Starting phenix.real_space_refine on Wed Nov 19 03:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbm_21593/11_2025/6wbm_21593.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbm_21593/11_2025/6wbm_21593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbm_21593/11_2025/6wbm_21593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbm_21593/11_2025/6wbm_21593.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbm_21593/11_2025/6wbm_21593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbm_21593/11_2025/6wbm_21593.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 12943 2.51 5 N 2863 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19201 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 2, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'DGA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.14, per 1000 atoms: 0.16 Number of scatterers: 19201 At special positions: 0 Unit cell: (108.808, 108.808, 120.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3297 8.00 N 2863 7.00 C 12943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 824.4 milliseconds 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 71.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.691A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.740A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 3.542A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.691A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 99 through 131 removed outlier: 4.083A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 304 through 311 removed outlier: 4.182A pdb=" N VAL B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.690A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 removed outlier: 3.585A pdb=" N PHE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 304 through 311 removed outlier: 4.180A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.691A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 295 removed outlier: 3.585A pdb=" N PHE D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 304 through 311 removed outlier: 4.180A pdb=" N VAL D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.690A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.081A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 256 removed outlier: 3.740A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.702A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.567A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.691A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 256 removed outlier: 3.740A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE F 273 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 358 removed outlier: 3.541A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.566A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.691A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 99 through 131 removed outlier: 4.081A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 256 removed outlier: 3.741A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 295 removed outlier: 3.584A pdb=" N PHE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 304 through 311 removed outlier: 4.181A pdb=" N VAL G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.703A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 358 removed outlier: 3.542A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.566A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 1212 hydrogen bonds defined for protein. 3552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2859 1.32 - 1.44: 4862 1.44 - 1.57: 11767 1.57 - 1.69: 42 1.69 - 1.81: 91 Bond restraints: 19621 Sorted by residual: bond pdb=" N VAL C 342 " pdb=" CA VAL C 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.98e+00 bond pdb=" N VAL D 342 " pdb=" CA VAL D 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL E 342 " pdb=" CA VAL E 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.97e+00 bond pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.95e+00 ... (remaining 19616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 25827 2.02 - 4.03: 675 4.03 - 6.05: 91 6.05 - 8.06: 21 8.06 - 10.08: 14 Bond angle restraints: 26628 Sorted by residual: angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 112.12 109.05 3.07 8.40e-01 1.42e+00 1.33e+01 angle pdb=" N ILE E 58 " pdb=" CA ILE E 58 " pdb=" C ILE E 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.30e+01 angle pdb=" N ILE G 58 " pdb=" CA ILE G 58 " pdb=" C ILE G 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.29e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 112.12 109.10 3.02 8.40e-01 1.42e+00 1.29e+01 angle pdb=" N ILE D 58 " pdb=" CA ILE D 58 " pdb=" C ILE D 58 " ideal model delta sigma weight residual 112.12 109.11 3.01 8.40e-01 1.42e+00 1.28e+01 ... (remaining 26623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.50: 12054 31.50 - 63.00: 539 63.00 - 94.50: 28 94.50 - 125.99: 0 125.99 - 157.49: 21 Dihedral angle restraints: 12642 sinusoidal: 5537 harmonic: 7105 Sorted by residual: dihedral pdb=" N1 PTY B 402 " pdb=" C2 PTY B 402 " pdb=" C3 PTY B 402 " pdb=" O11 PTY B 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.18 -157.49 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" N1 PTY E 402 " pdb=" C2 PTY E 402 " pdb=" C3 PTY E 402 " pdb=" O11 PTY E 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.18 -157.49 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" N1 PTY F 402 " pdb=" C2 PTY F 402 " pdb=" C3 PTY F 402 " pdb=" O11 PTY F 402 " ideal model delta sinusoidal sigma weight residual 65.33 -137.20 -157.47 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1991 0.034 - 0.067: 