Starting phenix.real_space_refine on Thu Feb 5 15:07:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hf1_52104/02_2026/9hf1_52104.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hf1_52104/02_2026/9hf1_52104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hf1_52104/02_2026/9hf1_52104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hf1_52104/02_2026/9hf1_52104.map" model { file = "/net/cci-nas-00/data/ceres_data/9hf1_52104/02_2026/9hf1_52104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hf1_52104/02_2026/9hf1_52104.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 11942 2.51 5 N 2744 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 17913 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2559 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.10, per 1000 atoms: 0.12 Number of scatterers: 17913 At special positions: 0 Unit cell: (110.528, 111.936, 113.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3129 8.00 N 2744 7.00 C 11942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 264 " distance=2.02 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.02 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.02 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.02 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.02 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 536.3 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 77.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.230A pdb=" N HIS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 55 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.366A pdb=" N GLN A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 131 removed outlier: 4.482A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 156 removed outlier: 3.693A pdb=" N ALA A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 206 through 236 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.780A pdb=" N ASP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 removed outlier: 4.052A pdb=" N ILE A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.507A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.761A pdb=" N VAL A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 removed outlier: 4.001A pdb=" N SER A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 32 through 55 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 90 removed outlier: 4.367A pdb=" N GLN B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 131 removed outlier: 4.481A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 156 removed outlier: 3.693A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 206 through 236 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.780A pdb=" N ASP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 295 removed outlier: 4.052A pdb=" N ILE B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.507A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.762A pdb=" N VAL B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 removed outlier: 4.001A pdb=" N SER B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 363 through 369 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 32 through 55 Proline residue: C 46 - end of helix removed outlier: 3.500A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.367A pdb=" N GLN C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 131 removed outlier: 4.482A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 156 removed outlier: 3.693A pdb=" N ALA C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 206 through 236 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.780A pdb=" N ASP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 295 removed outlier: 4.052A pdb=" N ILE C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.507A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.761A pdb=" N VAL C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 339 removed outlier: 4.001A pdb=" N SER C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 32 through 55 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 90 removed outlier: 4.368A pdb=" N GLN D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 131 removed outlier: 4.481A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 156 removed outlier: 3.693A pdb=" N ALA D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 206 through 236 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 249 through 255 removed outlier: 3.781A pdb=" N ASP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 295 removed outlier: 4.052A pdb=" N ILE D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.508A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.762A