Starting phenix.real_space_refine on Mon Dec 30 22:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2o_26317/12_2024/7u2o_26317_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2o_26317/12_2024/7u2o_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_26317/12_2024/7u2o_26317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2o_26317/12_2024/7u2o_26317.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2o_26317/12_2024/7u2o_26317_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2o_26317/12_2024/7u2o_26317_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS: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: C, B, E, D, J, N, R, V Time building chain proxies: 6.87, per 1000 atoms: 0.49 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=2, 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 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: 4.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.83 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: 4.64 Time building geometry restraints manager: 4.74 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: 8524 22.49 - 44.98: 196 44.98 - 67.47: 6 67.47 - 89.97: 40 89.97 - 112.46: 20 Dihedral angle restraints: 8786 sinusoidal: 3671 harmonic: 5115 Sorted by residual: 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 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual 288.71 176.25 112.46 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual 288.71 176.27 112.44 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 8783 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: 2.02 - 2.60: 163 2.60 - 3.17: 13443 3.17 - 3.75: 20893 3.75 - 4.32: 31358 4.32 - 4.90: 48833 Nonbonded interactions: 114690 Sorted by model distance: nonbonded pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " model vdw 2.032 3.760 ... (remaining 114685 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: 0.00 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: 1.410 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 33.340 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- 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 14415 Z= 0.416 Angle : 0.837 11.097 19585 Z= 0.455 Chirality : 0.048 0.269 2260 Planarity : 0.005 0.051 2425 Dihedral : 13.058 112.457 5460 Min Nonbonded Distance : 2.022 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP B 422 HIS 0.003 0.002 HIS C 217 PHE 0.017 0.002 PHE C 309 TYR 0.017 0.003 TYR C 144 ARG 0.007 0.001 ARG B 407 *********************** 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 : 1.654 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: 0.8394 (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: 0.3016 time to fit residues: 235.0165 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 : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 D 202 GLN E 77 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14415 Z= 0.258 Angle : 0.792 7.562 19585 Z= 0.410 Chirality : 0.050 0.239 2260 Planarity : 0.005 0.047 2425 Dihedral : 11.427 72.352 2195 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.78 % Allowed : 10.86 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.18), residues: 1710 helix: -1.44 (0.19), residues: 595 sheet: -1.93 (0.21), residues: 390 loop : -2.03 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 422 HIS 0.003 0.001 HIS C 217 PHE 0.023 0.002 PHE D 322 TYR 0.022 0.002 TYR A 421 ARG 0.003 0.001 ARG C 398 *********************** 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 529 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 487 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7807 (tptt) REVERT: A 43 ARG cc_start: 0.8973 (mtm-85) cc_final: 0.8507 (mtm-85) REVERT: A 133 LEU cc_start: 0.8581 (tp) cc_final: 0.8284 (tt) REVERT: A 159 LYS cc_start: 0.8481 (mttt) cc_final: 0.8216 (mtmt) REVERT: A 206 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8246 (mttp) REVERT: A 227 GLU cc_start: 0.8213 (pt0) cc_final: 0.7996 (pt0) REVERT: B 32 LYS cc_start: 0.8541 (pttp) cc_final: 0.7925 (tptt) REVERT: B 104 SER cc_start: 0.8474 (p) cc_final: 0.7855 (t) REVERT: B 133 LEU cc_start: 0.8611 (tp) cc_final: 0.8306 (tt) REVERT: B 159 LYS cc_start: 0.8615 (mttt) cc_final: 0.8385 (mtpt) REVERT: B 206 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8249 (mttp) REVERT: B 208 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7280 (tm-30) REVERT: B 239 TYR cc_start: 0.8603 (m-80) cc_final: 0.8366 (m-80) REVERT: C 32 LYS cc_start: 0.8419 (pttp) cc_final: 0.7746 (tptt) REVERT: C 133 LEU cc_start: 0.8601 (tp) cc_final: 0.8269 (tt) REVERT: C 137 SER