786 0.067 - 0.101: 255 0.101 - 0.135: 89 0.135 - 0.168: 36 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CA LEU F 200 " pdb=" N LEU F 200 " pdb=" C LEU F 200 " pdb=" CB LEU F 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA LEU A 200 " pdb=" N LEU A 200 " pdb=" C LEU A 200 " pdb=" CB LEU A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA LEU E 200 " pdb=" N LEU E 200 " pdb=" C LEU E 200 " pdb=" CB LEU E 200 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 3154 not shown) Planarity restraints: 3115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 93 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C SER B 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER B 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU B 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 93 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C SER C 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER C 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 93 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C SER A 93 " 0.023 2.00e-02 2.50e+03 pdb=" O SER A 93 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.008 2.00e-02 2.50e+03 ... (remaining 3112 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1513 2.73 - 3.27: 20315 3.27 - 3.82: 31173 3.82 - 4.36: 36916 4.36 - 4.90: 63155 Nonbonded interactions: 153072 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.237 3.040 ... (remaining 153067 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 2 through 403 or resid 405)) selection = (chain 'B' and (resid 2 through 403 or resid 405)) selection = (chain 'C' and (resid 2 through 403 or resid 405)) selection = (chain 'D' and (resid 2 through 403 or resid 405)) selection = (chain 'E' and (resid 2 through 403 or resid 405)) selection = (chain 'F' and (resid 2 through 403 or resid 405)) selection = (chain 'G' and (resid 2 through 403 or resid 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.050 19635 Z= 0.366 Angle : 0.803 10.076 26656 Z= 0.454 Chirality : 0.045 0.168 3157 Planarity : 0.004 0.026 3115 Dihedral : 17.310 157.493 7980 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.80 % Allowed : 13.15 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2359 helix: -0.23 (0.12), residues: 1568 sheet: None (None), residues: 0 loop : -2.33 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 254 TYR 0.011 0.001 TYR B 345 PHE 0.008 0.001 PHE D 67 TRP 0.008 0.001 TRP E 104 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00681 (19621) covalent geometry : angle 0.80318 (26628) SS BOND : bond 0.00065 ( 14) SS BOND : angle 0.65739 ( 28) hydrogen bonds : bond 0.13572 ( 1212) hydrogen bonds : angle 5.55503 ( 3552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.733 Fit side-chains REVERT: A 29 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8250 (mmt90) REVERT: A 57 GLU cc_start: 0.8556 (mp0) cc_final: 0.8099 (mp0) REVERT: A 337 GLU cc_start: 0.9110 (tp30) cc_final: 0.8532 (tm-30) REVERT: A 352 GLU cc_start: 0.9312 (tt0) cc_final: 0.9020 (tm-30) REVERT: B 9 GLU cc_start: 0.8521 (tt0) cc_final: 0.8214 (tt0) REVERT: B 29 ARG cc_start: 0.8685 (mmt-90) cc_final: 0.7842 (mmt-90) REVERT: B 31 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 57 GLU cc_start: 0.8776 (mp0) cc_final: 0.8258 (mp0) REVERT: B 337 GLU cc_start: 0.9058 (tp30) cc_final: 0.8360 (tm-30) REVERT: B 352 GLU cc_start: 0.9250 (tt0) cc_final: 0.8895 (tm-30) REVERT: C 9 GLU cc_start: 0.8523 (tt0) cc_final: 0.8198 (tt0) REVERT: C 29 ARG cc_start: 0.8712 (mmt-90) cc_final: 0.8016 (mmt-90) REVERT: C 57 GLU cc_start: 0.8724 (mp0) cc_final: 0.8313 (mp0) REVERT: C 128 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8471 (ttp80) REVERT: C 337 GLU cc_start: 0.9061 (tp30) cc_final: 0.8362 (tm-30) REVERT: C 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.8951 (tm-30) REVERT: D 9 GLU cc_start: 0.8477 (tt0) cc_final: 0.8188 (tt0) REVERT: D 29 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.7976 (mmt-90) REVERT: D 31 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 337 GLU cc_start: 0.9122 (tp30) cc_final: 0.8400 (tm-30) REVERT: D 352 GLU cc_start: 0.9321 (tt0) cc_final: 0.8963 (tm-30) REVERT: E 9 GLU cc_start: 0.8563 (tt0) cc_final: 0.8270 (tt0) REVERT: E 29 ARG cc_start: 0.8723 (mmt-90) cc_final: 0.7903 (mmt-90) REVERT: E 57 GLU cc_start: 0.8767 (mp0) cc_final: 0.8266 (mp0) REVERT: E 128 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8524 (ttp80) REVERT: E 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8429 (tm-30) REVERT: E 352 GLU cc_start: 0.9293 (tt0) cc_final: 0.9004 (tm-30) REVERT: F 9 GLU cc_start: 0.8553 (tt0) cc_final: 0.8241 (tt0) REVERT: F 29 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.7906 (mmt-90) REVERT: F 31 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8262 (mt-10) REVERT: F 337 GLU cc_start: 0.9115 (tp30) cc_final: 0.8297 (tm-30) REVERT: F 352 GLU cc_start: 0.9285 (tt0) cc_final: 0.8942 (tm-30) REVERT: G 9 GLU cc_start: 0.8490 (tt0) cc_final: 0.8051 (tt0) REVERT: G 29 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.7887 (mmt-90) REVERT: G 31 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8218 (mt-10) REVERT: G 57 GLU cc_start: 0.8731 (mp0) cc_final: 0.8429 (mp0) REVERT: G 337 GLU cc_start: 0.9102 (tp30) cc_final: 0.8420 (tm-30) REVERT: G 352 GLU cc_start: 0.9294 (tt0) cc_final: 0.8999 (tm-30) outliers start: 14 outliers final: 0 residues processed: 194 average time/residue: 0.7928 time to fit residues: 169.0127 Evaluate side-chains 113 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 208 ASN B 76 GLN B 208 ASN C 76 GLN D 76 GLN D 208 ASN E 76 GLN E 208 ASN F 76 