pdb=" N VAL D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 removed outlier: 4.000A pdb=" N SER D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 32 through 55 Proline residue: E 46 - end of helix removed outlier: 3.500A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 90 removed outlier: 4.367A pdb=" N GLN E 89 " --> pdb=" O TRP E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.482A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 156 removed outlier: 3.693A pdb=" N ALA E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 206 through 236 Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.780A pdb=" N ASP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 295 removed outlier: 4.053A pdb=" N ILE E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.508A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 303 through 310 removed outlier: 3.761A pdb=" N VAL E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 339 removed outlier: 4.000A pdb=" N SER E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 363 through 369 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 32 through 55 Proline residue: F 46 - end of helix removed outlier: 3.500A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 90 removed outlier: 4.367A pdb=" N GLN F 89 " --> pdb=" O TRP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 131 removed outlier: 4.481A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 156 removed outlier: 3.693A pdb=" N ALA F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 206 through 236 Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.780A pdb=" N ASP F 255 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 295 removed outlier: 4.052A pdb=" N ILE F 271 " --> pdb=" O ILE F 267 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.508A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 303 through 310 removed outlier: 3.762A pdb=" N VAL F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 339 removed outlier: 4.001A pdb=" N SER F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 355 Processing helix chain 'F' and resid 363 through 369 Processing helix chain 'G' and resid 2 through 11 Processing helix chain 'G' and resid 32 through 55 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 90 removed outlier: 4.367A pdb=" N GLN G 89 " --> pdb=" O TRP G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 131 removed outlier: 4.481A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 156 removed outlier: 3.692A pdb=" N ALA G 156 " --> pdb=" O ARG G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 206 through 236 Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 249 through 255 removed outlier: 3.781A pdb=" N ASP G 255 " --> pdb=" O VAL G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 295 removed outlier: 4.052A pdb=" N ILE G 271 " --> pdb=" O ILE G 267 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.507A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 303 through 310 removed outlier: 3.761A pdb=" N VAL G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 339 removed outlier: 4.001A pdb=" N SER G 339 " --> pdb=" O GLU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 355 Processing helix chain 'G' and resid 363 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.452A pdb=" N GLN A 263 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.452A pdb=" N GLN B 263 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.452A pdb=" N GLN C 263 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.452A pdb=" N GLN D 263 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.452A pdb=" N GLN E 263 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.453A pdb=" N GLN F 263 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.452A pdb=" N GLN G 263 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5264 1.34 - 1.46: 3974 1.46 - 1.58: 8955 1.58 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 18326 Sorted by residual: bond pdb=" CA ILE E 287 " pdb=" CB ILE E 287 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.55e+00 bond pdb=" CA ILE A 287 " pdb=" CB ILE A 287 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.47e+00 bond pdb=" CA ILE G 287 " pdb=" CB ILE G 287 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.27e+00 bond pdb=" CA ILE C 287 " pdb=" CB ILE C 287 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.22e+00 bond pdb=" CA ILE F 287 " pdb=" CB ILE F 287 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.17e+00 ... (remaining 