Starting phenix.real_space_refine on Mon Dec 30 01:51:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvu_42629/12_2024/8uvu_42629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvu_42629/12_2024/8uvu_42629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvu_42629/12_2024/8uvu_42629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvu_42629/12_2024/8uvu_42629.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvu_42629/12_2024/8uvu_42629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvu_42629/12_2024/8uvu_42629.cif" } resolution = 3.0 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= 0.003 sd= 0.102 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 120 5.16 5 C 7784 2.51 5 N 2000 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 ABDF A 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF A 501 " occ=0.75 residue: pdb=" C1 BFRU A 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU A 502 " occ=0.25 residue: pdb=" C1 ABDF B 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF B 501 " occ=0.75 residue: pdb=" C1 BFRU B 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU B 502 " occ=0.25 residue: pdb=" C1 ABDF C 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF C 501 " occ=0.75 residue: pdb=" C1 BFRU C 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU C 502 " occ=0.25 residue: pdb=" C1 ABDF D 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF D 501 " occ=0.75 residue: pdb=" C1 BFRU D 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU D 502 " occ=0.25 Time building chain proxies: 6.86, per 1000 atoms: 0.57 Number of scatterers: 11976 At special positions: 0 Unit cell: (110.004, 110.004, 93.984, 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 120 16.00 O 2072 8.00 N 2000 7.00 C 7784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 85.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.817A pdb=" N PHE A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.531A pdb=" N TYR A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 134 removed outlier: 3.916A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 176 removed outlier: 3.773A pdb=" N SER A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 186 through 225 removed outlier: 4.051A pdb=" N TYR A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 341 removed outlier: 3.645A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 344 through 390 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 394 through 410 removed outlier: 4.121A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.816A pdb=" N PHE B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 79 removed outlier: 3.532A pdb=" N TYR B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 95 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 134 removed outlier: 3.916A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 176 removed outlier: 3.773A pdb=" N SER B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 186 through 225 removed outlier: 4.052A pdb=" N TYR B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 341 removed outlier: 3.645A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 344 through 390 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 394 through 410 removed outlier: 4.122A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.817A pdb=" N PHE C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 79 removed outlier: 3.532A pdb=" N TYR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 95 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 134 removed outlier: 3.917A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 176 removed outlier: 3.773A pdb=" N SER C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 186 through 225 removed outlier: 4.051A pdb=" N TYR C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 341 removed outlier: 3.646A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 344 through 390 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 394 through 410 removed outlier: 4.122A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.817A pdb=" N PHE D 24 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 79 removed outlier: 3.533A pdb=" N TYR D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 95 " --> pdb=" O MET D 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 134 removed outlier: 3.916A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 176 removed outlier: 3.774A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 