GLN F 208 ASN G 76 GLN G 208 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.079623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057470 restraints weight = 56612.772| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.04 r_work: 0.2913 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19635 Z= 0.129 Angle : 0.573 6.981 26656 Z= 0.284 Chirality : 0.039 0.130 3157 Planarity : 0.004 0.031 3115 Dihedral : 15.709 136.829 4347 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 16.90 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2359 helix: 1.09 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.09 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 152 TYR 0.012 0.001 TYR A 345 PHE 0.007 0.001 PHE B 12 TRP 0.012 0.001 TRP B 104 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00288 (19621) covalent geometry : angle 0.57320 (26628) SS BOND : bond 0.00172 ( 14) SS BOND : angle 0.38033 ( 28) hydrogen bonds : bond 0.03888 ( 1212) hydrogen bonds : angle 4.34096 ( 3552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.749 Fit side-chains REVERT: A 5 GLN cc_start: 0.8123 (mp10) cc_final: 0.7674 (mp10) REVERT: A 9 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 29 ARG cc_start: 0.8786 (mmt-90) cc_final: 0.8159 (mmm-85) REVERT: A 138 ASP cc_start: 0.8717 (m-30) cc_final: 0.8322 (t0) REVERT: A 337 GLU cc_start: 0.9247 (tp30) cc_final: 0.8596 (tm-30) REVERT: A 352 GLU cc_start: 0.9417 (tt0) cc_final: 0.9161 (tm-30) REVERT: B 9 GLU cc_start: 0.8798 (tt0) cc_final: 0.8517 (tt0) REVERT: B 29 ARG cc_start: 0.8652 (mmt-90) cc_final: 0.8166 (mmt-90) REVERT: B 337 GLU cc_start: 0.9211 (tp30) cc_final: 0.8459 (tm-30) REVERT: B 352 GLU cc_start: 0.9386 (tt0) cc_final: 0.9114 (tm-30) REVERT: C 9 GLU cc_start: 0.8806 (tt0) cc_final: 0.8507 (tt0) REVERT: C 29 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.8024 (mmt-90) REVERT: C 57 GLU cc_start: 0.8884 (mp0) cc_final: 0.8471 (mp0) REVERT: C 128 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8668 (ttp80) REVERT: C 337 GLU cc_start: 0.9207 (tp30) cc_final: 0.8404 (tm-30) REVERT: C 352 GLU cc_start: 0.9391 (tt0) cc_final: 0.9106 (tm-30) REVERT: D 9 GLU cc_start: 0.8771 (tt0) cc_final: 0.8504 (tt0) REVERT: D 29 ARG cc_start: 0.8617 (mmt-90) cc_final: 0.7985 (mmt-90) REVERT: D 57 GLU cc_start: 0.8981 (mp0) cc_final: 0.8758 (mt-10) REVERT: D 337 GLU cc_start: 0.9190 (tp30) cc_final: 0.8429 (tm-30) REVERT: D 352 GLU cc_start: 0.9402 (tt0) cc_final: 0.9108 (tm-30) REVERT: E 9 GLU cc_start: 0.8776 (tt0) cc_final: 0.8461 (tt0) REVERT: E 29 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8056 (mmt-90) REVERT: E 128 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8710 (ttp80) REVERT: E 337 GLU cc_start: 0.9217 (tp30) cc_final: 0.8450 (tm-30) REVERT: E 352 GLU cc_start: 0.9378 (tt0) cc_final: 0.9115 (tm-30) REVERT: F 9 GLU cc_start: 0.8785 (tt0) cc_final: 0.8498 (tt0) REVERT: F 29 ARG cc_start: 0.8637 (mmt-90) cc_final: 0.8209 (mmt-90) REVERT: F 337 GLU cc_start: 0.9230 (tp30) cc_final: 0.8488 (tm-30) REVERT: F 352 GLU cc_start: 0.9380 (tt0) cc_final: 0.9100 (tm-30) REVERT: G 9 GLU cc_start: 0.8692 (tt0) cc_final: 0.8365 (tt0) REVERT: G 29 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.8004 (mmt-90) REVERT: G 57 GLU cc_start: 0.8884 (mp0) cc_final: 0.8456 (pm20) REVERT: G 337 GLU cc_start: 0.9230 (tp30) cc_final: 0.8385 (tm-30) REVERT: G 352 GLU cc_start: 0.9394 (tt0) cc_final: 0.9149 (tm-30) outliers start: 40 outliers final: 19 residues processed: 197 average time/residue: 0.7591 time to fit residues: 165.0497 Evaluate side-chains 128 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 159 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 101 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN C 89 GLN C 208 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.078673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056263 restraints weight = 58113.475| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.11 r_work: 0.2881 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19635 Z= 0.158 Angle : 0.568 6.670 26656 Z= 0.280 Chirality : 0.039 0.117 3157 Planarity : 0.004 0.040 3115 Dihedral : 13.166 92.846 4347 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.93 % Allowed : 16.33 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.18), residues: 2359 helix: 1.74 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.83 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 152 TYR 0.012 0.001 TYR B 345 PHE 0.009 0.001 PHE D 67 TRP 0.012 0.001 TRP G 104 HIS 0.002 0.000 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00371 (19621) covalent geometry : angle 0.56857 (26628) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.42825 ( 28) hydrogen bonds : bond 0.03752 ( 1212) hydrogen bonds : angle 4.23412 ( 3552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 112 time to evaluate : 0.749 Fit side-chains REVERT: A 5 GLN cc_start: 0.8376 (mp10) cc_final: 0.7869 (mp10) REVERT: A 29 ARG cc_start: 0.8755 (mmt-90) cc_final: 0.8221 (mmt-90) REVERT: A 336 GLU cc_start: 0.8914 (tt0) cc_final: 0.8693 (tt0) REVERT: A 337 GLU cc_start: 0.9181 (tp30) cc_final: 0.8524 (tm-30) REVERT: A 352 GLU cc_start: 0.9434 (tt0) cc_final: 0.9227 (tm-30) REVERT: B 9 GLU cc_start: 0.8750 (tt0) cc_final: 0.8474 (tt0) REVERT: B 29 ARG cc_start: 0.8649 (mmt-90) cc_final: 0.8017 (mmt-90) REVERT: B 89 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: B 337 GLU cc_start: 0.9175 (tp30) cc_final: 0.8364 (tm-30) REVERT: B 352 GLU cc_start: 0.9408 (tt0) cc_final: 0.9181 (tm-30) REVERT: C 9 GLU cc_start: 0.8780 (tt0) cc_final: 0.8498 (tt0) REVERT: C 29 ARG cc_start: 