Starting phenix.real_space_refine on Sun Feb 8 01:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oqj_70763/02_2026/9oqj_70763_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oqj_70763/02_2026/9oqj_70763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oqj_70763/02_2026/9oqj_70763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oqj_70763/02_2026/9oqj_70763.map" model { file = "/net/cci-nas-00/data/ceres_data/9oqj_70763/02_2026/9oqj_70763_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oqj_70763/02_2026/9oqj_70763_trim.cif" } resolution = 2.66 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= 0.001 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 77 5.16 5 C 12754 2.51 5 N 2898 2.21 5 O 3234 1.98 5 H 17927 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36897 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 6.06, per 1000 atoms: 0.16 Number of scatterers: 36897 At special positions: 0 Unit cell: (109.65, 109.65, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 7 15.00 O 3234 8.00 N 2898 7.00 C 12754 6.00 H 17927 1.00 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 Links applied NAG-ASN " NAG A 504 " - " ASN A 255 " " NAG B 504 " - " ASN B 255 " " NAG C 504 " - " ASN C 255 " " NAG D 504 " - " ASN D 255 " " NAG E 504 " - " ASN E 255 " " NAG F 504 " - " ASN F 255 " " NAG G 504 " - " ASN G 255 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 70.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.610A 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 100 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 removed outlier: 4.213A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.616A pdb=" N VAL A 308 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.659A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.610A 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 100 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 removed outlier: 3.532A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.796A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 254 removed outlier: 4.216A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.616A pdb=" N VAL B 308 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 356 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.657A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.611A 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 100 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.617A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.904A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 356 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.660A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.610A 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 100 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.797A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.619A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 356 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.611A 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 100 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.617A pdb=" N VAL E 308 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.900A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 356 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.657A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.609A 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 100 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 305 through 312 removed outlier: 3.614A pdb=" N VAL F 308 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 356 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.610A 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 100 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 removed outlier: 3.533A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 254 removed outlier: 4.216A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.615A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 356 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.659A 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 removed outlier: 3.599A pdb=" N VAL A 245 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.601A pdb=" N VAL B 245 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL C 245 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL D 245 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.597A pdb=" N VAL E 245 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL F 245 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.601A pdb=" N VAL G 245 " --> pdb=" O GLN G 95 