18321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 23560 1.30 - 2.60: 1038 2.60 - 3.90: 159 3.90 - 5.21: 59 5.21 - 6.51: 20 Bond angle restraints: 24836 Sorted by residual: angle pdb=" CA TYR E 10 " pdb=" CB TYR E 10 " pdb=" CG TYR E 10 " ideal model delta sigma weight residual 113.90 107.39 6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TYR F 10 " pdb=" CB TYR F 10 " pdb=" CG TYR F 10 " ideal model delta sigma weight residual 113.90 107.41 6.49 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CA TYR G 10 " pdb=" CB TYR G 10 " pdb=" CG TYR G 10 " ideal model delta sigma weight residual 113.90 107.41 6.49 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CA TYR A 10 " pdb=" CB TYR A 10 " pdb=" CG TYR A 10 " ideal model delta sigma weight residual 113.90 107.42 6.48 1.80e+00 3.09e-01 1.30e+01 angle pdb=" CA TYR D 10 " pdb=" CB TYR D 10 " pdb=" CG TYR D 10 " ideal model delta sigma weight residual 113.90 107.44 6.46 1.80e+00 3.09e-01 1.29e+01 ... (remaining 24831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 10053 16.30 - 32.60: 716 32.60 - 48.90: 179 48.90 - 65.20: 28 65.20 - 81.50: 14 Dihedral angle restraints: 10990 sinusoidal: 4319 harmonic: 6671 Sorted by residual: dihedral pdb=" CA SER B 249 " pdb=" C SER B 249 " pdb=" N GLY B 250 " pdb=" CA GLY B 250 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA SER D 249 " pdb=" C SER D 249 " pdb=" N GLY D 250 " pdb=" CA GLY D 250 " ideal model delta harmonic sigma weight residual 180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA SER G 249 " pdb=" C SER G 249 " pdb=" N GLY G 250 " pdb=" CA GLY G 250 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 10987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2142 0.039 - 0.078: 601 0.078 - 0.116: 181 0.116 - 0.155: 26 0.155 - 0.194: 11 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA GLN D 89 " pdb=" N GLN D 89 " pdb=" C GLN D 89 " pdb=" CB GLN D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA GLN E 89 " pdb=" N GLN E 89 " pdb=" C GLN E 89 " pdb=" CB GLN E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA GLN G 89 " pdb=" N GLN G 89 " pdb=" C GLN G 89 " pdb=" CB GLN G 89 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 2958 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 10 " -0.023 2.00e-02 2.50e+03 1.93e-02 7.46e+00 pdb=" CG TYR D 10 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 10 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 10 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 10 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 10 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 10 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR D 10 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 10 " -0.023 2.00e-02 2.50e+03 1.93e-02 7.46e+00 pdb=" CG TYR G 10 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR G 10 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR G 10 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR G 10 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR G 10 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 10 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR G 10 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 10 " -0.023 2.00e-02 2.50e+03 1.93e-02 7.44e+00 pdb=" CG TYR C 10 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR C 10 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 10 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 10 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 10 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 10 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR C 10 " -0.024 2.00e-02 2.50e+03 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 78 2.49 - 3.09: 13794 3.09 - 3.69: 29150 3.69 - 4.30: 42745 4.30 - 4.90: 67138 Nonbonded interactions: 152905 Sorted by model distance: nonbonded pdb=" NE2 GLN F 90 " pdb=" OD2 ASP G 241 " model vdw 1.883 3.120 nonbonded pdb=" NE2 GLN C 90 " pdb=" OD2 ASP D 241 " model vdw 1.887 3.120 nonbonded pdb=" OD2 ASP A 241 " pdb=" NE2 GLN G 90 " model vdw 1.889 3.120 nonbonded pdb=" NE2 GLN B 90 " pdb=" OD2 ASP C 241 " model vdw 1.889 3.120 nonbonded pdb=" NE2 GLN E 90 " pdb=" OD2 ASP F 241 " model vdw 1.889 3.120 ... (remaining 152900 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 0.032 18340 Z= 0.142 Angle : 0.666 6.508 24864 Z= 0.389 Chirality : 0.041 0.194 2961 Planarity : 0.005 0.047 2975 Dihedral : 13.078 81.504 6594 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.03 % Allowed : 3.45 % Favored : 95.52 % 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: 0.20 (0.17), residues: 