0.8689 (mmt-90) cc_final: 0.8014 (mmt-90) REVERT: C 128 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8757 (ttp80) REVERT: C 337 GLU cc_start: 0.9169 (tp30) cc_final: 0.8348 (tm-30) REVERT: C 352 GLU cc_start: 0.9425 (tt0) cc_final: 0.9174 (tm-30) REVERT: D 9 GLU cc_start: 0.8721 (tt0) cc_final: 0.8473 (tt0) REVERT: D 29 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.7794 (mmt-90) REVERT: D 57 GLU cc_start: 0.8940 (mp0) cc_final: 0.8563 (mp0) REVERT: D 337 GLU cc_start: 0.9124 (tp30) cc_final: 0.8342 (tm-30) REVERT: D 352 GLU cc_start: 0.9414 (tt0) cc_final: 0.9169 (tm-30) REVERT: E 9 GLU cc_start: 0.8758 (tt0) cc_final: 0.8448 (tt0) REVERT: E 29 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.7915 (mmt-90) REVERT: E 128 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8724 (ttp80) REVERT: E 336 GLU cc_start: 0.9033 (tt0) cc_final: 0.8808 (mt-10) REVERT: E 337 GLU cc_start: 0.9166 (tp30) cc_final: 0.8340 (tm-30) REVERT: E 352 GLU cc_start: 0.9393 (tt0) cc_final: 0.9172 (tm-30) REVERT: F 9 GLU cc_start: 0.8792 (tt0) cc_final: 0.8534 (tt0) REVERT: F 29 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8061 (mmt-90) REVERT: F 337 GLU cc_start: 0.9132 (tp30) cc_final: 0.8350 (tm-30) REVERT: F 352 GLU cc_start: 0.9407 (tt0) cc_final: 0.9150 (tm-30) REVERT: G 5 GLN cc_start: 0.8332 (mp10) cc_final: 0.8122 (mp10) REVERT: G 9 GLU cc_start: 0.8615 (tt0) cc_final: 0.8309 (tt0) REVERT: G 29 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.7826 (mmt-90) REVERT: G 57 GLU cc_start: 0.8756 (mp0) cc_final: 0.8485 (mp0) REVERT: G 336 GLU cc_start: 0.8947 (tt0) cc_final: 0.8740 (mt-10) REVERT: G 337 GLU cc_start: 0.9123 (tp30) cc_final: 0.8248 (tm-30) REVERT: G 352 GLU cc_start: 0.9415 (tt0) cc_final: 0.9193 (tm-30) outliers start: 69 outliers final: 23 residues processed: 180 average time/residue: 0.6501 time to fit residues: 131.5092 Evaluate side-chains 132 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 43 optimal weight: 0.0870 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN B 274 GLN D 89 GLN G 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057464 restraints weight = 57343.156| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.09 r_work: 0.2912 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19635 Z= 0.116 Angle : 0.532 7.145 26656 Z= 0.263 Chirality : 0.038 0.109 3157 Planarity : 0.004 0.035 3115 Dihedral : 12.311 90.834 4347 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.07 % Allowed : 17.93 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2359 helix: 1.97 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 152 TYR 0.011 0.001 TYR A 345 PHE 0.009 0.001 PHE C 109 TRP 0.014 0.001 TRP C 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00263 (19621) covalent geometry : angle 0.53248 (26628) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.34575 ( 28) hydrogen bonds : bond 0.03386 ( 1212) hydrogen bonds : angle 4.09389 ( 3552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.740 Fit side-chains REVERT: A 5 GLN cc_start: 0.8303 (mp10) cc_final: 0.7875 (mp10) REVERT: A 29 ARG cc_start: 0.8706 (mmt-90) cc_final: 0.8045 (mmt-90) REVERT: A 57 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: A 337 GLU cc_start: 0.9198 (tp30) cc_final: 0.8459 (tm-30) REVERT: B 9 GLU cc_start: 0.8757 (tt0) cc_final: 0.8500 (tt0) REVERT: B 29 ARG cc_start: 0.8615 (mmt-90) cc_final: 0.8079 (mmt-90) REVERT: B 31 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8587 (mm-30) REVERT: B 152 ARG cc_start: 0.8885 (tmm-80) cc_final: 0.8616 (ttp80) REVERT: B 337 GLU cc_start: 0.9156 (tp30) cc_final: 0.8401 (tm-30) REVERT: C 9 GLU cc_start: 0.8769 (tt0) cc_final: 0.8514 (tt0) REVERT: C 29 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8111 (mmt-90) REVERT: C 128 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8727 (ttp80) REVERT: C 337 GLU cc_start: 0.9152 (tp30) cc_final: 0.8380 (tm-30) REVERT: C 352 GLU cc_start: 0.9415 (tt0) cc_final: 0.9185 (tm-30) REVERT: D 9 GLU cc_start: 0.8708 (tt0) cc_final: 0.8462 (tt0) REVERT: D 29 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.7906 (mmt-90) REVERT: D 31 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8478 (mm-30) REVERT: D 337 GLU cc_start: 0.9096 (tp30) cc_final: 0.8331 (tm-30) REVERT: D 352 GLU cc_start: 0.9425 (tt0) cc_final: 0.9178 (tm-30) REVERT: E 9 GLU cc_start: 0.8746 (tt0) cc_final: 0.8478 (tt0) REVERT: E 29 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8038 (mmt-90) REVERT: E 57 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: E 128 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8719 (ttp80) REVERT: E 337 GLU cc_start: 0.9159 (tp30) cc_final: 0.8339 (tm-30) REVERT: E 352 GLU cc_start: 0.9397 (tt0) cc_final: 0.9188 (tm-30) REVERT: F 9 GLU cc_start: 0.8737 (tt0) cc_final: 0.8489 (tt0) REVERT: F 29 ARG cc_start: 0.8574 (mmt-90) cc_final: 0.8031 (mmt-90) REVERT: F 31 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8484 (mm-30) REVERT: F 147 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8962 (p0) REVERT: F 337 GLU cc_start: 0.9105 (tp30) cc_final: 0.8306 (tm-30) REVERT: F 352 GLU cc_start: 0.9400 (tt0) cc_final: 0.9165 (tm-30) REVERT: G 5 GLN cc_start: 0.8385 (mp10) cc_final: 0.8185 (mp10) REVERT: G 9 GLU cc_start: 0.8604 (tt0) cc_final: 0.8330 (tt0) REVERT: G 29 ARG cc_start: 0.8525 (mmt-90) cc_final: 0.7822 (mmt-90) REVERT: G 31 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8628 (mm-30) REVERT: G 57 GLU cc_start: 0.8705 (mp0) cc_final: 0.8458 (mp0) REVERT: G 337 GLU cc_start: 0.9108 (tp30) cc_final: 0.8236 (tm-30) outliers start: 54 outliers final: 26 residues processed: 167 