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3531 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: 8.47 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17892 1.03 - 1.23: 57 1.23 - 1.42: 7745 1.42 - 1.62: 11553 1.62 - 1.81: 105 Bond restraints: 37352 Sorted by residual: bond pdb=" CA TYR C 83 " pdb=" C TYR C 83 " ideal model delta sigma weight residual 1.524 1.515 0.008 1.27e-02 6.20e+03 4.47e-01 bond pdb=" CB TRP B 74 " pdb=" CG TRP B 74 " ideal model delta sigma weight residual 1.498 1.518 -0.020 3.10e-02 1.04e+03 4.12e-01 bond pdb=" CB TRP D 74 " pdb=" CG TRP D 74 " ideal model delta sigma weight residual 1.498 1.518 -0.020 3.10e-02 1.04e+03 4.08e-01 bond pdb=" C GLU B 310 " pdb=" N ILE B 311 " ideal model delta sigma weight residual 1.338 1.331 0.007 1.05e-02 9.07e+03 4.06e-01 bond pdb=" CG PRO E 110 " pdb=" CD PRO E 110 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.01e-01 ... (remaining 37347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 62382 1.05 - 2.10: 4669 2.10 - 3.14: 199 3.14 - 4.19: 69 4.19 - 5.24: 28 Bond angle restraints: 67347 Sorted by residual: angle pdb=" N ILE C 311 " pdb=" CA ILE C 311 " pdb=" C ILE C 311 " ideal model delta sigma weight residual 112.80 110.02 2.78 1.15e+00 7.56e-01 5.82e+00 angle pdb=" N ILE A 311 " pdb=" CA ILE A 311 " pdb=" C ILE A 311 " ideal model delta sigma weight residual 112.80 110.06 2.74 1.15e+00 7.56e-01 5.68e+00 angle pdb=" N ILE D 311 " pdb=" CA ILE D 311 " pdb=" C ILE D 311 " ideal model delta sigma weight residual 112.80 110.06 2.74 1.15e+00 7.56e-01 5.67e+00 angle pdb=" N ILE B 311 " pdb=" CA ILE B 311 " pdb=" C ILE B 311 " ideal model delta sigma weight residual 112.80 110.09 2.71 1.15e+00 7.56e-01 5.54e+00 angle pdb=" N ILE G 311 " pdb=" CA ILE G 311 " pdb=" C ILE G 311 " ideal model delta sigma weight residual 112.80 110.13 2.67 1.15e+00 7.56e-01 5.41e+00 ... (remaining 67342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 17342 16.16 - 32.33: 995 32.33 - 48.49: 294 48.49 - 64.65: 101 64.65 - 80.82: 21 Dihedral angle restraints: 18753 sinusoidal: 10192 harmonic: 8561 Sorted by residual: dihedral pdb=" CA GLU D 9 " pdb=" C GLU D 9 " pdb=" N TYR D 10 " pdb=" CA TYR D 10 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU C 9 " pdb=" C GLU C 9 " pdb=" N TYR C 10 " pdb=" CA TYR C 10 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU E 9 " pdb=" C GLU E 9 " pdb=" N TYR E 10 " pdb=" CA TYR E 10 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 18750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2540 0.040 - 0.080: 524 0.080 - 0.120: 149 0.120 - 0.159: 14 0.159 - 0.199: 7 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG F 504 " pdb=" ND2 ASN F 255 " pdb=" C2 NAG F 504 " pdb=" O5 NAG F 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 255 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" C1 NAG D 504 " pdb=" ND2 ASN D 255 " pdb=" C2 NAG D 504 " pdb=" O5 NAG D 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 3231 not shown) Planarity restraints: 5432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 122 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO F 123 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO F 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 123 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 123 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO D 123 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.018 5.00e-02 4.00e+02 ... (remaining 5429 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 19307 2.43 - 2.97: 84975 2.97 - 3.52: 101675 3.52 - 4.06: 127336 4.06 - 4.60: 195461 Nonbonded interactions: 528754 Sorted by model distance: nonbonded pdb=" HE1 TYR A 309 " pdb=" HD1 TYR A 345 " model vdw 1.889 2.100 nonbonded pdb=" HE1 TYR C 309 " pdb=" HD1 TYR C 345 " model vdw 1.890 2.100 nonbonded pdb=" HE1 TYR G 309 " pdb=" HD1 TYR G 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR D 309 " pdb=" HD1 TYR D 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR B 309 " pdb=" HD1 TYR B 345 " model vdw 1.892 2.100 ... (remaining 528749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.180 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: 0.200 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 33.