186 through 225 removed outlier: 4.052A pdb=" N TYR D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 341 removed outlier: 3.646A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 344 through 390 Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 394 through 410 removed outlier: 4.121A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 removed outlier: 4.267A pdb=" N CYS A 16 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 49 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.268A pdb=" N CYS B 16 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 49 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 16 through 18 removed outlier: 4.268A pdb=" N CYS C 16 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 49 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 16 through 18 removed outlier: 4.269A pdb=" N CYS D 16 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 49 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2916 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: 3.79 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3716 1.34 - 1.46: 2834 1.46 - 1.58: 5478 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 12208 Sorted by residual: bond pdb=" C2 BFRU B 502 " pdb=" O2 BFRU B 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C2 BFRU A 502 " pdb=" O2 BFRU A 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C2 BFRU C 502 " pdb=" O2 BFRU C 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C2 BFRU D 502 " pdb=" O2 BFRU D 502 " ideal model delta sigma weight residual 1.388 1.425 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" C2 ABDF A 501 " pdb=" O2 ABDF A 501 " ideal model delta sigma weight residual 1.390 1.425 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 12203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 16272 1.84 - 3.67: 230 3.67 - 5.51: 62 5.51 - 7.35: 16 7.35 - 9.18: 4 Bond angle restraints: 16584 Sorted by residual: angle pdb=" N ALA B 23 " pdb=" CA ALA B 23 " pdb=" C ALA B 23 " ideal model delta sigma weight residual 114.62 108.80 5.82 1.14e+00 7.69e-01 2.61e+01 angle pdb=" N ALA A 23 " pdb=" CA ALA A 23 " pdb=" C ALA A 23 " ideal model delta sigma weight residual 114.62 108.83 5.79 1.14e+00 7.69e-01 2.58e+01 angle pdb=" N ALA D 23 " pdb=" CA ALA D 23 " pdb=" C ALA D 23 " ideal model delta sigma weight residual 114.62 108.83 5.79 1.14e+00 7.69e-01 2.58e+01 angle pdb=" N ALA C 23 " pdb=" CA ALA C 23 " pdb=" C ALA C 23 " ideal model delta sigma weight residual 114.62 108.86 5.76 1.14e+00 7.69e-01 2.55e+01 angle pdb=" CA ALA A 23 " pdb=" C ALA A 23 " pdb=" N PHE A 24 " ideal model delta sigma weight residual 119.71 116.12 3.59 1.17e+00 7.31e-01 9.41e+00 ... (remaining 16579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6640 17.96 - 35.91: 599 35.91 - 53.87: 145 53.87 - 71.82: 32 71.82 - 89.78: 8 Dihedral angle restraints: 7424 sinusoidal: 3000 harmonic: 4424 Sorted by residual: dihedral pdb=" CA LYS D 52 " pdb=" C LYS D 52 " pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS A 52 " pdb=" C LYS A 52 " pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS C 52 " pdb=" C LYS C 52 " pdb=" N GLY C 53 " pdb=" CA GLY C 53 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1846 0.062 - 0.124: 186 0.124 - 0.186: 8 0.186 - 0.248: 8 0.248 - 0.309: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C3 BFRU A 502 " pdb=" C2 BFRU A 502 " pdb=" C4 BFRU A 502 " pdb=" O3 BFRU A 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3 BFRU C 502 " pdb=" C2 BFRU C 502 " pdb=" C4 BFRU C 502 " pdb=" O3 BFRU C 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3 BFRU B 502 " pdb=" C2 BFRU B 502 " pdb=" C4 BFRU B 502 " pdb=" O3 BFRU B 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2049 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 285 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 286 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 285 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 286 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 285 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO C 286 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " -0.019 5.00e-02 4.00e+02 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2385 2.78 - 3.31: 12351 3.31 - 3.84: 20664 3.84 - 4.37: 23759 4.37 - 4.90: 42018 Nonbonded interactions: 101177 Sorted by model distance: nonbonded pdb=" OD1 ASN A 218 " pdb=" OG1 THR A 379 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN B 218 " pdb=" OG1 THR B 379 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN D 218 " pdb=" OG1 THR D 379 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN C 218 " pdb=" OG1 THR C 379 " model vdw 2.246 3.040 nonbonded pdb=" N GLN B 179 " pdb=" OE1 GLN B 179 " model vdw 2.256 3.120 ... (remaining 101172 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' and resid 14 through 446) selection = (chain 'B' and resid 14 through 446) selection = (chain 'C' and resid 14 through 446) selection = (chain 'D' and resid 14 through 446) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 3.050 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.910 Find NCS groups from input model: 0.750 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: 0.000 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.003 0.038 12208 Z= 0.209 Angle : 0.601 9.182 16584 Z= 0.304 Chirality : 0.041 0.309 2052 Planarity : 0.004 0.035 1992 Dihedral : 14.700 89.777 4568 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.22), residues: 1500 helix: 2.06 (0.14), residues: 1224 sheet: -4.55 (0.58), residues: 44 loop : -2.92 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.000 HIS D 307 PHE 0.014 0.001 PHE C 189 TYR 0.019 0.001 TYR D 124 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.381 Fit side-chains REVERT: A 389 LEU cc_start: 0.8293 (mt) cc_final: 0.8018 (mt) REVERT: B 121 MET cc_start: 0.8756 (tmm) cc_final: 0.8540 (tmt) REVERT: B 389 LEU cc_start: 0.8310 (mt) cc_final: 0.8022 (mt) REVERT: C 389 LEU cc_start: 0.8322 (mt) cc_final: 0.8045 (mt) REVERT: D 389 LEU cc_start: 0.8328 (mt) cc_final: 0.8062 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 1.4345 time to fit residues: 343.3000 Evaluate side-chains 178 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12208 Z= 0.281 Angle : 0.584 6.679 16584 Z= 0.301 Chirality : 0.039 0.129 2052 Planarity : 0.004 0.036 1992 Dihedral : 4.173 21.445 1856 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.89 % Allowed : 8.41 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.22), residues: 1500 helix: 2.36 (0.14), residues: 1224 sheet: -4.46 (0.55), residues: 44 loop : -3.15 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 193 HIS 0.004 0.001 HIS C 358 PHE 0.014 0.001 PHE A 203 TYR 0.018 0.002 TYR D 124 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.332 Fit side-chains REVERT: A 179 GLN cc_start: 0.7980 (pm20) cc_final: 0.7730 (pm20) REVERT: A 389 LEU cc_start: 0.8596 (mt) cc_final: 0.8331 (mt) REVERT: B 121 MET cc_start: 0.8825 (tmm) cc_final: 0.8602 (tmt) REVERT: B 179 GLN cc_start: 0.8026 (pm20) cc_final: 0.7781 (pm20) REVERT: B 389 LEU cc_start: 0.8596 (mt) cc_final: 0.8331 (mt) REVERT: C 179 GLN cc_start: 0.7983 (pm20) cc_final: 0.7735 (pm20) REVERT: C 389 LEU cc_start: 0.8651 (mt) cc_final: 0.8395 (mt) REVERT: D 179 GLN cc_start: 0.7983 (pm20) cc_final: 0.7735 (pm20) REVERT: D 389 LEU cc_start: 0.8650 (mt) cc_final: 0.8390 (mt) outliers start: 25 outliers final: 12 residues processed: 211 average time/residue: 1.3198 time to fit residues: 301.6683 Evaluate side-chains 191 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 392 HIS B 222 ASN B 392 HIS C 222 ASN C 392 HIS D 222 ASN D 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12208 Z= 0.281 Angle : 0.585 7.111 16584 Z= 0.301 Chirality : 0.039 0.133 2052 Planarity : 0.004 0.037 1992 Dihedral : 4.182 18.376 1856 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.82 % Allowed : 12.65 % Favored : 85.53 % 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: 2.00 (0.22), residues: 1500 helix: 2.32 (0.14), residues: 1224 sheet: -4.38 (0.55), residues: 44 loop : -3.23 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 193 HIS 0.003 0.001 HIS D 22 PHE 0.015 0.001 PHE D 205 TYR 0.021 0.002 TYR D 124 ARG 0.003 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.333 Fit side-chains REVERT: A 179 GLN cc_start: 0.7893 (pm20) cc_final: 0.7647 (pm20) REVERT: A 389 LEU cc_start: 0.8609 (mt) cc_final: 0.8306 (mt) REVERT: B 121 MET cc_start: 0.8838 (tmm) cc_final: 0.8603 (tmt) REVERT: B 179 GLN cc_start: 0.7897 (pm20) cc_final: 0.7647 (pm20) REVERT: B 389 LEU cc_start: 0.8606 (mt) cc_final: 0.8303 (mt) REVERT: C 179 GLN cc_start: 0.7895 (pm20) cc_final: 0.7646 (pm20) REVERT: C 389 LEU cc_start: 0.8611 (mt) cc_final: 0.8330 (mt) REVERT: D 179 GLN cc_start: 0.7896 (pm20) cc_final: 0.7650 (pm20) REVERT: D 389 LEU cc_start: 0.8613 (mt) cc_final: 0.8329 (mt) outliers start: 24 outliers final: 16 residues processed: 198 average time/residue: 1.4444 time to fit residues: 308.6542 Evaluate side-chains 191 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12208 Z= 0.195 Angle : 0.528 5.100 16584 Z= 0.275 Chirality : 0.036 0.119 2052 Planarity : 0.004 0.037 1992 Dihedral : 4.089 18.615 1856 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.89 % Allowed : 14.47 % Favored : 83.64 % 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: 2.36 (0.22), residues: 1500 helix: 2.45 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : -3.01 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.003 0.001 HIS D 22 PHE 0.014 0.001 PHE C 205 TYR 0.018 0.001 TYR A 124 ARG 0.002 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.296 Fit side-chains REVERT: A 129 VAL cc_start: 0.7879 (t) cc_final: 0.7333 (m) REVERT: A 365 VAL cc_start: 0.8744 (t) cc_final: 0.8410 (t) REVERT: A 389 LEU cc_start: 0.8570 (mt) cc_final: 0.8268 (mt) REVERT: B 121 MET cc_start: 0.8775 (tmm) cc_final: 0.8554 (tmt) REVERT: B 365 VAL cc_start: 0.8745 (t) cc_final: 0.8410 (t) REVERT: B 389 LEU cc_start: 0.8569 (mt) cc_final: 0.8268 (mt) REVERT: C 125 MET cc_start: 0.7303 (mmm) cc_final: 0.6969 (mmt) REVERT: C 365 VAL cc_start: 0.8746 (t) cc_final: 0.8410 (t) REVERT: C 389 LEU cc_start: 0.8574 (mt) cc_final: 0.8274 (mt) REVERT: D 365 VAL cc_start: 0.8745 (t) cc_final: 0.8411 (t) REVERT: D 389 LEU cc_start: 0.8574 (mt) cc_final: 0.8269 (mt) outliers start: 25 outliers final: 17 residues processed: 206 average time/residue: 1.4059 time to fit residues: 312.4942 Evaluate side-chains 199 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12208 Z= 0.242 Angle : 0.569 7.222 16584 Z= 0.293 Chirality : 0.037 0.124 2052 Planarity : 0.004 0.037 1992 Dihedral : 4.115 17.769 1856 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.03 % Allowed : 15.00 % Favored : 81.97 % 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: 2.31 (0.21), residues: 1500 helix: 2.39 (0.14), residues: 1236 sheet: None (None), residues: 0 loop : -2.96 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 354 HIS 0.003 0.001 HIS D 22 PHE 0.015 0.001 PHE B 205 TYR 0.019 0.001 TYR A 124 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.384 Fit side-chains REVERT: A 365 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8431 (t) REVERT: A 389 LEU cc_start: 0.8635 (mt) cc_final: 0.8345 (mt) REVERT: B 121 MET cc_start: 0.8818 (tmm) cc_final: 0.8612 (tmt) REVERT: B 179 GLN cc_start: 0.8042 (pm20) cc_final: 0.7827 (pm20) REVERT: B 365 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (t) REVERT: B 389 LEU cc_start: 0.8633 (mt) cc_final: 0.8343 (mt) REVERT: C 179 GLN cc_start: 0.8039 (pm20) cc_final: 0.7823 (pm20) REVERT: C 365 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8472 (t) REVERT: C 389 LEU cc_start: 0.8641 (mt) cc_final: 0.8373 (mt) REVERT: D 179 GLN cc_start: 0.8025 (pm20) cc_final: 0.7815 (pm20) REVERT: D 365 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8472 (t) REVERT: D 389 LEU cc_start: 0.8637 (mt) cc_final: 0.8366 (mt) outliers start: 40 outliers final: 20 residues processed: 207 average time/residue: 1.3262 time to fit residues: 297.0167 Evaluate side-chains 205 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN B 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12208 Z= 0.252 Angle : 0.573 6.408 16584 Z= 0.295 Chirality : 0.038 0.129 2052 Planarity : 0.004 0.037 1992 Dihedral : 4.188 19.366 1856 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.33 % Allowed : 15.00 % Favored : 81.67 % 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: 2.28 (0.21), residues: 1500 helix: 2.38 (0.14), residues: 1236 sheet: None (None), residues: 0 loop : -3.03 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 354 HIS 0.004 0.001 HIS A 22 PHE 0.016 0.001 PHE D 205 TYR 0.019 0.001 TYR A 124 ARG 0.003 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.212 Fit side-chains REVERT: A 365 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 389 LEU cc_start: 0.8638 (mt) cc_final: 0.8394 (mt) REVERT: B 121 MET cc_start: 0.8870 (tmm) cc_final: 0.8616 (tmt) REVERT: B 365 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8514 (t) REVERT: B 389 LEU cc_start: 0.8634 (mt) cc_final: 0.8390 (mt) REVERT: C 121 MET cc_start: 0.8598 (tmt) cc_final: 0.8269 (tmt) REVERT: C 179 GLN cc_start: 0.7976 (pm20) cc_final: 0.7758 (pm20) REVERT: C 365 