average time/residue: 0.7060 time to fit residues: 131.0025 Evaluate side-chains 137 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 184 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 195 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 67 optimal weight: 0.0030 chunk 232 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN G 89 GLN G 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.080839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059241 restraints weight = 56845.514| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.11 r_work: 0.2966 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19635 Z= 0.101 Angle : 0.537 8.944 26656 Z= 0.259 Chirality : 0.038 0.108 3157 Planarity : 0.004 0.037 3115 Dihedral : 11.590 82.840 4347 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.05 % Allowed : 19.41 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 2359 helix: 2.18 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 152 TYR 0.011 0.001 TYR B 345 PHE 0.009 0.001 PHE G 109 TRP 0.015 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00210 (19621) covalent geometry : angle 0.53742 (26628) SS BOND : bond 0.00074 ( 14) SS BOND : angle 0.25903 ( 28) hydrogen bonds : bond 0.03022 ( 1212) hydrogen bonds : angle 3.96473 ( 3552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.674 Fit side-chains REVERT: A 29 ARG cc_start: 0.8632 (mmt-90) cc_final: 0.8028 (mmt-90) REVERT: A 57 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8636 (pm20) REVERT: A 337 GLU cc_start: 0.9200 (tp30) cc_final: 0.8451 (tm-30) REVERT: B 9 GLU cc_start: 0.8787 (tt0) cc_final: 0.8534 (tt0) REVERT: B 29 ARG cc_start: 0.8514 (mmt-90) cc_final: 0.7955 (mmt-90) REVERT: B 57 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8791 (pm20) REVERT: B 152 ARG cc_start: 0.8887 (tmm-80) cc_final: 0.8595 (ttp80) REVERT: B 337 GLU cc_start: 0.9157 (tp30) cc_final: 0.8292 (tm-30) REVERT: C 9 GLU cc_start: 0.8783 (tt0) cc_final: 0.8558 (tt0) REVERT: C 29 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.7787 (mmt-90) REVERT: C 128 ARG cc_start: 0.9051 (ttp80) cc_final: 0.8740 (ttp80) REVERT: C 337 GLU cc_start: 0.9160 (tp30) cc_final: 0.8265 (tm-30) REVERT: C 352 GLU cc_start: 0.9410 (tt0) cc_final: 0.9166 (tm-30) REVERT: D 29 ARG cc_start: 0.8517 (mmt-90) cc_final: 0.7990 (mmt-90) REVERT: D 337 GLU cc_start: 0.9085 (tp30) cc_final: 0.8271 (tm-30) REVERT: D 352 GLU cc_start: 0.9431 (tt0) cc_final: 0.9179 (tm-30) REVERT: E 9 GLU cc_start: 0.8687 (tt0) cc_final: 0.8457 (tt0) REVERT: E 29 ARG cc_start: 0.8549 (mmt-90) cc_final: 0.7972 (mmt-90) REVERT: E 57 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: E 128 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8692 (ttp80) REVERT: E 337 GLU cc_start: 0.9107 (tp30) cc_final: 0.8213 (tm-30) REVERT: E 352 GLU cc_start: 0.9398 (tt0) cc_final: 0.9181 (tm-30) REVERT: F 9 GLU cc_start: 0.8742 (tt0) cc_final: 0.8490 (tt0) REVERT: F 29 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.7937 (mmt-90) REVERT: F 147 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8952 (p0) REVERT: F 337 GLU cc_start: 0.9082 (tp30) cc_final: 0.8288 (tm-30) REVERT: F 352 GLU cc_start: 0.9388 (tt0) cc_final: 0.9156 (tm-30) REVERT: G 5 GLN cc_start: 0.8418 (mp10) cc_final: 0.8181 (mp10) REVERT: G 9 GLU cc_start: 0.8665 (tt0) cc_final: 0.8434 (tt0) REVERT: G 29 ARG cc_start: 0.8429 (mmt-90) cc_final: 0.7776 (mmt-90) REVERT: G 57 GLU cc_start: 0.8617 (mp0) cc_final: 0.8358 (mp0) REVERT: G 337 GLU cc_start: 0.9073 (tp30) cc_final: 0.8234 (tm-30) outliers start: 36 outliers final: 16 residues processed: 151 average time/residue: 0.7600 time to fit residues: 126.9693 Evaluate side-chains 123 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 71 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 135 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.080513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.058560 restraints weight = 56924.699| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.13 r_work: 0.2948 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19635 Z= 0.110 Angle : 0.534 7.177 26656 Z= 0.260 Chirality : 0.038 0.110 3157 Planarity : 0.004 0.038 3115 Dihedral : 11.105 74.081 4347 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.50 % Allowed : 20.09 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.19), residues: 2359 helix: 2.26 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.69 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 152 TYR 0.009 0.001 TYR A 345 PHE 0.007 0.001 PHE C 54 TRP 0.009 0.001 TRP F 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00249 (19621) covalent geometry : angle 0.53407 (26628) SS BOND : bond 0.00114 ( 14) SS BOND : angle 0.32732 ( 28) hydrogen bonds : bond 0.03070 ( 1212) hydrogen bonds : angle 3.91716 ( 3552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.734 Fit side-chains REVERT: A 29 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.7998 (mmt-90) REVERT: A 57 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: A 337 GLU cc_start: 0.9179 (tp30) cc_final: 0.8412 (tm-30) REVERT: B 9 GLU cc_start: 0.8785 (tt0) cc_final: 0.8547 (tt0) REVERT: B 29 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.7905 (mmt-90) REVERT: B 57 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8763 (pm20) REVERT: B 152 ARG cc_start: 0.8860 (tmm-80) cc_final: 0.8561 (ttp80) REVERT: B 337 GLU cc_start: 0.9133 (tp30) cc_final: 0.8335 (tm-30) REVERT: C 9 GLU cc_start: 0.8759 (tt0) cc_final: 0.8555 (tt0) REVERT: C 29 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.7884 (mmt-90) REVERT: C 128 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8752 (ttp80) REVERT: C 336 GLU cc_start: 0.8957 (tt0) cc_final: 0.8757 (mt-10) REVERT: C 337 GLU cc_start: 0.9134 (tp30) cc_final: 0.8191 (tm-30) REVERT: C 352 GLU cc_start: 0.9425 (tt0) cc_final: 0.9166 (tm-30) REVERT: D 29 ARG cc_start: 0.8533 (mmt-90) cc_final: 0.7924 (mmt-90) REVERT: D 337 GLU cc_start: 0.9071 (tp30) cc_final: 0.8344 (tm-30) REVERT: D 352 GLU cc_start: 0.9434 (tt0) cc_final: 0.9194 (tm-30) REVERT: E 9 GLU cc_start: 0.8662 (tt0) cc_final: 0.8455 (tt0) REVERT: E 29 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.7970 (mmt-90) REVERT: E 57 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: E 128 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8709 (ttp80) REVERT: E 337 GLU cc_start: 0.9103 (tp30) cc_final: 0.8246 (tm-30) REVERT: E 352 GLU cc_start: 0.9402 (tt0) cc_final: 0.9187 (tm-30) REVERT: F 9 GLU cc_start: 0.8743 (tt0) cc_final: 0.8496 (tt0) REVERT: F 29 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.8047 (mmt-90) REVERT: F 152 ARG cc_start: 0.8891 (tmm-80) cc_final: 0.8640 (ttp80) REVERT: F 337 GLU cc_start: 0.9079 (tp30) cc_final: 0.8313 (tm-30) REVERT: F 352 GLU cc_start: 0.9412 (tt0) cc_final: 0.9182 (tm-30) REVERT: G 5 GLN cc_start: 0.8428 (mp10) cc_final: 0.8177 (mp10) REVERT: G 9 GLU cc_start: 0.8711 (tt0) cc_final: 0.8482 (tt0) REVERT: G 29 ARG cc_start: 0.8523 (mmt-90) cc_final: 0.7806 (mmt-90) REVERT: G 31 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 57 GLU cc_start: 0.8634 (mp0) cc_final: 0.8357 (mt-10) REVERT: G 337 GLU cc_start: 0.9099 (tp30) cc_final: 0.8210 (tm-30) outliers start: 44 outliers final: 19 residues processed: 146 average time/residue: 0.7713 time to fit residues: 124.9149 Evaluate side-chains 124 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.078755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056540 restraints weight = 57748.805| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.14 r_work: 0.2890 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19635 Z= 0.167 Angle : 0.570 7.264 26656 Z= 0.280 Chirality : 0.039 0.123 3157 Planarity : 0.004 0.036 3115 Dihedral : 11.102 80.368 4347 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.73 % Allowed : 20.20 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 2359 helix: 2.22 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.62 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 152 TYR 0.010 0.001 TYR B 345 PHE 0.011 0.001 PHE A 67 TRP 0.008 0.001 TRP G 104 HIS 0.001 0.000 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00394 (19621) covalent geometry : angle 0.57004 (26628) SS BOND : bond 0.00247 ( 14) SS BOND : angle 0.47481 ( 28) hydrogen bonds : bond 0.03497 ( 1212) hydrogen bonds : angle 4.03104 ( 3552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 103 time to evaluate : 0.733 Fit side-chains REVERT: A 29 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.7994 (mmt-90) REVERT: A 89 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8642 (mt0) REVERT: A 337 GLU cc_start: 0.9173 (tp30) cc_final: 0.8458 (tm-30) REVERT: B 9 GLU cc_start: 0.8750 (tt0) cc_final: 0.8547 (tt0) REVERT: B 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.8038 (mmt-90) REVERT: B 152 ARG cc_start: 0.8883 (tmm-80) cc_final: 0.8574 (ttp80) REVERT: B 337 GLU cc_start: 0.9136 (tp30) cc_final: 0.8326 (tm-30) REVERT: C 9 GLU cc_start: 0.8717 (tt0) cc_final: 0.8477 (tt0) REVERT: C 29 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.7889 (mmt-90) REVERT: C 128 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8777 (ttp80) REVERT: C 337 GLU cc_start: 0.9103 (tp30) cc_final: 0.8272 (tm-30) REVERT: C 352 GLU cc_start: 0.9447 (tt0) cc_final: 0.9183 (tm-30) REVERT: D 29 ARG cc_start: 0.8616 (mmt-90) cc_final: 0.7852 (mmt-90) REVERT: D 337 GLU cc_start: 0.9079 (tp30) cc_final: 0.8337 (tm-30) REVERT: D 352 GLU cc_start: 0.9449 (tt0) cc_final: 0.9194 (tm-30) REVERT: E 9 GLU cc_start: 0.8695 (tt0) cc_final: 0.8462 (tt0) REVERT: E 29 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.7919 (mmt-90) REVERT: E 57 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8594 (pm20) REVERT: E 89 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8626 (mt0) REVERT: E 128 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8722 (ttp80) REVERT: E 337 GLU cc_start: 0.9079 (tp30) cc_final: 0.8234 (tm-30) REVERT: E 352 GLU cc_start: 0.9405 (tt0) cc_final: 0.9175 (tm-30) REVERT: F 9 GLU cc_start: 0.8743 (tt0) cc_final: 0.8539 (tt0) REVERT: F 29 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8042 (mmt-90) REVERT: F 152 ARG cc_start: 0.8877 (tmm-80) cc_final: 0.8570 (ttp80) REVERT: F 337 GLU cc_start: 0.9073 (tp30) cc_final: 0.8336 (tm-30) REVERT: F 352 GLU cc_start: 0.9431 (tt0) cc_final: 0.9184 (tm-30) REVERT: G 5 GLN cc_start: 0.8463 (mp10) cc_final: 0.8172 (mp10) REVERT: G 9 GLU cc_start: 0.8645 (tt0) cc_final: 0.8364 (tt0) REVERT: G 29 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.7933 (mmt-90) REVERT: G 31 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8099 (mm-30) REVERT: G 57 GLU cc_start: 0.8675 (mp0) cc_final: 0.8340 (mt-10) REVERT: G 337 GLU cc_start: 0.9096 (tp30) cc_final: 0.8294 (tm-30) outliers start: 48 outliers final: 22 residues processed: 148 average time/residue: 0.7686 time to fit residues: 126.1090 Evaluate side-chains 125 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 76 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057033 restraints weight = 57210.745| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.17 r_work: 0.2897 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19635 Z= 0.123 Angle : 0.547 7.186 26656 Z= 0.269 Chirality : 