cc_start: 0.9030 (m) cc_final: 0.8199 (p) REVERT: C 206 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8340 (mttp) REVERT: C 208 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7012 (pp20) REVERT: C 210 ASP cc_start: 0.8442 (m-30) cc_final: 0.8106 (m-30) REVERT: C 282 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8415 (mm-40) REVERT: D 43 ARG cc_start: 0.9103 (mtm-85) cc_final: 0.8526 (mtm-85) REVERT: D 69 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: D 130 ASP cc_start: 0.8305 (m-30) cc_final: 0.8087 (m-30) REVERT: D 133 LEU cc_start: 0.8562 (tp) cc_final: 0.8255 (tt) REVERT: D 159 LYS cc_start: 0.8575 (mttt) cc_final: 0.8333 (mtpt) REVERT: D 165 VAL cc_start: 0.9232 (t) cc_final: 0.9013 (p) REVERT: D 206 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8424 (mttp) REVERT: E 32 LYS cc_start: 0.8436 (pttp) cc_final: 0.7776 (tptt) REVERT: E 43 ARG cc_start: 0.9105 (mtm-85) cc_final: 0.8622 (mtm-85) REVERT: E 133 LEU cc_start: 0.8434 (tp) cc_final: 0.8099 (tt) REVERT: E 159 LYS cc_start: 0.8554 (mttt) cc_final: 0.8311 (mtpt) REVERT: E 206 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8453 (mttp) REVERT: E 248 LEU cc_start: 0.8528 (tt) cc_final: 0.8319 (tp) outliers start: 42 outliers final: 31 residues processed: 499 average time/residue: 0.2617 time to fit residues: 189.8892 Evaluate side-chains 434 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 401 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 C residue 33 LEU 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 33 LEU 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 E residue 24 MET 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 85 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 C 85 ASN D 85 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14415 Z= 0.228 Angle : 0.755 7.376 19585 Z= 0.388 Chirality : 0.057 0.721 2260 Planarity : 0.005 0.045 2425 Dihedral : 9.074 54.595 2195 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.90 % Allowed : 12.45 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.19), residues: 1710 helix: -0.38 (0.20), residues: 595 sheet: -1.20 (0.25), residues: 345 loop : -1.94 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 422 HIS 0.002 0.001 HIS C 125 PHE 0.024 0.001 PHE A 322 TYR 0.020 0.002 TYR A 421 ARG 0.004 0.000 ARG A 43 *********************** 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 489 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 415 time to evaluate : 1.648 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 32 LYS cc_start: 0.8526 (pttp) cc_final: 0.7802 (tptt) REVERT: A 43 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8429 (mtm-85) REVERT: A 133 LEU cc_start: 0.8602 (tp) cc_final: 0.8353 (tt) REVERT: A 159 LYS cc_start: 0.8502 (mttt) cc_final: 0.8238 (mtpt) REVERT: A 206 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8216 (mttp) REVERT: A 240 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8722 (mp) REVERT: B 32 LYS cc_start: 0.8550 (pttp) cc_final: 0.7887 (tptt) REVERT: B 159 LYS cc_start: 0.8642 (mttt) cc_final: 0.8386 (mtpt) REVERT: B 206 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8273 (mttp) REVERT: B 208 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7255 (tm-30) REVERT: B 239 TYR cc_start: 0.8575 (m-80) cc_final: 0.8274 (m-80) REVERT: B 250 ILE cc_start: 0.8277 (mm) cc_final: 0.7858 (mt) REVERT: C 105 MET cc_start: 0.5960 (mmp) cc_final: 0.5733 (mmp) REVERT: C 133 LEU cc_start: 0.8700 (tp) cc_final: 0.8433 (tt) REVERT: C 137 SER cc_start: 0.9045 (m) cc_final: 0.8226 (p) REVERT: C 159 LYS cc_start: 0.8521 (mttt) cc_final: 0.8252 (mtpt) REVERT: C 208 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7094 (pp20) REVERT: C 210 ASP cc_start: 0.8388 (m-30) cc_final: 0.8086 (m-30) REVERT: C 250 ILE cc_start: 0.8439 (mm) cc_final: 0.8053 (mt) REVERT: C 282 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8457 (mm-40) REVERT: D 43 ARG cc_start: 0.9014 (mtm-85) cc_final: 0.8511 (mtm-85) REVERT: D 159 LYS cc_start: 0.8578 (mttt) cc_final: 0.8328 (mtpt) REVERT: D 206 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8428 (mttp) REVERT: D 282 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8288 (mm-40) REVERT: E 159 LYS cc_start: 0.8565 (mttt) cc_final: 0.8309 (mtpt) outliers start: 74 outliers final: 60 residues processed: 439 average time/residue: 0.2555 time to fit residues: 164.9330 Evaluate side-chains 452 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 391 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET 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 