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19446 Z= 0.142 Angle : 0.518 5.239 26572 Z= 0.274 Chirality : 0.037 0.199 3234 Planarity : 0.004 0.034 3136 Dihedral : 11.768 80.816 7679 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.76 % Allowed : 4.18 % Favored : 95.06 % 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: 1.79 (0.19), residues: 2380 helix: 2.34 (0.14), residues: 1610 sheet: None (None), residues: 0 loop : -1.43 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 300 TYR 0.008 0.001 TYR E 83 PHE 0.008 0.001 PHE F 109 TRP 0.008 0.002 TRP A 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00310 (19425) covalent geometry : angle 0.51634 (26523) SS BOND : bond 0.00236 ( 14) SS BOND : angle 0.97044 ( 28) hydrogen bonds : bond 0.10207 ( 1212) hydrogen bonds : angle 4.19473 ( 3531) link_NAG-ASN : bond 0.00447 ( 7) link_NAG-ASN : angle 1.36252 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 215 average time/residue: 1.1998 time to fit residues: 294.5834 Evaluate side-chains 133 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain G residue 74 TRP 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: 8.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN D 280 ASN E 280 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.101127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073559 restraints weight = 130140.998| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.64 r_work: 0.3028 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19446 Z= 0.184 Angle : 0.532 6.199 26572 Z= 0.277 Chirality : 0.037 0.178 3234 Planarity : 0.004 0.037 3136 Dihedral : 6.976 65.987 3865 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.09 % Allowed : 9.40 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 2380 helix: 2.54 (0.14), residues: 1561 sheet: None (None), residues: 0 loop : -1.13 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 75 TYR 0.019 0.001 TYR B 10 PHE 0.011 0.001 PHE G 67 TRP 0.008 0.001 TRP E 74 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00410 (19425) covalent geometry : angle 0.52967 (26523) SS BOND : bond 0.00245 ( 14) SS BOND : angle 1.02465 ( 28) hydrogen bonds : bond 0.03679 ( 1212) hydrogen bonds : angle 4.05259 ( 3531) link_NAG-ASN : bond 0.00218 ( 7) link_NAG-ASN : angle 1.33928 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.8682 (tt0) cc_final: 0.8477 (tt0) REVERT: C 9 GLU cc_start: 0.8726 (tt0) cc_final: 0.8518 (tt0) REVERT: E 209 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8866 (tp) REVERT: F 9 GLU cc_start: 0.8759 (tt0) cc_final: 0.8533 (tt0) outliers start: 20 outliers final: 8 residues processed: 162 average time/residue: 1.2872 time to fit residues: 237.6759 Evaluate side-chains 140 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 151 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 129 optimal weight: 0.0670 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070401 restraints weight = 131105.683| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.60 r_work: 0.2947 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 19446 Z= 0.213 Angle : 0.540 5.246 26572 Z= 0.285 Chirality : 0.037 0.183 3234 Planarity : 0.004 0.039 3136 Dihedral : 6.823 64.446 3859 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.54 % Allowed : 9.51 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 2380 helix: 2.57 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.11 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.024 0.001 TYR A 10 PHE 0.014 0.001 PHE E 67 TRP 0.010 0.002 TRP G 74 HIS 0.004 0.002 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00473 (19425) covalent geometry : angle 0.53794 (26523) SS BOND : bond 0.00267 ( 14) SS BOND : angle 1.28575 ( 28) hydrogen bonds : bond 0.03889 ( 1212) hydrogen bonds : angle 4.18734 ( 3531) link_NAG-ASN : bond 0.00311 ( 7) link_NAG-ASN : angle 1.29011 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8805 (tt0) cc_final: 0.8570 (tm-30) REVERT: B 9 GLU cc_start: 0.8715 (tt0) cc_final: 0.8495 (tt0) REVERT: D 9 GLU cc_start: 0.8797 (tt0) cc_final: 0.8580 (tt0) REVERT: E 9 GLU cc_start: 0.8784 (tt0) cc_final: 0.8493 (tm-30) REVERT: E 209 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8874 (tp) REVERT: F 9 GLU cc_start: 0.8742 (tt0) cc_final: 0.8505 (tm-30) outliers start: 10 outliers final: 7 residues processed: 146 average time/residue: 1.2685 time to fit residues: 210.8377 Evaluate side-chains 135 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 216 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.099358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071205 restraints weight = 130456.592| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.57 r_work: 0.2963 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19446 Z= 0.145 Angle : 0.501 5.426 26572 Z= 0.259 Chirality : 0.036 0.176 3234 Planarity : 0.004 0.038 