0.038 0.113 3157 Planarity : 0.004 0.037 3115 Dihedral : 10.813 85.463 4347 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.16 % Allowed : 21.12 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 2359 helix: 2.25 (0.13), residues: 1631 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 152 TYR 0.009 0.001 TYR A 345 PHE 0.007 0.001 PHE A 67 TRP 0.011 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00285 (19621) covalent geometry : angle 0.54765 (26628) SS BOND : bond 0.00138 ( 14) SS BOND : angle 0.35676 ( 28) hydrogen bonds : bond 0.03212 ( 1212) hydrogen bonds : angle 3.95729 ( 3552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.746 Fit side-chains REVERT: A 29 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.7848 (mmt-90) REVERT: A 337 GLU cc_start: 0.9179 (tp30) cc_final: 0.8374 (tm-30) REVERT: B 9 GLU cc_start: 0.8757 (tt0) cc_final: 0.8542 (tt0) REVERT: B 29 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.8007 (mmt-90) REVERT: B 152 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8575 (ttp80) REVERT: B 337 GLU cc_start: 0.9124 (tp30) cc_final: 0.8313 (tm-30) REVERT: C 29 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.7876 (mmt-90) REVERT: C 128 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8728 (ttp80) REVERT: C 336 GLU cc_start: 0.8966 (tt0) cc_final: 0.8757 (mt-10) REVERT: C 337 GLU cc_start: 0.9081 (tp30) cc_final: 0.8269 (tm-30) REVERT: C 352 GLU cc_start: 0.9434 (tt0) cc_final: 0.9189 (tm-30) REVERT: D 29 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.7945 (mmt-90) REVERT: D 337 GLU cc_start: 0.9071 (tp30) cc_final: 0.8324 (tm-30) REVERT: D 352 GLU cc_start: 0.9441 (tt0) cc_final: 0.9197 (tm-30) REVERT: E 9 GLU cc_start: 0.8652 (tt0) cc_final: 0.8435 (tt0) REVERT: E 29 ARG cc_start: 0.8583 (mmt-90) cc_final: 0.7976 (mmt-90) REVERT: E 57 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: E 128 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8717 (ttp80) REVERT: E 337 GLU cc_start: 0.9059 (tp30) cc_final: 0.8275 (tm-30) REVERT: E 352 GLU cc_start: 0.9416 (tt0) cc_final: 0.9208 (tm-30) REVERT: F 9 GLU cc_start: 0.8714 (tt0) cc_final: 0.8474 (tt0) REVERT: F 29 ARG cc_start: 0.8653 (mmt-90) cc_final: 0.8118 (mmt-90) REVERT: F 152 ARG cc_start: 0.8891 (tmm-80) cc_final: 0.8575 (ttp80) REVERT: F 337 GLU cc_start: 0.9051 (tp30) cc_final: 0.8336 (tm-30) REVERT: F 352 GLU cc_start: 0.9411 (tt0) cc_final: 0.9173 (tm-30) REVERT: G 5 GLN cc_start: 0.8441 (mp10) cc_final: 0.8157 (mp10) REVERT: G 9 GLU cc_start: 0.8658 (tt0) cc_final: 0.8393 (tt0) REVERT: G 29 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: G 31 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8098 (mm-30) REVERT: G 57 GLU cc_start: 0.8673 (mp0) cc_final: 0.8298 (mt-10) REVERT: G 254 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8834 (ttm110) REVERT: G 337 GLU cc_start: 0.9059 (tp30) cc_final: 0.8172 (tm-30) outliers start: 38 outliers final: 23 residues processed: 141 average time/residue: 0.7796 time to fit residues: 121.5466 Evaluate side-chains 122 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 116 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.077944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055766 restraints weight = 57458.960| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.15 r_work: 0.2866 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19635 Z= 0.169 Angle : 0.584 7.215 26656 Z= 0.289 Chirality : 0.039 0.170 3157 Planarity : 0.004 0.036 3115 Dihedral : 10.867 89.680 4347 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.94 % Allowed : 21.51 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.19), residues: 2359 helix: 2.20 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.56 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 152 TYR 0.009 0.001 TYR A 345 PHE 0.011 0.001 PHE A 67 TRP 0.009 0.001 TRP G 104 HIS 0.001 0.000 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00400 (19621) covalent geometry : angle 0.58404 (26628) SS BOND : bond 0.00237 ( 14) SS BOND : angle 0.45684 ( 28) hydrogen bonds : bond 0.03519 ( 1212) hydrogen bonds : angle 4.04878 ( 3552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.716 Fit side-chains REVERT: A 29 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.7955 (mmt-90) REVERT: A 337 GLU cc_start: 0.9174 (tp30) cc_final: 0.8457 (tm-30) REVERT: B 9 GLU cc_start: 0.8753 (tt0) cc_final: 0.8540 (tt0) REVERT: B 29 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8027 (mmt-90) REVERT: B 152 ARG cc_start: 0.8893 (tmm-80) cc_final: 0.8571 (ttp80) REVERT: B 337 GLU cc_start: 0.9128 (tp30) cc_final: 0.8329 (tm-30) REVERT: C 29 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.7872 (mmt-90) REVERT: C 128 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8745 (ttp80) REVERT: C 337 GLU cc_start: 0.9072 (tp30) cc_final: 0.8256 (tm-30) REVERT: C 352 GLU cc_start: 0.9437 (tt0) cc_final: 0.9187 (tm-30) REVERT: D 29 ARG cc_start: 0.8623 (mmt-90) cc_final: 0.7873 (mmt-90) REVERT: D 337 GLU cc_start: 0.9072 (tp30) cc_final: 0.8334 (tm-30) REVERT: D 352 GLU cc_start: 0.9451 (tt0) cc_final: 0.9221 (tm-30) REVERT: E 9 GLU cc_start: 0.8680 (tt0) cc_final: 0.8455 (tt0) REVERT: E 29 ARG cc_start: 0.8649 (mmt-90) cc_final: 0.8008 (mmt90) REVERT: E 57 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: E 128 ARG cc_start: 0.9071 (ttp80) cc_final: 0.8717 (ttp80) REVERT: E 337 GLU cc_start: 0.9065 (tp30) cc_final: 0.8246 (tm-30) REVERT: E 352 GLU cc_start: 0.9425 (tt0) cc_final: 0.9193 (tm-30) REVERT: F 9 GLU cc_start: 0.8712 (tt0) cc_final: 0.8507 (tt0) REVERT: F 29 ARG cc_start: 0.8661 (mmt-90) cc_final: 