2170 helix: 0.51 (0.12), residues: 1540 sheet: None (None), residues: 0 loop : -0.56 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG E 216 TYR 0.031 0.005 TYR D 10 PHE 0.026 0.002 PHE G 54 TRP 0.015 0.003 TRP E 85 HIS 0.007 0.001 HIS F 318 Details of bonding type rmsd covalent geometry : bond 0.00313 (18326) covalent geometry : angle 0.66464 (24836) SS BOND : bond 0.00464 ( 14) SS BOND : angle 1.37767 ( 28) hydrogen bonds : bond 0.21496 ( 1208) hydrogen bonds : angle 7.14701 ( 3582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 681 time to evaluate : 0.717 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5053 (tmt) cc_final: 0.3406 (tpt) REVERT: A 37 MET cc_start: 0.9237 (mmp) cc_final: 0.8897 (mmp) REVERT: A 45 LEU cc_start: 0.9612 (tp) cc_final: 0.9338 (tp) REVERT: A 49 LEU cc_start: 0.9635 (mt) cc_final: 0.9381 (mt) REVERT: A 119 LEU cc_start: 0.9611 (mt) cc_final: 0.9370 (mt) REVERT: A 134 HIS cc_start: 0.8975 (t70) cc_final: 0.8737 (t-170) REVERT: A 147 ASP cc_start: 0.9559 (m-30) cc_final: 0.9355 (m-30) REVERT: B 1 MET cc_start: 0.5018 (tmt) cc_final: 0.3755 (tpt) REVERT: B 37 MET cc_start: 0.9225 (mmp) cc_final: 0.8897 (mmp) REVERT: B 45 LEU cc_start: 0.9613 (tp) cc_final: 0.9352 (tp) REVERT: B 49 LEU cc_start: 0.9638 (mt) cc_final: 0.9348 (mt) REVERT: B 119 LEU cc_start: 0.9593 (mt) cc_final: 0.9355 (mt) REVERT: B 134 HIS cc_start: 0.8981 (t70) cc_final: 0.8737 (t-170) REVERT: B 147 ASP cc_start: 0.9562 (m-30) cc_final: 0.9343 (m-30) REVERT: C 1 MET cc_start: 0.5008 (tmt) cc_final: 0.3365 (tpt) REVERT: C 37 MET cc_start: 0.9205 (mmp) cc_final: 0.8886 (mmp) REVERT: C 45 LEU cc_start: 0.9614 (tp) cc_final: 0.9343 (tp) REVERT: C 49 LEU cc_start: 0.9616 (mt) cc_final: 0.9354 (mt) REVERT: C 119 LEU cc_start: 0.9599 (mt) cc_final: 0.9367 (mt) REVERT: C 134 HIS cc_start: 0.9030 (t70) cc_final: 0.8797 (t-170) REVERT: D 1 MET cc_start: 0.4949 (tmt) cc_final: 0.3281 (tpt) REVERT: D 37 MET cc_start: 0.9208 (mmp) cc_final: 0.8879 (mmp) REVERT: D 45 LEU cc_start: 0.9613 (tp) cc_final: 0.9324 (tp) REVERT: D 49 LEU cc_start: 0.9636 (mt) cc_final: 0.9371 (mt) REVERT: D 81 ASP cc_start: 0.8874 (m-30) cc_final: 0.8540 (m-30) REVERT: D 119 LEU cc_start: 0.9595 (mt) cc_final: 0.9353 (mt) REVERT: D 134 HIS cc_start: 0.9029 (t70) cc_final: 0.8781 (t-170) REVERT: D 147 ASP cc_start: 0.9548 (m-30) cc_final: 0.9339 (m-30) REVERT: E 1 MET cc_start: 0.5209 (tmt) cc_final: 0.3606 (tpt) REVERT: E 37 MET cc_start: 0.9169 (mmp) cc_final: 0.8840 (mmp) REVERT: E 81 ASP cc_start: 0.8877 (m-30) cc_final: 0.8625 (m-30) REVERT: E 85 TRP cc_start: 0.9444 (t-100) cc_final: 0.8946 (t-100) REVERT: E 119 LEU cc_start: 0.9608 (mt) cc_final: 0.9364 (mt) REVERT: E 134 HIS cc_start: 0.8990 (t70) cc_final: 0.8755 (t-170) REVERT: E 147 ASP cc_start: 0.9563 (m-30) cc_final: 0.9346 (m-30) REVERT: F 1 MET cc_start: 0.5150 (tmt) cc_final: 0.3464 (tpt) REVERT: F 37 MET cc_start: 0.9214 (mmp) cc_final: 0.8873 (mmp) REVERT: F 49 LEU cc_start: 0.9617 (mt) cc_final: 0.9383 (mt) REVERT: F 81 ASP cc_start: 0.8892 (m-30) cc_final: 0.8677 (m-30) REVERT: F 119 LEU cc_start: 0.9589 (mt) cc_final: 0.9345 (mt) REVERT: F 134 HIS cc_start: 0.8993 (t70) cc_final: 0.8771 (t-170) REVERT: F 147 ASP cc_start: 0.9566 (m-30) cc_final: 0.9350 (m-30) REVERT: G 1 MET cc_start: 0.5041 (tmt) cc_final: 0.3841 (tpt) REVERT: G 37 MET cc_start: 0.9221 (mmp) cc_final: 0.8919 (mmp) REVERT: G 81 ASP cc_start: 0.8880 (m-30) cc_final: 0.8665 (m-30) REVERT: G 85 TRP cc_start: 0.9440 (t-100) cc_final: 0.9063 (t-100) REVERT: G 119 LEU cc_start: 0.9608 (mt) cc_final: 0.9363 (mt) REVERT: G 134 HIS cc_start: 0.9009 (t70) cc_final: 0.8785 (t-170) REVERT: G 147 ASP cc_start: 0.9569 (m-30) cc_final: 0.9368 (m-30) outliers start: 21 outliers final: 4 residues processed: 688 average time/residue: 0.1410 time to fit residues: 144.8055 Evaluate side-chains 427 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 423 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain G residue 279 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 134 HIS B 279 ASN C 134 HIS C 279 ASN D 134 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN E 134 HIS F 134 HIS G 134 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060736 restraints weight = 75517.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.062738 restraints weight = 43471.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.064122 restraints weight = 30196.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.065052 restraints weight = 23500.