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 B residue 24 MET Chi-restraints excluded: chain B residue 54 ASN 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 174 SER 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 33 LEU 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 227 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 C residue 428 ILE Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 54 ASN 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 119 GLU 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 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 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 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 81 optimal weight: 0.0010 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN D 231 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14415 Z= 0.231 Angle : 0.720 7.748 19585 Z= 0.373 Chirality : 0.052 0.342 2260 Planarity : 0.005 0.044 2425 Dihedral : 7.448 48.607 2195 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.70 % Allowed : 14.04 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1710 helix: 0.27 (0.21), residues: 590 sheet: -0.75 (0.25), residues: 335 loop : -1.88 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS B 217 PHE 0.026 0.001 PHE A 322 TYR 0.018 0.002 TYR A 421 ARG 0.003 0.000 ARG A 43 *********************** 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 480 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 394 time to evaluate : 1.656 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: A 29 PHE cc_start: 0.8241 (t80) cc_final: 0.7941 (t80) REVERT: A 133 LEU cc_start: 0.8582 (tp) cc_final: 0.8354 (tt) REVERT: A 159 LYS cc_start: 0.8532 (mttt) cc_final: 0.8287 (mtpt) REVERT: A 206 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8203 (mttp) REVERT: A 240 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 282 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8358 (mm-40) REVERT: A 428 ILE cc_start: 0.7203 (mp) cc_final: 0.6942 (mt) REVERT: B 32 LYS cc_start: 0.8539 (pttp) cc_final: 0.7929 (tptt) REVERT: B 133 LEU cc_start: 0.8509 (tp) cc_final: 0.8265 (tt) REVERT: B 159 LYS cc_start: 0.8644 (mttt) cc_final: 0.8369 (mtpt) REVERT: B 206 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8274 (mttp) REVERT: B 208 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 239 TYR cc_start: 0.8581 (m-80) cc_final: 0.8232 (m-80) REVERT: B 240 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 243 MET cc_start: 0.8620 (mtt) cc_final: 0.8355 (mtt) REVERT: B 282 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8408 (mm-40) REVERT: B 295 TYR cc_start: 0.8921 (p90) cc_final: 0.8694 (p90) REVERT: C 47 ASN cc_start: 0.8671 (m-40) cc_final: 0.8449 (m-40) REVERT: C 133 LEU cc_start: 0.8672 (tp) cc_final: 0.8430 (tt) REVERT: C 159 LYS cc_start: 0.8543 (mttt) cc_final: 0.8256 (mtpt) REVERT: C 210 ASP cc_start: 0.8405 (m-30) cc_final: 0.8181 (m-30) REVERT: C 282 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8534 (mm-40) REVERT: D 113 ASP cc_start: 0.9202 (p0) cc_final: 0.8993 (p0) REVERT: D 159 LYS cc_start: 0.8605 (mttt) cc_final: 0.8325 (mtpt) REVERT: D 206 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8432 (mttm) REVERT: D 248 LEU cc_start: 0.8421 (tt) cc_final: 0.8200 (tp) REVERT: D 250 ILE cc_start: 0.8443 (mm) cc_final: 0.8117 (mt) REVERT: E 159 LYS cc_start: 0.8594 (mttt) cc_final: 0.8317 (mtpt) REVERT: E 240 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8715 (mp) REVERT: E 282 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8445 (mm-40) outliers start: 86 outliers final: 71 residues processed: 422 average time/residue: 0.2491 time to fit residues: 157.0579 Evaluate side-chains 448 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 374 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET 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 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 301 ILE 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 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 174 SER 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 33 LEU Chi-restraints excluded: chain C residue 37 VAL 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 127 VAL Chi-restraints excluded: chain C residue 149 THR 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 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 54 ASN 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 119 GLU 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 307 LEU 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 69 GLU Chi-restraints excluded: chain E residue 101 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 0.0010 overall best weight: 0.