3136 Dihedral : 6.419 60.837 3857 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.03 % Allowed : 11.24 % Favored : 87.72 % 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: 2.24 (0.19), residues: 2380 helix: 2.73 (0.14), residues: 1540 sheet: None (None), residues: 0 loop : -1.00 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.015 0.001 TYR G 10 PHE 0.010 0.001 PHE F 67 TRP 0.009 0.001 TRP A 74 HIS 0.002 0.000 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00321 (19425) covalent geometry : angle 0.49845 (26523) SS BOND : bond 0.00214 ( 14) SS BOND : angle 0.99467 ( 28) hydrogen bonds : bond 0.03472 ( 1212) hydrogen bonds : angle 4.02963 ( 3531) link_NAG-ASN : bond 0.00367 ( 7) link_NAG-ASN : angle 1.36708 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8838 (tt0) cc_final: 0.8542 (tm-30) REVERT: B 9 GLU cc_start: 0.8754 (tt0) cc_final: 0.8552 (tt0) REVERT: C 9 GLU cc_start: 0.8795 (tt0) cc_final: 0.8457 (tm-30) REVERT: E 9 GLU cc_start: 0.8773 (tt0) cc_final: 0.8496 (tm-30) REVERT: E 209 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8866 (tp) REVERT: F 9 GLU cc_start: 0.8784 (tt0) cc_final: 0.8534 (tm-30) REVERT: G 9 GLU cc_start: 0.8827 (tt0) cc_final: 0.8523 (tt0) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 1.2791 time to fit residues: 214.4106 Evaluate side-chains 138 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 193 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 213 optimal weight: 0.0050 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069661 restraints weight = 131087.371| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.55 r_work: 0.2924 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 19446 Z= 0.203 Angle : 0.527 7.921 26572 Z= 0.274 Chirality : 0.037 0.184 3234 Planarity : 0.004 0.040 3136 Dihedral : 6.593 61.213 3857 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.36 % Allowed : 11.52 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 2380 helix: 2.61 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.05 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 254 TYR 0.016 0.001 TYR G 10 PHE 0.014 0.001 PHE F 67 TRP 0.007 0.001 TRP E 74 HIS 0.003 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00451 (19425) covalent geometry : angle 0.52520 (26523) SS BOND : bond 0.00208 ( 14) SS BOND : angle 0.96551 ( 28) hydrogen bonds : bond 0.03639 ( 1212) hydrogen bonds : angle 4.10266 ( 3531) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.29806 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8724 (tt0) cc_final: 0.8495 (tm-30) REVERT: B 9 GLU cc_start: 0.8761 (tt0) cc_final: 0.8453 (tm-30) REVERT: C 9 GLU cc_start: 0.8746 (tt0) cc_final: 0.8439 (tm-30) REVERT: D 9 GLU cc_start: 0.8799 (tt0) cc_final: 0.8449 (tm-30) REVERT: E 9 GLU cc_start: 0.8788 (tt0) cc_final: 0.8506 (tm-30) REVERT: E 209 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8894 (tp) REVERT: F 9 GLU cc_start: 0.8764 (tt0) cc_final: 0.8492 (tm-30) REVERT: G 9 GLU cc_start: 0.8827 (tt0) cc_final: 0.8448 (tt0) outliers start: 25 outliers final: 14 residues processed: 147 average time/residue: 1.1881 time to fit residues: 201.0431 Evaluate side-chains 137 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068765 restraints weight = 131624.308| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.53 r_work: 0.2901 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19446 Z= 0.224 Angle : 0.536 5.205 26572 Z= 0.280 Chirality : 0.037 0.185 3234 Planarity : 0.004 0.062 3136 Dihedral : 6.780 61.635 3857 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.25 % Allowed : 11.84 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.19), residues: 2380 helix: 2.78 (0.14), residues: 1512 sheet: 0.35 (0.55), residues: 84 loop : -0.78 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.012 0.001 TYR G 10 PHE 0.016 0.001 PHE G 67 TRP 0.007 0.002 TRP A 74 HIS 0.003 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00496 (19425) covalent geometry : angle 0.53417 (26523) SS BOND : bond 0.00288 ( 14) SS BOND : angle 0.91954 ( 28) hydrogen bonds : bond 0.03696 ( 1212) hydrogen bonds : angle 4.15438 ( 3531) link_NAG-ASN : bond 0.00278 ( 7) link_NAG-ASN : angle 1.22850 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8795 (tt0) cc_final: 0.8523 (tm-30) REVERT: B 9 GLU cc_start: 0.8926 (tt0) cc_final: 0.8577 (tm-30) REVERT: C 9 GLU cc_start: 0.8860 (tt0) cc_final: 0.8519 (tm-30) REVERT: D 9 GLU cc_start: 0.8879 (tt0) cc_final: 0.8525 (tm-30) REVERT: E 9 GLU cc_start: 0.8940 (tt0) cc_final: 0.8644 (tm-30) REVERT: E 209 