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.065648 restraints weight = 19733.929| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18340 Z= 0.202 Angle : 0.789 9.475 24864 Z= 0.407 Chirality : 0.045 0.178 2961 Planarity : 0.004 0.030 2975 Dihedral : 6.071 28.528 2374 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.76 % Allowed : 12.56 % Favored : 84.68 % 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: 1.36 (0.18), residues: 2170 helix: 1.33 (0.13), residues: 1568 sheet: 2.47 (0.86), residues: 42 loop : -0.29 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 128 TYR 0.020 0.003 TYR G 233 PHE 0.032 0.002 PHE F 54 TRP 0.013 0.003 TRP B 127 HIS 0.004 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00414 (18326) covalent geometry : angle 0.78814 (24836) SS BOND : bond 0.00388 ( 14) SS BOND : angle 1.46908 ( 28) hydrogen bonds : bond 0.06951 ( 1208) hydrogen bonds : angle 5.79316 ( 3582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 485 time to evaluate : 0.697 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3989 (tmt) cc_final: 0.2512 (tpt) REVERT: A 37 MET cc_start: 0.9247 (mmp) cc_final: 0.8877 (mmp) REVERT: A 49 LEU cc_start: 0.9540 (mt) cc_final: 0.9092 (mp) REVERT: A 283 TYR cc_start: 0.9708 (m-10) cc_final: 0.9438 (m-80) REVERT: A 329 LEU cc_start: 0.9582 (tp) cc_final: 0.9369 (pp) REVERT: B 1 MET cc_start: 0.4074 (tmt) cc_final: 0.2085 (tpt) REVERT: B 37 MET cc_start: 0.9266 (mmp) cc_final: 0.8924 (mmp) REVERT: B 210 MET cc_start: 0.8927 (mmm) cc_final: 0.8563 (mmm) REVERT: B 233 TYR cc_start: 0.8302 (t80) cc_final: 0.7874 (t80) REVERT: B 283 TYR cc_start: 0.9696 (m-10) cc_final: 0.9321 (m-10) REVERT: B 329 LEU cc_start: 0.9581 (tp) cc_final: 0.9362 (pp) REVERT: C 1 MET cc_start: 0.3743 (tmt) cc_final: 0.2152 (tpt) REVERT: C 37 MET cc_start: 0.9254 (mmp) cc_final: 0.8892 (mmp) REVERT: C 49 LEU cc_start: 0.9520 (mt) cc_final: 0.9298 (mp) REVERT: C 283 TYR cc_start: 0.9671 (m-10) cc_final: 0.9328 (m-10) REVERT: C 329 LEU cc_start: 0.9601 (tp) cc_final: 0.9368 (pp) REVERT: D 1 MET cc_start: 0.4135 (tmt) cc_final: 0.2222 (tpt) REVERT: D 37 MET cc_start: 0.9276 (mmp) cc_final: 0.8913 (mmp) REVERT: D 49 LEU cc_start: 0.9555 (mt) cc_final: 0.9251 (mt) REVERT: D 210 MET cc_start: 0.8942 (mmm) cc_final: 0.8443 (mmm) REVERT: D 283 TYR cc_start: 0.9684 (m-10) cc_final: 0.9324 (m-10) REVERT: D 329 LEU cc_start: 0.9591 (tp) cc_final: 0.9367 (pp) REVERT: E 1 MET cc_start: 0.3798 (tmt) cc_final: 0.2079 (tpt) REVERT: E 37 MET cc_start: 0.9261 (mmp) cc_final: 0.8911 (mmp) REVERT: E 279 ASN cc_start: 0.9529 (OUTLIER) cc_final: 0.8828 (t0) REVERT: E 283 TYR cc_start: 0.9677 (m-10) cc_final: 0.9237 (m-10) REVERT: E 329 LEU cc_start: 0.9570 (tp) cc_final: 0.9360 (pp) REVERT: F 1 MET cc_start: 0.4066 (tmt) cc_final: 0.2275 (tpt) REVERT: F 37 MET cc_start: 0.9261 (mmp) cc_final: 0.8900 (mmp) REVERT: F 49 LEU cc_start: 0.9557 (mt) cc_final: 0.9308 (mt) REVERT: F 81 ASP cc_start: 0.9031 (m-30) cc_final: 0.8817 (m-30) REVERT: F 279 ASN cc_start: 0.9590 (t160) cc_final: 0.9096 (t0) REVERT: F 283 TYR cc_start: 0.9676 (m-10) cc_final: 0.9246 (m-10) REVERT: F 332 LEU cc_start: 0.9688 (mt) cc_final: 0.9423 (pp) REVERT: G 1 MET cc_start: 0.3988 (tmt) cc_final: 0.2136 (tpt) REVERT: G 37 MET cc_start: 0.9262 (mmp) cc_final: 0.8891 (mmp) REVERT: G 48 LEU cc_start: 0.9404 (pp) cc_final: 0.9103 (mm) REVERT: G 49 LEU cc_start: 0.9504 (mt) cc_final: 0.9197 (mp) REVERT: G 63 GLN cc_start: 0.8960 (mp10) cc_final: 0.8751 (mp10) REVERT: G 279 ASN cc_start: 0.9568 (t160) cc_final: 0.9005 (t0) REVERT: G 283 TYR cc_start: 0.9677 (m-10) cc_final: 0.9240 (m-10) REVERT: G 329 LEU cc_start: 0.9570 (tp) cc_final: 0.9340 (pp) outliers start: 56 outliers final: 30 residues processed: 524 average time/residue: 0.1334 time to fit residues: 108.2063 Evaluate side-chains 403 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 372 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 142 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 138 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN B 134 HIS ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN C 134 HIS C 204 ASN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN D 134 HIS D 204 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN E 134 HIS ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 204 ASN ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 ASN G 134 HIS G 204 ASN ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.082105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063320 restraints weight = 74161.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.065698 restraints weight = 38356.