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14415 Z= 0.192 Angle : 0.686 8.079 19585 Z= 0.355 Chirality : 0.050 0.596 2260 Planarity : 0.004 0.049 2425 Dihedral : 6.858 58.495 2195 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.17 % Allowed : 15.70 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1710 helix: 0.57 (0.22), residues: 595 sheet: -0.41 (0.26), residues: 335 loop : -1.85 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS C 217 PHE 0.026 0.001 PHE A 322 TYR 0.017 0.001 TYR A 421 ARG 0.004 0.000 ARG D 43 *********************** 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 473 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 395 time to evaluate : 1.527 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: A 159 LYS cc_start: 0.8545 (mttt) cc_final: 0.8284 (mtpt) REVERT: A 206 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8220 (mttp) REVERT: A 240 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8720 (mp) REVERT: A 250 ILE cc_start: 0.8208 (mm) cc_final: 0.7865 (mt) REVERT: A 282 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8405 (mm-40) REVERT: A 428 ILE cc_start: 0.7223 (mp) cc_final: 0.6974 (mt) REVERT: B 32 LYS cc_start: 0.8527 (pttp) cc_final: 0.7931 (tptt) REVERT: B 133 LEU cc_start: 0.8530 (tp) cc_final: 0.8311 (tt) REVERT: B 141 ASN cc_start: 0.8510 (m-40) cc_final: 0.8232 (m-40) REVERT: B 159 LYS cc_start: 0.8621 (mttt) cc_final: 0.8352 (mtpt) REVERT: B 206 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8274 (mttp) REVERT: B 208 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 239 TYR cc_start: 0.8506 (m-80) cc_final: 0.7994 (m-80) REVERT: B 240 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8624 (mp) REVERT: B 243 MET cc_start: 0.8607 (mtt) cc_final: 0.8355 (mtt) REVERT: B 250 ILE cc_start: 0.8458 (mm) cc_final: 0.8097 (mt) REVERT: B 282 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8353 (mm-40) REVERT: B 428 ILE cc_start: 0.7166 (mp) cc_final: 0.6749 (mt) REVERT: C 133 LEU cc_start: 0.8625 (tp) cc_final: 0.8403 (tt) REVERT: C 159 LYS cc_start: 0.8552 (mttt) cc_final: 0.8259 (mtpt) REVERT: C 208 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7104 (pp20) REVERT: C 210 ASP cc_start: 0.8289 (m-30) cc_final: 0.8030 (m-30) REVERT: C 240 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 250 ILE cc_start: 0.8486 (mm) cc_final: 0.8181 (mt) REVERT: C 282 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8495 (mm-40) REVERT: D 159 LYS cc_start: 0.8622 (mttt) cc_final: 0.8331 (mtpt) REVERT: D 206 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8436 (mttm) REVERT: D 248 LEU cc_start: 0.8437 (tt) cc_final: 0.8234 (tp) REVERT: D 282 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8382 (mm-40) REVERT: E 159 LYS cc_start: 0.8559 (mttt) cc_final: 0.8297 (mtpt) REVERT: E 250 ILE cc_start: 0.8309 (mm) cc_final: 0.8021 (mt) REVERT: E 282 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8453 (mm-40) outliers start: 78 outliers final: 61 residues processed: 423 average time/residue: 0.2378 time to fit residues: 151.2502 Evaluate side-chains 445 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 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 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 308 LEU Chi-restraints excluded: chain A residue 415 LEU 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 104 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 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 37 VAL 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 171 GLN Chi-restraints excluded: chain C residue 227 GLU 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 37 VAL Chi-restraints excluded: chain D residue 54 ASN 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 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 149 THR 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 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 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 55 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14415 Z= 0.248 Angle : 0.687 8.469 19585 Z= 0.358 Chirality : 0.049 0.373 2260 Planarity : 0.004 0.043 2425 Dihedral : 6.697 58.302 2195 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.56 % Allowed : 15.96 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1710 helix: 0.80 (0.22), residues: 595 sheet: -0.00 (0.27), residues: 320 loop : -1.70 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.003 0.001 HIS E 125 PHE 0.028 