (mp) REVERT: C 295 TYR cc_start: 0.8850 (p90) cc_final: 0.8463 (p90) REVERT: D 105 MET cc_start: 0.8544 (ppp) cc_final: 0.7591 (ptm) REVERT: D 133 LEU cc_start: 0.8613 (tp) cc_final: 0.8357 (tt) REVERT: D 159 LYS cc_start: 0.8749 (mttt) cc_final: 0.8453 (mtpt) REVERT: D 206 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8572 (mttm) REVERT: D 240 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8562 (mp) REVERT: E 105 MET cc_start: 0.8645 (ppp) cc_final: 0.7947 (ptm) REVERT: E 107 ASP cc_start: 0.8652 (t0) cc_final: 0.8290 (m-30) REVERT: E 159 LYS cc_start: 0.8676 (mttt) cc_final: 0.8384 (mtpt) REVERT: E 240 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8591 (mp) REVERT: E 250 ILE cc_start: 0.8300 (mm) cc_final: 0.7996 (mt) REVERT: E 282 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8534 (mm-40) outliers start: 72 outliers final: 59 residues processed: 407 average time/residue: 0.0875 time to fit residues: 55.6199 Evaluate side-chains 442 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 377 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN B 235 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126917 restraints weight = 20917.708| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.15 r_work: 0.3188 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14440 Z= 0.162 Angle : 0.770 11.955 19650 Z= 0.388 Chirality : 0.050 0.364 2260 Planarity : 0.004 0.035 2425 Dihedral : 6.302 58.531 2195 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.10 % Allowed : 19.14 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.46 (0.20), residues: 1710 helix: 0.89 (0.22), residues: 595 sheet: 0.08 (0.28), residues: 320 loop : -1.42 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.022 0.002 TYR A 421 PHE 0.029 0.001 PHE A 322 TRP 0.012 0.001 TRP D 186 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00370 (14415) covalent geometry : angle 0.73130 (19585) SS BOND : bond 0.00541 ( 10) SS BOND : angle 2.97839 ( 20) hydrogen bonds : bond 0.04173 ( 655) hydrogen bonds : angle 4.73503 ( 2190) link_BETA1-4 : bond 0.00699 ( 10) link_BETA1-4 : angle 1.86895 ( 30) link_NAG-ASN : bond 0.00863 ( 5) link_NAG-ASN : angle 7.70703 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 380 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8567 (ppp) cc_final: 0.7709 (ptt) REVERT: A 107 ASP cc_start: 0.8853 (m-30) cc_final: 0.8612 (t0) REVERT: A 133 LEU cc_start: 0.8653 (tp) cc_final: 0.8346 (tt) REVERT: A 206 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8164 (mttp) REVERT: A 240 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 105 MET cc_start: 0.8641 (ppp) cc_final: 0.7863 (ptm) REVERT: B 179 MET cc_start: 0.8671 (mmm) cc_final: 0.8441 (mmm) REVERT: B 206 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8272 (mttp) REVERT: B 239 TYR cc_start: 0.8529 (m-80) cc_final: 0.7980 (m-80) REVERT: B 240 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 282 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8471 (mm-40) REVERT: C 47 ASN cc_start: 0.8948 (m-40) cc_final: 0.8702 (m-40) REVERT: C 105 MET cc_start: 0.8721 (ppp) cc_final: 0.7919 (ptt) REVERT: C 159 LYS cc_start: 0.8689 (mttt) cc_final: 0.8420 (mtpt) REVERT: C 163 MET cc_start: 0.9025 (mtm) cc_final: 0.8743 (mtm) REVERT: C 236 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6085 (tpp) REVERT: C 240 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 105 MET cc_start: 0.8565 (ppp) cc_final: 0.7941 (ptm) REVERT: D 133 LEU cc_start: 0.8675 (tp) cc_final: 0.8424 (tt) REVERT: D 159 LYS cc_start: 0.8745 (mttt) cc_final: 0.8443 (mtpt) REVERT: D 206 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8572 (mttm) REVERT: D 240 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8564 (mp) REVERT: E 41 ASP cc_start: 0.8327 (t0) cc_final: 0.7959 (t0) REVERT: E 96 ASP cc_start: 0.8036 (m-30) cc_final: 0.7812 (m-30) REVERT: E 105 MET cc_start: 0.8708 (ppp) cc_final: 0.7943 (ptm) REVERT: E 107 ASP cc_start: 0.8594 (t0) cc_final: 0.8246 (m-30) REVERT: E 159 LYS cc_start: 0.8682 (mttt) cc_final: 0.8386 (mtpt) REVERT: E 236 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6586 (mtp) REVERT: E 240 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8592 (mp) REVERT: E 250 ILE cc_start: 0.8280 (mm) cc_final: 0.7976 (mt) REVERT: E 282 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8522 (mm-40) outliers start: 77 outliers final: 61 residues processed: 410 average time/residue: 0.0933 time to fit residues: 59.6849 Evaluate side-chains 444 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 376 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125063 restraints weight = 21053.062| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.15 r_work: 0.3166 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14440 