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.067308 restraints weight = 24981.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.068386 restraints weight = 18413.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.069143 restraints weight = 14862.489| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18340 Z= 0.189 Angle : 0.760 9.056 24864 Z= 0.390 Chirality : 0.048 0.368 2961 Planarity : 0.004 0.027 2975 Dihedral : 5.698 22.879 2370 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.99 % Allowed : 16.60 % Favored : 79.41 % 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: 1.05 (0.18), residues: 2170 helix: 1.08 (0.13), residues: 1589 sheet: 2.73 (0.78), residues: 42 loop : -0.44 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 216 TYR 0.018 0.002 TYR G 233 PHE 0.034 0.002 PHE E 54 TRP 0.019 0.002 TRP G 85 HIS 0.008 0.002 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00397 (18326) covalent geometry : angle 0.75869 (24836) SS BOND : bond 0.00317 ( 14) SS BOND : angle 1.30312 ( 28) hydrogen bonds : bond 0.06222 ( 1208) hydrogen bonds : angle 5.62143 ( 3582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 420 time to evaluate : 0.677 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4087 (tmt) cc_final: 0.2444 (tpt) REVERT: A 37 MET cc_start: 0.9258 (mmp) cc_final: 0.8815 (mmm) REVERT: A 49 LEU cc_start: 0.9539 (mt) cc_final: 0.9277 (mt) REVERT: A 54 PHE cc_start: 0.8898 (m-10) cc_final: 0.8657 (m-10) REVERT: A 57 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 233 TYR cc_start: 0.8264 (t80) cc_final: 0.8050 (t80) REVERT: A 279 ASN cc_start: 0.9600 (OUTLIER) cc_final: 0.9051 (t0) REVERT: A 283 TYR cc_start: 0.9669 (m-10) cc_final: 0.9255 (m-10) REVERT: B 1 MET cc_start: 0.3817 (tmt) cc_final: 0.2236 (tpt) REVERT: B 37 MET cc_start: 0.9237 (mmp) cc_final: 0.8861 (mmm) REVERT: B 49 LEU cc_start: 0.9599 (mt) cc_final: 0.9339 (mt) REVERT: B 233 TYR cc_start: 0.8273 (t80) cc_final: 0.7808 (t80) REVERT: C 1 MET cc_start: 0.3845 (tmt) cc_final: 0.2257 (tpt) REVERT: C 37 MET cc_start: 0.9248 (mmp) cc_final: 0.8812 (mmm) REVERT: C 210 MET cc_start: 0.8863 (mmm) cc_final: 0.8350 (mmm) REVERT: C 279 ASN cc_start: 0.9041 (t0) cc_final: 0.8610 (t0) REVERT: C 283 TYR cc_start: 0.9621 (m-10) cc_final: 0.9260 (m-10) REVERT: D 1 MET cc_start: 0.3899 (tmt) cc_final: 0.2120 (tpt) REVERT: D 37 MET cc_start: 0.9252 (mmp) cc_final: 0.8813 (mmm) REVERT: D 279 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8659 (t0) REVERT: D 283 TYR cc_start: 0.9620 (m-10) cc_final: 0.9278 (m-10) REVERT: D 332 LEU cc_start: 0.9747 (mm) cc_final: 0.9520 (pp) REVERT: E 1 MET cc_start: 0.4019 (tmt) cc_final: 0.2099 (tpt) REVERT: E 37 MET cc_start: 0.9240 (mmp) cc_final: 0.8823 (mmm) REVERT: E 279 ASN cc_start: 0.9541 (OUTLIER) cc_final: 0.9024 (t0) REVERT: E 283 TYR cc_start: 0.9711 (m-10) cc_final: 0.9285 (m-10) REVERT: E 332 LEU cc_start: 0.9752 (mm) cc_final: 0.9526 (pp) REVERT: F 1 MET cc_start: 0.3868 (tmt) cc_final: 0.2202 (tpt) REVERT: F 37 MET cc_start: 0.9249 (mmp) cc_final: 0.8852 (mmm) REVERT: F 210 MET cc_start: 0.8676 (mmm) cc_final: 0.8162 (mmm) REVERT: F 332 LEU cc_start: 0.9693 (mt) cc_final: 0.9463 (pp) REVERT: G 1 MET cc_start: 0.3884 (tmt) cc_final: 0.2310 (tpt) REVERT: G 37 MET cc_start: 0.9251 (mmp) cc_final: 0.8829 (mmm) REVERT: G 279 ASN cc_start: 0.9589 (t160) cc_final: 0.9102 (t0) REVERT: G 283 TYR cc_start: 0.9711 (m-10) cc_final: 0.9244 (m-10) REVERT: G 332 LEU cc_start: 0.9744 (mm) cc_final: 0.9522 (pp) outliers start: 81 outliers final: 36 residues processed: 470 average time/residue: 0.1181 time to fit residues: 86.2329 Evaluate side-chains 397 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 357 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN B 279 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN D 352 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 ASN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN G 352 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.079540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061231 restraints weight = 73992.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063374 restraints weight = 40429.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.064811 restraints weight = 27241.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.065759 restraints weight = 20688.