0.001 PHE B 414 TYR 0.017 0.002 TYR A 421 ARG 0.003 0.000 ARG A 43 *********************** 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 479 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 395 time to evaluate : 1.557 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 206 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8211 (mttp) REVERT: A 240 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 282 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 133 LEU cc_start: 0.8588 (tp) cc_final: 0.8371 (tt) REVERT: B 159 LYS cc_start: 0.8674 (mttt) cc_final: 0.8391 (mtpt) REVERT: B 206 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8302 (mttp) REVERT: B 239 TYR cc_start: 0.8561 (m-80) cc_final: 0.7992 (m-80) REVERT: B 240 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 243 MET cc_start: 0.8644 (mtt) cc_final: 0.8405 (mtt) REVERT: B 250 ILE cc_start: 0.8519 (mm) cc_final: 0.8162 (mt) REVERT: B 282 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8392 (mm-40) REVERT: B 428 ILE cc_start: 0.7167 (mp) cc_final: 0.6792 (mt) REVERT: C 123 ASN cc_start: 0.9041 (p0) cc_final: 0.8823 (p0) REVERT: C 159 LYS cc_start: 0.8562 (mttt) cc_final: 0.8315 (mtpt) REVERT: C 240 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 250 ILE cc_start: 0.8524 (mm) cc_final: 0.8218 (mt) REVERT: C 282 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8485 (mm-40) REVERT: D 159 LYS cc_start: 0.8670 (mttt) cc_final: 0.8375 (mtpt) REVERT: D 206 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8462 (mttm) REVERT: D 248 LEU cc_start: 0.8423 (tt) cc_final: 0.8218 (tp) REVERT: E 159 LYS cc_start: 0.8590 (mttt) cc_final: 0.8310 (mtpt) REVERT: E 240 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8685 (mp) REVERT: E 250 ILE cc_start: 0.8378 (mm) cc_final: 0.8081 (mt) REVERT: E 282 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8493 (mm-40) outliers start: 84 outliers final: 67 residues processed: 423 average time/residue: 0.2324 time to fit residues: 150.3502 Evaluate side-chains 452 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 381 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 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 214 CYS 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 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 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 104 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 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 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 227 GLU 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 54 ASN 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 119 GLU 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 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 101 LEU Chi-restraints excluded: chain E residue 119 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN C 171 GLN C 231 HIS ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14415 Z= 0.251 Angle : 0.705 9.117 19585 Z= 0.367 Chirality : 0.050 0.376 2260 Planarity : 0.004 0.052 2425 Dihedral : 6.571 59.382 2195 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.23 % Allowed : 16.75 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1710 helix: 0.89 (0.22), residues: 595 sheet: 0.02 (0.27), residues: 320 loop : -1.66 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.003 0.001 HIS B 217 PHE 0.028 0.001 PHE E 48 TYR 0.017 0.002 TYR A 421 ARG 0.003 0.000 ARG A 229 *********************** 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 466 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 387 time to evaluate : 1.544 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 105 MET cc_start: 0.8458 (ppp) cc_final: 0.7449 (ptm) REVERT: A 206 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8196 (mttp) REVERT: A 240 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8753 (mp) REVERT: A 282 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8413 (mm-40) REVERT: B 133 LEU cc_start: 0.8589 (tp) cc_final: 0.8381 (tt) REVERT: B 159 LYS cc_start: 0.8677 (mttt) cc_final: 0.8383 (mtpt) REVERT: B 206 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8303 (mttp) REVERT: B 239 TYR cc_start: 0.8545 (m-80) cc_final: 0.7960 (m-80) REVERT: B 240 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8649 (mp) REVERT: B 243 MET cc_start: 0.8646 (mtt) cc_final: 0.8437 (mtt) REVERT: B 282 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8423 (mm-40) REVERT: C 123 ASN cc_start: 0.9008 (p0) cc_final: 0.8784 (p0) REVERT: C 159 LYS cc_start: 0.8583 (mttt) cc_final: 0.8321 (mtpt) REVERT: C 