Z= 0.185 Angle : 0.796 12.187 19650 Z= 0.401 Chirality : 0.051 0.371 2260 Planarity : 0.004 0.032 2425 Dihedral : 6.204 58.860 2195 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.44 % Allowed : 20.46 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.39 (0.20), residues: 1710 helix: 0.94 (0.22), residues: 595 sheet: 0.16 (0.28), residues: 320 loop : -1.39 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 392 TYR 0.022 0.002 TYR A 421 PHE 0.029 0.002 PHE A 322 TRP 0.017 0.001 TRP C 422 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00427 (14415) covalent geometry : angle 0.75805 (19585) SS BOND : bond 0.00619 ( 10) SS BOND : angle 3.06478 ( 20) hydrogen bonds : bond 0.04256 ( 655) hydrogen bonds : angle 4.70313 ( 2190) link_BETA1-4 : bond 0.00684 ( 10) link_BETA1-4 : angle 1.75852 ( 30) link_NAG-ASN : bond 0.00769 ( 5) link_NAG-ASN : angle 7.81853 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 383 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8562 (ppp) cc_final: 0.8050 (ptm) REVERT: A 107 ASP cc_start: 0.8858 (m-30) cc_final: 0.8647 (t0) REVERT: A 133 LEU cc_start: 0.8684 (tp) cc_final: 0.8352 (tt) REVERT: A 206 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8384 (mtpp) REVERT: A 240 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 32 LYS cc_start: 0.8735 (pttp) cc_final: 0.8074 (tptt) REVERT: B 105 MET cc_start: 0.8653 (ppp) cc_final: 0.8050 (ptm) REVERT: B 159 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8421 (tttp) REVERT: B 206 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8273 (mttp) REVERT: B 239 TYR cc_start: 0.8585 (m-80) cc_final: 0.7978 (m-80) REVERT: B 240 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8589 (mp) REVERT: B 282 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8467 (mm-40) REVERT: C 47 ASN cc_start: 0.8944 (m-40) cc_final: 0.8672 (m-40) REVERT: C 105 MET cc_start: 0.8731 (ppp) cc_final: 0.8295 (ptm) REVERT: C 159 LYS cc_start: 0.8759 (mttt) cc_final: 0.8473 (mtpt) REVERT: C 163 MET cc_start: 0.9062 (mtm) cc_final: 0.8801 (mtm) REVERT: C 236 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6172 (tpp) REVERT: C 240 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8492 (mp) REVERT: D 105 MET cc_start: 0.8596 (ppp) cc_final: 0.8054 (ptm) REVERT: D 113 ASP cc_start: 0.9008 (p0) cc_final: 0.8764 (p0) REVERT: D 133 LEU cc_start: 0.8706 (tp) cc_final: 0.8443 (tt) REVERT: D 159 LYS cc_start: 0.8780 (mttt) cc_final: 0.8538 (mtpt) REVERT: D 206 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8581 (mttm) REVERT: D 240 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8573 (mp) REVERT: E 41 ASP cc_start: 0.8235 (t0) cc_final: 0.7933 (t0) REVERT: E 96 ASP cc_start: 0.8050 (m-30) cc_final: 0.7829 (m-30) REVERT: E 105 MET cc_start: 0.8596 (ppp) cc_final: 0.7960 (ptt) REVERT: E 159 LYS cc_start: 0.8681 (mttt) cc_final: 0.8449 (mtpt) REVERT: E 179 MET cc_start: 0.8637 (mmm) cc_final: 0.8386 (mmm) REVERT: E 236 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6764 (mtp) REVERT: E 240 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8638 (mp) REVERT: E 282 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8491 (mm-40) outliers start: 67 outliers final: 58 residues processed: 411 average time/residue: 0.0941 time to fit residues: 60.3880 Evaluate side-chains 436 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 161 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 22 optimal weight: 0.0000 chunk 90 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN C 282 GLN E 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127764 restraints weight = 20880.607| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.23 r_work: 0.3208 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14440 Z= 0.141 Angle : 0.771 11.787 19650 Z= 0.386 Chirality : 0.049 0.355 2260 Planarity : 0.004 0.030 2425 Dihedral : 6.169 59.890 2195 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.97 % Allowed : 21.19 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.38 (0.20), residues: 1710 helix: 1.02 (0.22), residues: 590 sheet: 0.21 (0.28), residues: 320 loop : -1.45 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.021 0.001 TYR A 421 PHE 0.029 0.001 PHE A 322 TRP 0.014 0.001 TRP D 186 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00316 (14415) covalent geometry : angle 0.73223 (19585) SS BOND : bond 0.00459 ( 10) SS BOND : angle 3.46406 ( 20) hydrogen bonds : bond 0.04058 ( 655) hydrogen bonds : angle 4.59591 ( 2190) link_BETA1-4 : bond 0.00748 ( 10) link_BETA1-4 : angle 1.70721 ( 30) link_NAG-ASN : bond 0.00887 ( 5) link_NAG-ASN : angle 7.49856 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.20 seconds wall clock time: 58 minutes 11.45 seconds (3491.45 seconds total)