0.8072 (mmt-90) REVERT: F 31 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8274 (mm-30) REVERT: F 89 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: F 152 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8570 (ttp80) REVERT: F 337 GLU cc_start: 0.9060 (tp30) cc_final: 0.8312 (tm-30) REVERT: F 352 GLU cc_start: 0.9431 (tt0) cc_final: 0.9195 (tm-30) REVERT: G 5 GLN cc_start: 0.8470 (mp10) cc_final: 0.8165 (mp10) REVERT: G 9 GLU cc_start: 0.8625 (tt0) cc_final: 0.8337 (tt0) REVERT: G 29 ARG cc_start: 0.8618 (mmt-90) cc_final: 0.7905 (mmt-90) REVERT: G 31 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8096 (mm-30) REVERT: G 337 GLU cc_start: 0.9049 (tp30) cc_final: 0.8231 (tm-30) outliers start: 34 outliers final: 23 residues processed: 134 average time/residue: 0.7979 time to fit residues: 117.9676 Evaluate side-chains 119 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 50.0000 chunk 192 optimal weight: 0.1980 chunk 146 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.079595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057682 restraints weight = 57313.454| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.17 r_work: 0.2915 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19635 Z= 0.113 Angle : 0.559 9.053 26656 Z= 0.277 Chirality : 0.038 0.144 3157 Planarity : 0.004 0.087 3115 Dihedral : 10.485 89.725 4347 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.54 % Allowed : 22.03 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 2359 helix: 2.24 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.53 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 254 TYR 0.009 0.001 TYR D 345 PHE 0.008 0.001 PHE F 54 TRP 0.012 0.001 TRP G 104 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00257 (19621) covalent geometry : angle 0.55948 (26628) SS BOND : bond 0.00103 ( 14) SS BOND : angle 0.30353 ( 28) hydrogen bonds : bond 0.03101 ( 1212) hydrogen bonds : angle 3.92959 ( 3552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.680 Fit side-chains REVERT: A 29 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.7937 (mmt-90) REVERT: A 337 GLU cc_start: 0.9181 (tp30) cc_final: 0.8460 (tm-30) REVERT: B 9 GLU cc_start: 0.8765 (tt0) cc_final: 0.8553 (tt0) REVERT: B 29 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.8031 (mmt-90) REVERT: B 152 ARG cc_start: 0.8884 (tmm-80) cc_final: 0.8626 (ttp80) REVERT: B 337 GLU cc_start: 0.9112 (tp30) cc_final: 0.8355 (tm-30) REVERT: C 29 ARG cc_start: 0.8543 (mmt-90) cc_final: 0.7867 (mmt-90) REVERT: C 128 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8728 (ttp80) REVERT: C 337 GLU cc_start: 0.9073 (tp30) cc_final: 0.8300 (tm-30) REVERT: C 352 GLU cc_start: 0.9427 (tt0) cc_final: 0.9196 (tm-30) REVERT: D 29 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.7996 (mmt-90) REVERT: D 337 GLU cc_start: 0.9050 (tp30) cc_final: 0.8345 (tm-30) REVERT: D 352 GLU cc_start: 0.9439 (tt0) cc_final: 0.9212 (tm-30) REVERT: E 9 GLU cc_start: 0.8648 (tt0) cc_final: 0.8439 (tt0) REVERT: E 29 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.7961 (mmt-90) REVERT: E 57 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8605 (pm20) REVERT: E 128 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8730 (ttp80) REVERT: E 337 GLU cc_start: 0.9048 (tp30) cc_final: 0.8268 (tm-30) REVERT: E 352 GLU cc_start: 0.9406 (tt0) cc_final: 0.9201 (tm-30) REVERT: F 9 GLU cc_start: 0.8711 (tt0) cc_final: 0.8484 (tt0) REVERT: F 29 ARG cc_start: 0.8638 (mmt-90) cc_final: 0.8041 (mmt-90) REVERT: F 31 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8219 (mm-30) REVERT: F 152 ARG cc_start: 0.8849 (tmm-80) cc_final: 0.8589 (ttp80) REVERT: F 337 GLU cc_start: 0.9057 (tp30) cc_final: 0.8302 (tm-30) REVERT: F 352 GLU cc_start: 0.9416 (tt0) cc_final: 0.9177 (tm-30) REVERT: G 5 GLN cc_start: 0.8431 (mp10) cc_final: 0.8123 (mp10) REVERT: G 9 GLU cc_start: 0.8623 (tt0) cc_final: 0.8398 (tt0) REVERT: G 29 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.7784 (mmt-90) REVERT: G 31 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8050 (mm-30) REVERT: G 337 GLU cc_start: 0.9031 (tp30) cc_final: 0.8176 (tm-30) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.7766 time to fit residues: 109.3488 Evaluate side-chains 118 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 59 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 175 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 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 89 GLN E 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.080993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059376 restraints weight = 56970.494| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.19 r_work: 0.2966 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19635 Z= 0.102 Angle : 0.541 8.480 26656 Z= 0.266 Chirality : 0.037 0.126 3157 Planarity : 0.004 0.037 3115 Dihedral : 9.658 75.798 4347 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.42 % Allowed : 22.25 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 2359 helix: 2.38 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -1.57 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 254 TYR 0.009 0.001 TYR D 345 PHE 0.007 0.001 PHE D 334 TRP 0.010 0.001 TRP G 104 HIS 0.001 0.000 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00229 (19621) covalent geometry : angle 0.54085 (26628) SS BOND : bond 0.00083 ( 14) SS BOND : angle 0.26772 ( 28) hydrogen bonds : bond 0.02824 ( 1212) hydrogen bonds : angle 3.82133 ( 3552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5454.86 seconds wall clock time: 93 minutes 57.19 seconds (5637.19 seconds total)