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8511 (t) REVERT: C 389 LEU cc_start: 0.8630 (mt) cc_final: 0.8386 (mt) REVERT: D 365 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8514 (t) REVERT: D 389 LEU cc_start: 0.8629 (mt) cc_final: 0.8381 (mt) outliers start: 44 outliers final: 21 residues processed: 214 average time/residue: 1.4045 time to fit residues: 323.4573 Evaluate side-chains 203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12208 Z= 0.261 Angle : 0.599 8.813 16584 Z= 0.303 Chirality : 0.038 0.130 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.231 18.294 1856 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.64 % Allowed : 15.83 % Favored : 80.53 % 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: 2.03 (0.22), residues: 1500 helix: 2.31 (0.14), residues: 1236 sheet: -4.66 (0.48), residues: 52 loop : -3.10 (0.36), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.003 0.001 HIS C 22 PHE 0.014 0.001 PHE C 205 TYR 0.019 0.001 TYR C 124 ARG 0.003 0.000 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.287 Fit side-chains REVERT: A 151 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7066 (tp) REVERT: A 365 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8536 (t) REVERT: A 389 LEU cc_start: 0.8613 (mt) cc_final: 0.8356 (mt) REVERT: B 121 MET cc_start: 0.8855 (tmm) cc_final: 0.8602 (tmt) REVERT: B 151 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7069 (tp) REVERT: B 365 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8535 (t) REVERT: B 389 LEU cc_start: 0.8607 (mt) cc_final: 0.8328 (mt) REVERT: C 151 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7072 (tp) REVERT: C 179 GLN cc_start: 0.7953 (pm20) cc_final: 0.7751 (pm20) REVERT: C 365 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8536 (t) REVERT: C 389 LEU cc_start: 0.8609 (mt) cc_final: 0.8354 (mt) REVERT: D 121 MET cc_start: 0.8558 (tmt) cc_final: 0.8300 (tmt) REVERT: D 151 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7071 (tp) REVERT: D 365 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8536 (t) REVERT: D 389 LEU cc_start: 0.8607 (mt) cc_final: 0.8326 (mt) outliers start: 48 outliers final: 22 residues processed: 218 average time/residue: 1.3854 time to fit residues: 325.9641 Evaluate side-chains 205 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.0050 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12208 Z= 0.243 Angle : 0.581 8.767 16584 Z= 0.296 Chirality : 0.037 0.126 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.225 19.282 1856 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.79 % Allowed : 15.91 % Favored : 80.30 % 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: 2.20 (0.21), residues: 1500 helix: 2.32 (0.14), residues: 1236 sheet: None (None), residues: 0 loop : -3.03 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.003 0.001 HIS D 22 PHE 0.014 0.001 PHE C 205 TYR 0.017 0.001 TYR C 124 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 1.250 Fit side-chains REVERT: A 151 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7044 (tp) REVERT: A 179 GLN cc_start: 0.8029 (pm20) cc_final: 0.7810 (pm20) REVERT: A 365 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (t) REVERT: A 389 LEU cc_start: 0.8612 (mt) cc_final: 0.8387 (mt) REVERT: B 121 MET cc_start: 0.8854 (tmm) cc_final: 0.8622 (tmt) REVERT: B 151 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7046 (tp) REVERT: B 365 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8529 (t) REVERT: B 389 LEU cc_start: 0.8605 (mt) cc_final: 0.8376 (mt) REVERT: C 151 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7046 (tp) REVERT: C 365 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8533 (t) REVERT: C 389 LEU cc_start: 0.8615 (mt) cc_final: 0.8390 (mt) REVERT: D 151 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7046 (tp) REVERT: D 365 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8529 (t) REVERT: D 389 LEU cc_start: 0.8606 (mt) cc_final: 0.8377 (mt) outliers start: 50 outliers final: 24 residues processed: 218 average time/residue: 1.3506 time to fit residues: 318.2066 Evaluate side-chains 209 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 0.0060 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12208 Z= 0.222 Angle : 0.583 8.467 16584 Z= 0.296 Chirality : 0.037 0.121 2052 Planarity : 0.004 0.037 1992 Dihedral : 4.181 17.980 1856 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.64 % Allowed : 