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8918 (tp) REVERT: F 9 GLU cc_start: 0.8906 (tt0) cc_final: 0.8584 (tm-30) REVERT: G 9 GLU cc_start: 0.9011 (tt0) cc_final: 0.8704 (tm-30) outliers start: 23 outliers final: 13 residues processed: 145 average time/residue: 1.3344 time to fit residues: 219.7554 Evaluate side-chains 133 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 169 optimal weight: 40.0000 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.097669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068895 restraints weight = 131421.749| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.54 r_work: 0.2906 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19446 Z= 0.187 Angle : 0.523 5.077 26572 Z= 0.272 Chirality : 0.036 0.183 3234 Planarity : 0.004 0.041 3136 Dihedral : 6.650 60.370 3857 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.14 % Allowed : 12.17 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.19), residues: 2380 helix: 2.79 (0.14), residues: 1512 sheet: 0.41 (0.54), residues: 84 loop : -0.79 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 254 TYR 0.011 0.001 TYR G 10 PHE 0.014 0.001 PHE G 67 TRP 0.007 0.001 TRP A 74 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00413 (19425) covalent geometry : angle 0.52184 (26523) SS BOND : bond 0.00239 ( 14) SS BOND : angle 0.83909 ( 28) hydrogen bonds : bond 0.03589 ( 1212) hydrogen bonds : angle 4.12584 ( 3531) link_NAG-ASN : bond 0.00306 ( 7) link_NAG-ASN : angle 1.25377 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.146 Fit side-chains REVERT: A 9 GLU cc_start: 0.8670 (tt0) cc_final: 0.8435 (tm-30) REVERT: B 9 GLU cc_start: 0.8755 (tt0) cc_final: 0.8447 (tm-30) REVERT: C 9 GLU cc_start: 0.8722 (tt0) cc_final: 0.8439 (tm-30) REVERT: D 9 GLU cc_start: 0.8710 (tt0) cc_final: 0.8416 (tm-30) REVERT: E 9 GLU cc_start: 0.8774 (tt0) cc_final: 0.8514 (tm-30) REVERT: E 209 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8879 (tp) REVERT: F 9 GLU cc_start: 0.8754 (tt0) cc_final: 0.8551 (tm-30) REVERT: G 9 GLU cc_start: 0.8812 (tt0) cc_final: 0.8546 (tm-30) outliers start: 21 outliers final: 16 residues processed: 137 average time/residue: 1.2383 time to fit residues: 195.2516 Evaluate side-chains 134 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS 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 147 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.098504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070270 restraints weight = 130507.648| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.53 r_work: 0.2943 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19446 Z= 0.126 Angle : 0.501 5.188 26572 Z= 0.259 Chirality : 0.035 0.172 3234 Planarity : 0.004 0.040 3136 Dihedral : 6.198 57.594 3857 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.36 % Allowed : 12.44 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 2380 helix: 2.62 (0.14), residues: 1561 sheet: None (None), residues: 0 loop : -0.99 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 254 TYR 0.011 0.001 TYR A 230 PHE 0.009 0.001 PHE F 54 TRP 0.007 0.001 TRP D 74 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00282 (19425) covalent geometry : angle 0.49862 (26523) SS BOND : bond 0.00132 ( 14) SS BOND : angle 0.90461 ( 28) hydrogen bonds : bond 0.03330 ( 1212) hydrogen bonds : angle 4.00672 ( 3531) link_NAG-ASN : bond 0.00388 ( 7) link_NAG-ASN : angle 1.37190 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.123 Fit side-chains REVERT: A 9 GLU cc_start: 0.8659 (tt0) cc_final: 0.8410 (tm-30) REVERT: B 9 GLU cc_start: 0.8786 (tt0) cc_final: 0.8473 (tm-30) REVERT: C 9 GLU cc_start: 0.8725 (tt0) cc_final: 0.8425 (tm-30) REVERT: D 9 GLU cc_start: 0.8724 (tt0) cc_final: 0.8410 (tm-30) REVERT: E 9 GLU cc_start: 0.8765 (tt0) cc_final: 0.8528 (tm-30) REVERT: E 209 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8865 (tp) REVERT: F 9 GLU cc_start: 0.8747 (tt0) cc_final: 0.8481 (tm-30) REVERT: G 9 GLU cc_start: 0.8841 (tt0) cc_final: 0.8586 (tm-30) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 1.1358 time to fit residues: 187.8661 Evaluate side-chains 134 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS 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 177 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 219 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.068812 restraints weight = 131414.757| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.51 r_work: 0.2905 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19446 Z= 0.207 Angle : 0.535 