240 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 282 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8495 (mm-40) REVERT: D 159 LYS cc_start: 0.8664 (mttt) cc_final: 0.8355 (mtpt) REVERT: D 206 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8472 (mttm) REVERT: E 41 ASP cc_start: 0.8294 (t0) cc_final: 0.8038 (t0) REVERT: E 159 LYS cc_start: 0.8596 (mttt) cc_final: 0.8301 (mtpt) REVERT: E 240 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8669 (mp) REVERT: E 250 ILE cc_start: 0.8373 (mm) cc_final: 0.8077 (mt) REVERT: E 282 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8483 (mm-40) outliers start: 79 outliers final: 70 residues processed: 416 average time/residue: 0.2397 time to fit residues: 150.4253 Evaluate side-chains 444 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 370 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 214 CYS 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 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 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 240 LEU Chi-restraints excluded: chain B residue 245 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 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 227 GLU 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 29 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 ASN 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 119 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 171 GLN ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14415 Z= 0.234 Angle : 0.722 8.432 19585 Z= 0.372 Chirality : 0.050 0.520 2260 Planarity : 0.004 0.054 2425 Dihedral : 6.432 55.403 2195 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.30 % Allowed : 17.88 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1710 helix: 0.90 (0.22), residues: 595 sheet: 0.07 (0.27), residues: 320 loop : -1.63 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS B 217 PHE 0.029 0.001 PHE E 48 TYR 0.017 0.002 TYR A 421 ARG 0.003 0.000 ARG C 229 *********************** 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 470 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 390 time to evaluate : 1.646 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 105 MET cc_start: 0.8517 (ppp) cc_final: 0.7880 (ptm) REVERT: A 206 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8191 (mttp) REVERT: A 240 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 282 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8449 (mm-40) REVERT: B 159 LYS cc_start: 0.8669 (mttt) cc_final: 0.8353 (mtpt) REVERT: B 206 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8282 (mttp) REVERT: B 239 TYR cc_start: 0.8479 (m-80) cc_final: 0.7936 (m-80) REVERT: B 240 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 243 MET cc_start: 0.8630 (mtt) cc_final: 0.8399 (mtt) REVERT: B 250 ILE cc_start: 0.8544 (mm) cc_final: 0.8249 (mt) REVERT: B 282 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8366 (mm-40) REVERT: C 47 ASN cc_start: 0.8685 (m-40) cc_final: 0.8413 (m-40) REVERT: C 123 ASN cc_start: 0.8992 (p0) cc_final: 0.8772 (p0) REVERT: C 141 ASN cc_start: 0.8500 (m-40) cc_final: 0.8157 (m-40) REVERT: C 159 LYS cc_start: 0.8576 (mttt) cc_final: 0.8305 (mtpt) REVERT: C 240 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 282 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8531 (mm-40) REVERT: D 105 MET cc_start: 0.8345 (ppp) cc_final: 0.7205 (ptt) REVERT: D 133 LEU cc_start: 0.8592 (tp) cc_final: 0.8362 (tt) REVERT: D 159 LYS cc_start: 0.8641 (mttt) cc_final: 0.8330 (mtpt) REVERT: D 206 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8471 (mttm) REVERT: D 282 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8395 (mm-40) REVERT: E 133 LEU cc_start: 0.8438 (tp) cc_final: 0.8235 (tt) REVERT: E 149 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8643 (m) REVERT: E 159 LYS cc_start: 0.8593 (mttt) cc_final: 0.8301 (mtpt) REVERT: E 240 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8651 (mp) REVERT: E 250 ILE cc_start: 0.8353 (mm) cc_final: 0.8062 (mt) REVERT: E 282 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8482 (mm-40) outliers start: 80 outliers final: 68 residues processed: 420 average time/residue: 0.2609 time to fit residues: 167.3949 Evaluate side-chains 451 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 378 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 214 CYS 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 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 33 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 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 