16.74 % Favored : 79.62 % 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: 2.26 (0.21), residues: 1500 helix: 2.35 (0.14), residues: 1236 sheet: None (None), residues: 0 loop : -2.97 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.003 0.000 HIS C 22 PHE 0.014 0.001 PHE C 205 TYR 0.018 0.001 TYR B 124 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 1.401 Fit side-chains REVERT: A 151 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7085 (tp) REVERT: A 179 GLN cc_start: 0.8030 (pm20) cc_final: 0.7815 (pm20) REVERT: A 365 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8589 (t) REVERT: A 389 LEU cc_start: 0.8556 (mt) cc_final: 0.8323 (mt) REVERT: B 121 MET cc_start: 0.8845 (tmm) cc_final: 0.8611 (tmt) REVERT: B 151 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7088 (tp) REVERT: B 365 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8588 (t) REVERT: B 389 LEU cc_start: 0.8547 (mt) cc_final: 0.8292 (mt) REVERT: C 151 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7090 (tp) REVERT: C 365 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8592 (t) REVERT: C 389 LEU cc_start: 0.8584 (mt) cc_final: 0.8350 (mt) REVERT: D 151 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7088 (tp) REVERT: D 365 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8590 (t) REVERT: D 389 LEU cc_start: 0.8551 (mt) cc_final: 0.8294 (mt) outliers start: 48 outliers final: 24 residues processed: 222 average time/residue: 1.3868 time to fit residues: 331.8984 Evaluate side-chains 213 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12208 Z= 0.328 Angle : 0.643 8.588 16584 Z= 0.324 Chirality : 0.040 0.147 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.427 19.891 1856 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.03 % Allowed : 17.50 % Favored : 79.47 % 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: 1.87 (0.22), residues: 1500 helix: 2.15 (0.14), residues: 1240 sheet: -4.24 (0.55), residues: 44 loop : -3.18 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 193 HIS 0.005 0.001 HIS D 22 PHE 0.017 0.001 PHE C 205 TYR 0.017 0.002 TYR D 124 ARG 0.003 0.000 ARG D 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.383 Fit side-chains REVERT: A 151 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 179 GLN cc_start: 0.8050 (pm20) cc_final: 0.7811 (pm20) REVERT: A 193 TRP cc_start: 0.9511 (OUTLIER) cc_final: 0.7158 (m100) REVERT: A 365 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8618 (t) REVERT: B 121 MET cc_start: 0.8917 (tmm) cc_final: 0.8675 (tmt) REVERT: B 151 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6850 (tp) REVERT: B 193 TRP cc_start: 0.9510 (OUTLIER) cc_final: 0.7157 (m100) REVERT: B 365 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8617 (t) REVERT: B 389 LEU cc_start: 0.8677 (mt) cc_final: 0.8462 (mt) REVERT: C 151 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6797 (tp) REVERT: C 193 TRP cc_start: 0.9512 (OUTLIER) cc_final: 0.7159 (m100) REVERT: C 365 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8614 (t) REVERT: D 121 MET cc_start: 0.8625 (tmt) cc_final: 0.8300 (tmt) REVERT: D 151 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6790 (tp) REVERT: D 193 TRP cc_start: 0.9512 (OUTLIER) cc_final: 0.7161 (m100) REVERT: D 365 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8616 (t) outliers start: 40 outliers final: 25 residues processed: 220 average time/residue: 1.3974 time to fit residues: 331.0147 Evaluate side-chains 214 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 103 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117014 restraints weight = 21280.502| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.38 r_work: 0.3102 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12208 Z= 0.209 Angle : 0.614 13.861 16584 Z= 0.307 Chirality : 0.037 0.121 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.248 18.853 1856 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.73 % Allowed : 18.33 % Favored : 78.94 % 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: 2.20 (0.21), residues: 1500 helix: 2.31 (0.14), residues: 1236 sheet: None (None), residues: 0 loop : -2.97 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 193 HIS 0.002 0.000 HIS C 22 PHE 0.014 0.001 PHE C 205 TYR 0.018 0.001 TYR D 124 ARG 0.003 0.000 ARG C 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4854.02 seconds wall clock time: 93 minutes 32.88 seconds (5612.88 seconds total)