5.551 26572 Z= 0.280 Chirality : 0.036 0.180 3234 Planarity : 0.004 0.041 3136 Dihedral : 6.528 58.583 3857 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.09 % Allowed : 12.55 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.19), residues: 2380 helix: 2.56 (0.14), residues: 1561 sheet: None (None), residues: 0 loop : -1.11 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 254 TYR 0.011 0.001 TYR D 230 PHE 0.016 0.001 PHE G 67 TRP 0.007 0.001 TRP A 74 HIS 0.002 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00460 (19425) covalent geometry : angle 0.53363 (26523) SS BOND : bond 0.00250 ( 14) SS BOND : angle 1.06075 ( 28) hydrogen bonds : bond 0.03549 ( 1212) hydrogen bonds : angle 4.10965 ( 3531) link_NAG-ASN : bond 0.00254 ( 7) link_NAG-ASN : angle 1.24534 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.276 Fit side-chains REVERT: A 9 GLU cc_start: 0.8818 (tt0) cc_final: 0.8541 (tm-30) REVERT: B 9 GLU cc_start: 0.8921 (tt0) cc_final: 0.8554 (tm-30) REVERT: C 9 GLU cc_start: 0.8870 (tt0) cc_final: 0.8532 (tm-30) REVERT: D 9 GLU cc_start: 0.8923 (tt0) cc_final: 0.8592 (tm-30) REVERT: E 9 GLU cc_start: 0.8924 (tt0) cc_final: 0.8612 (tm-30) REVERT: E 209 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8894 (tp) REVERT: F 9 GLU cc_start: 0.8902 (tt0) cc_final: 0.8577 (tm-30) REVERT: G 9 GLU cc_start: 0.8969 (tt0) cc_final: 0.8674 (tm-30) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 1.2158 time to fit residues: 187.7879 Evaluate side-chains 132 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS 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 188 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070392 restraints weight = 131209.119| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.56 r_work: 0.2946 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19446 Z= 0.115 Angle : 0.504 6.132 26572 Z= 0.260 Chirality : 0.035 0.169 3234 Planarity : 0.004 0.040 3136 Dihedral : 6.052 58.717 3857 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.20 % Allowed : 12.66 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 2380 helix: 2.59 (0.14), residues: 1568 sheet: None (None), residues: 0 loop : -1.02 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 254 TYR 0.010 0.001 TYR A 230 PHE 0.008 0.001 PHE D 54 TRP 0.008 0.001 TRP F 74 HIS 0.001 0.000 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00257 (19425) covalent geometry : angle 0.50174 (26523) SS BOND : bond 0.00138 ( 14) SS BOND : angle 0.84359 ( 28) hydrogen bonds : bond 0.03252 ( 1212) hydrogen bonds : angle 3.97562 ( 3531) link_NAG-ASN : bond 0.00388 ( 7) link_NAG-ASN : angle 1.39574 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8706 (tt0) cc_final: 0.8455 (tm-30) REVERT: B 9 GLU cc_start: 0.8793 (tt0) cc_final: 0.8456 (tm-30) REVERT: C 9 GLU cc_start: 0.8707 (tt0) cc_final: 0.8398 (tm-30) REVERT: D 9 GLU cc_start: 0.8758 (tt0) cc_final: 0.8488 (tm-30) REVERT: E 209 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8858 (tp) REVERT: G 9 GLU cc_start: 0.8833 (tt0) cc_final: 0.8566 (tm-30) outliers start: 22 outliers final: 17 residues processed: 136 average time/residue: 1.2271 time to fit residues: 191.2824 Evaluate side-chains 133 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS 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: 7.9990 chunk 69 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 210 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.098054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069833 restraints weight = 130654.296| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.53 r_work: 0.2948 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19446 Z= 0.143 Angle : 0.512 6.102 26572 Z= 0.266 Chirality : 0.035 0.170 3234 Planarity : 0.004 0.040 3136 Dihedral : 6.040 59.709 3857 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.03 % Allowed : 12.98 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 2380 helix: 2.58 (0.14), residues: 1568 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 75 TYR 0.011 0.001 TYR F 10 PHE 0.010 0.001 PHE G 67 TRP 0.007 0.001 TRP F 74 HIS 0.001 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00323 (19425) covalent geometry : angle 0.51057 (26523) SS BOND : bond 0.00185 ( 14) SS BOND : angle 0.84276 ( 28) hydrogen bonds : bond 0.03280 ( 1212) hydrogen bonds : angle 3.97825 ( 3531) link_NAG-ASN : bond 0.00346 ( 7) link_NAG-ASN : angle 1.37940 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10181.56 seconds wall clock time: 173 minutes 22.65 seconds (10402.65 seconds total)