227 GLU 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 54 ASN 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 119 GLU 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 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 149 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.0370 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 171 GLN ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14415 Z= 0.207 Angle : 0.707 8.550 19585 Z= 0.363 Chirality : 0.050 0.480 2260 Planarity : 0.004 0.055 2425 Dihedral : 6.229 50.706 2195 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.77 % Allowed : 18.61 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1710 helix: 1.03 (0.22), residues: 590 sheet: 0.11 (0.28), residues: 315 loop : -1.66 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS D 217 PHE 0.028 0.001 PHE A 322 TYR 0.021 0.002 TYR B 238 ARG 0.003 0.000 ARG A 212 *********************** 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: 72 poor density : 385 time to evaluate : 1.730 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 105 MET cc_start: 0.8455 (ppp) cc_final: 0.7600 (ptt) REVERT: A 141 ASN cc_start: 0.8401 (m-40) cc_final: 0.8044 (m-40) REVERT: A 206 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8147 (mttp) REVERT: A 240 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 282 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8451 (mm-40) REVERT: B 159 LYS cc_start: 0.8652 (mttt) cc_final: 0.8344 (mtpt) REVERT: B 206 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8303 (mttp) REVERT: B 239 TYR cc_start: 0.8435 (m-80) cc_final: 0.7877 (m-80) REVERT: B 243 MET cc_start: 0.8622 (mtt) cc_final: 0.8387 (mtt) REVERT: B 282 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8367 (mm-40) REVERT: C 34 MET cc_start: 0.6255 (pmm) cc_final: 0.5632 (pmm) REVERT: C 105 MET cc_start: 0.8424 (ppp) cc_final: 0.7259 (ptt) REVERT: C 123 ASN cc_start: 0.8965 (p0) cc_final: 0.8754 (p0) REVERT: C 141 ASN cc_start: 0.8439 (m-40) cc_final: 0.8104 (m-40) REVERT: C 159 LYS cc_start: 0.8568 (mttt) cc_final: 0.8296 (mtpt) REVERT: C 236 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6393 (mtp) REVERT: C 240 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8569 (mp) REVERT: C 244 TYR cc_start: 0.8776 (m-80) cc_final: 0.8532 (m-80) REVERT: C 282 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8530 (mm-40) REVERT: D 105 MET cc_start: 0.8242 (ppp) cc_final: 0.7242 (ptt) REVERT: D 133 LEU cc_start: 0.8561 (tp) cc_final: 0.8348 (tt) REVERT: D 159 LYS cc_start: 0.8627 (mttt) cc_final: 0.8299 (mtpt) REVERT: D 206 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8476 (mttm) REVERT: E 149 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8639 (m) REVERT: E 159 LYS cc_start: 0.8577 (mttt) cc_final: 0.8281 (mtpt) REVERT: E 240 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8624 (mp) REVERT: E 250 ILE cc_start: 0.8347 (mm) cc_final: 0.8065 (mt) REVERT: E 282 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8513 (mm-40) outliers start: 72 outliers final: 60 residues processed: 415 average time/residue: 0.2490 time to fit residues: 157.1627 Evaluate side-chains 449 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 384 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 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 207 GLU Chi-restraints excluded: chain A residue 214 CYS 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 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 33 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 128 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 227 GLU 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 29 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 ASN 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 119 GLU 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 171 GLN 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 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 149 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.0670 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN C 171 GLN E 47 ASN E 85 ASN E 141 ASN ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14415 Z= 0.196 Angle : 0.708 8.659 19585 Z= 0.362 Chirality : 0.049 0.424 2260 Planarity : 0.004 0.057 2425 Dihedral : 6.063 47.603 2195 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.17 % Allowed : 19.60 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1710 helix: 1.05 (0.22), residues: 590 sheet: 0.15 (0.28), residues: 315 loop : -1.67 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 186 HIS 0.002 0.001 HIS D 125 PHE 0.029 0.001 PHE A 322 TYR 0.016 0.001 TYR A 421 ARG 0.002 0.000 ARG C 229 ********************** 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 459 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 396 time to evaluate : 1.613 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 105 MET cc_start: 0.8469 (ppp) cc_final: 0.7708 (ptt) REVERT: A 141 ASN cc_start: 0.8367 (m-40) cc_final: 0.8018 (m-40) REVERT: A 206 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8135 (mttp) REVERT: A 210 ASP cc_start: 0.8286 (m-30) cc_final: 0.7672 (m-30) REVERT: A 240 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 282 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8456 (mm-40) REVERT: B 105 MET cc_start: 0.8380 (ppp) cc_final: 0.7786 (ptm) REVERT: B 159 LYS cc_start: 0.8626 (mttt) cc_final: 0.8333 (mtpt) REVERT: B 206 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8304 (mttp) REVERT: B 239 TYR cc_start: 0.8384 (m-80) cc_final: 0.7894 (m-80) REVERT: B 243 MET cc_start: 0.8628 (mtt) cc_final: 0.8415 (mtt) REVERT: B 282 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8376 (mm-40) REVERT: B 428 ILE cc_start: 0.7087 (mp) cc_final: 0.6821 (mt) REVERT: C 34 MET cc_start: 0.6280 (pmm) cc_final: 0.5683 (pmm) REVERT: C 47 ASN cc_start: 0.8684 (m-40) cc_final: 0.8423 (m-40) REVERT: C 105 MET cc_start: 0.8467 (ppp) cc_final: 0.7491 (ptt) REVERT: C 123 ASN cc_start: 0.8951 (p0) cc_final: 0.8738 (p0) REVERT: C 141 ASN cc_start: 0.8431 (m-40) cc_final: 0.8091 (m-40) REVERT: C 159 LYS cc_start: 0.8554 (mttt) cc_final: 0.8294 (mtpt) REVERT: C 240 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 244 TYR cc_start: 0.8764 (m-80) cc_final: 0.8555 (m-80) REVERT: C 282 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8533 (mm-40) REVERT: C 295 TYR cc_start: 0.8801 (p90) cc_final: 0.8595 (p90) REVERT: D 105 MET cc_start: 0.8231 (ppp) cc_final: 0.7308 (ptm) REVERT: D 113 ASP cc_start: 0.8843 (p0) cc_final: 0.8598 (p0) REVERT: D 133 LEU cc_start: 0.8543 (tp) cc_final: 0.8334 (tt) REVERT: D 141 ASN cc_start: 0.8447 (m-40) cc_final: 0.8153 (m110) REVERT: D 159 LYS cc_start: 0.8639 (mttt) cc_final: 0.8331 (mtpt) REVERT: D 206 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8468 (mttm) REVERT: E 159 LYS cc_start: 0.8548 (mttt) cc_final: 0.8231 (mtpt) REVERT: E 177 TYR cc_start: 0.8941 (m-80) cc_final: 0.8543 (m-80) REVERT: E 236 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6027 (mtp) REVERT: E 240 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8592 (mp) REVERT: E 250 ILE cc_start: 0.8338 (mm) cc_final: 0.8069 (mt) REVERT: E 282 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8501 (mm-40) outliers start: 63 outliers final: 53 residues processed: 423 average time/residue: 0.2488 time to fit residues: 159.0923 Evaluate side-chains 444 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 387 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 170 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE 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 33 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 128 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU 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 227 GLU 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 29 PHE Chi-restraints excluded: chain D residue 54 ASN 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 119 GLU 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 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 149 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.0980 chunk 7 optimal weight: 0.0970 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 171 GLN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.174482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132108 restraints weight = 20808.697| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.24 r_work: 0.3387 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14415 Z= 0.186 Angle : 0.708 8.671 19585 Z= 0.361 Chirality : 0.049 0.395 2260 Planarity : 0.004 0.054 2425 Dihedral : 5.887 47.739 2195 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.58 % Allowed : 20.60 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1710 helix: 1.12 (0.22), residues: 590 sheet: 0.26 (0.28), residues: 315 loop : -1.67 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 186 HIS 0.002 0.001 HIS E 125 PHE 0.029 0.001 PHE A 322 TYR 0.017 0.001 TYR A 421 ARG 0.010 0.000 ARG A 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.63 seconds wall clock time: 72 minutes 27.64 seconds (4347.64 seconds total)