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.066393 restraints weight = 17135.865| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18340 Z= 0.218 Angle : 0.771 9.081 24864 Z= 0.393 Chirality : 0.046 0.350 2961 Planarity : 0.004 0.026 2975 Dihedral : 5.659 23.037 2370 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.79 % Allowed : 17.78 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2170 helix: 0.96 (0.13), residues: 1589 sheet: 2.83 (0.75), residues: 42 loop : -0.33 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 152 TYR 0.019 0.002 TYR E 233 PHE 0.031 0.002 PHE B 54 TRP 0.012 0.001 TRP G 85 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00459 (18326) covalent geometry : angle 0.76934 (24836) SS BOND : bond 0.00470 ( 14) SS BOND : angle 1.50216 ( 28) hydrogen bonds : bond 0.05762 ( 1208) hydrogen bonds : angle 5.71200 ( 3582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 388 time to evaluate : 0.729 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 revert: symmetry clash REVERT: A 1 MET cc_start: 0.4406 (tmt) cc_final: 0.3048 (tpt) REVERT: A 233 TYR cc_start: 0.8218 (t80) cc_final: 0.7962 (t80) REVERT: B 1 MET cc_start: 0.4021 (tmt) cc_final: 0.2551 (tpt) REVERT: B 54 PHE cc_start: 0.9049 (m-10) cc_final: 0.8819 (m-10) REVERT: B 210 MET cc_start: 0.8846 (mmm) cc_final: 0.8428 (mmm) REVERT: B 233 TYR cc_start: 0.8268 (t80) cc_final: 0.7735 (t80) REVERT: C 1 MET cc_start: 0.4222 (tmt) cc_final: 0.2771 (tpt) REVERT: C 210 MET cc_start: 0.8706 (mmm) cc_final: 0.8273 (mmm) REVERT: C 233 TYR cc_start: 0.8091 (t80) cc_final: 0.7853 (t80) REVERT: D 1 MET cc_start: 0.4236 (tmt) cc_final: 0.2777 (tpt) REVERT: D 37 MET cc_start: 0.9284 (mmp) cc_final: 0.8978 (mmp) REVERT: E 1 MET cc_start: 0.4218 (tmt) cc_final: 0.2663 (tpt) REVERT: F 1 MET cc_start: 0.4064 (tmt) cc_final: 0.2602 (tpt) REVERT: F 37 MET cc_start: 0.9248 (mmp) cc_final: 0.8960 (mmp) REVERT: G 1 MET cc_start: 0.4141 (tmt) cc_final: 0.2707 (tpt) REVERT: G 49 LEU cc_start: 0.9550 (mt) cc_final: 0.9320 (mt) outliers start: 77 outliers final: 37 residues processed: 438 average time/residue: 0.1093 time to fit residues: 75.9006 Evaluate side-chains 371 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 334 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 278 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 166 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 40.0000 chunk 126 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 128 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 325 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 325 ASN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN D 325 ASN D 352 ASN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN E 325 ASN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN F 325 ASN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 325 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.081299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063277 restraints weight = 73055.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065302 restraints weight = 40894.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.066688 restraints weight = 28313.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.067571 restraints weight = 21892.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.068182 restraints weight = 18335.007| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18340 Z= 0.165 Angle : 0.831 11.833 24864 Z= 0.398 Chirality : 0.050 0.391 2961 Planarity : 0.004 0.028 2975 Dihedral : 5.528 22.811 2366 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.74 % Allowed : 19.56 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2170 helix: 0.89 (0.12), residues: 1610 sheet: 3.04 (0.71), residues: 42 loop : -0.47 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 216 TYR 0.017 0.002 TYR D 233 PHE 0.040 0.002 PHE F 333 TRP 0.012 0.001 TRP G 85 HIS 0.010 0.002 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00343 (18326) covalent geometry : angle 0.83084 (24836) SS BOND : bond 0.00146 ( 14) SS BOND : angle 1.09785 ( 28) hydrogen bonds : bond 0.05366 ( 1208) hydrogen bonds : angle 5.49453 ( 3582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 405 time to evaluate : 0.862 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4433 (tmt) cc_final: 0.3064 (tpt) REVERT: A 49 LEU cc_start: 0.9469 (mt) cc_final: 0.9262 (mp) REVERT: A 210 MET cc_start: 0.8772 (mmm) cc_final: 0.8451 (mmm) REVERT: B 1 MET cc_start: 0.4093 (tmt) cc_final: 0.2783 (tpt) REVERT: B 210 MET cc_start: 0.8668 (mmm) cc_final: 0.8180 (mmm) REVERT: B 233 TYR cc_start: 0.8359 (t80) cc_final: 0.8021 (t80) REVERT: C 1 MET cc_start: 0.4068 (tmt) cc_final: 0.2679 (tpt) REVERT: C 210 MET cc_start: 0.8627 (mmm) cc_final: 0.8128 (mmm) REVERT: C 233 TYR cc_start: 0.8225 (t80) cc_final: 0.7994 (t80) REVERT: D 1 MET cc_start: 0.3902 (tmt) cc_final: 0.2633 (tpt) REVERT: D 37 MET cc_start: 0.9243 (mmp) cc_final: 0.8882 (mmp) REVERT: D 48 LEU cc_start: 0.9328 (pp) cc_final: 0.9084 (mm) REVERT: D 49 LEU cc_start: 0.9586 (mt) cc_final: 0.9369 (mp) REVERT: E 1 MET cc_start: 0.4070 (tmt) cc_final: 0.2629 (tpt) REVERT: F 1 MET cc_start: 0.3889 (tmt) cc_final: 0.2531 (tpt) REVERT: F 283 TYR cc_start: 0.9645 (m-10) cc_final: 0.9180 (m-10) REVERT: G 1 MET cc_start: 0.4033 (tmt) cc_final: 0.2697 (tpt) outliers start: 76 outliers final: 39 residues processed: 445 average time/residue: 0.1141 time to fit residues: 80.8382 Evaluate side-chains 388 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 349 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 186 optimal weight: 0.0470 chunk 124 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.078977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061192 restraints weight = 74905.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.063240 restraints weight = 41866.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064659 restraints weight = 28402.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.065583 restraints weight = 21768.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.066255 restraints weight = 18215.877| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18340 Z= 0.209 Angle : 0.838 16.698 24864 Z= 0.405 Chirality : 0.049 0.360 2961 Planarity : 0.004 0.028 2975 Dihedral : 5.511 22.990 2366 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.91 % Allowed : 22.56 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2170 helix: 0.90 (0.13), residues: 1596 sheet: 3.27 (0.72), residues: 42 loop : -0.61 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 75 TYR 0.030 0.002 TYR B 283 PHE 0.039 0.003 PHE B 333 TRP 0.012 0.002 TRP E 85 HIS 0.007 0.002 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00449 (18326) covalent geometry : angle 0.83665 (24836) SS BOND : bond 0.00458 ( 14) SS BOND : angle 1.45838 ( 28) hydrogen bonds : bond 0.05302 ( 1208) hydrogen bonds : angle 5.60677 ( 3582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 359 time to evaluate : 0.700 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4403 (tmt) cc_final: 0.3095 (tpt) REVERT: B 1 MET cc_start: 0.3980 (tmt) cc_final: 0.2720 (tpt) REVERT: B 210 MET cc_start: 0.8540 (mmm) cc_final: 0.8043 (mmm) REVERT: B 233 TYR cc_start: 0.8339 (t80) cc_final: 0.7934 (t80) REVERT: C 1 MET cc_start: 0.4145 (tmt) cc_final: 0.2838 (tpt) REVERT: C 210 MET cc_start: 0.8540 (mmm) cc_final: 0.8031 (mmm) REVERT: C 233 TYR cc_start: 0.8240 (t80) cc_final: 0.8020 (t80) REVERT: D 1 MET cc_start: 0.3960 (tmt) cc_final: 0.2797 (tpt) REVERT: D 37 MET cc_start: 0.9235 (mmp) cc_final: 0.8870 (mmp) REVERT: E 1 MET cc_start: 0.4143 (tmt) cc_final: 0.2856 (tpt) REVERT: E 111 TYR cc_start: 0.8623 (m-10) cc_final: 0.8407 (m-10) REVERT: E 115 LEU cc_start: 0.9693 (tp) cc_final: 0.9345 (mt) REVERT: E 332 LEU cc_start: 0.9631 (mt) cc_final: 0.9402 (pp) REVERT: F 1 MET cc_start: 0.3995 (tmt) cc_final: 0.2705 (tpt) REVERT: G 1 MET cc_start: 0.4103 (tmt) cc_final: 0.2792 (tpt) REVERT: G 233 TYR cc_start: 0.8091 (t80) cc_final: 0.7824 (t80) REVERT: G 332 LEU cc_start: 0.9627 (mt) cc_final: 0.9419 (pp) outliers start: 59 outliers final: 42 residues processed: 390 average time/residue: 0.1191 time to fit residues: 74.1935 Evaluate side-chains 390 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 348 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.080448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.062437 restraints weight = 75677.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.064545 restraints weight = 42045.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.065978 restraints weight = 28680.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.066943 restraints weight = 21898.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.067530 restraints weight = 18255.042| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 18340 Z= 0.170 Angle : 0.882 16.639 24864 Z= 0.412 Chirality : 0.053 0.379 2961 Planarity : 0.004 0.025 2975 Dihedral : 5.446 23.305 2366 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.66 % Allowed : 23.40 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2170 helix: 0.87 (0.13), residues: 1638 sheet: 2.85 (0.75), residues: 42 loop : -0.47 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 75 TYR 0.016 0.002 TYR D 233 PHE 0.032 0.002 PHE A 54 TRP 0.011 0.001 TRP E 85 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00377 (18326) covalent geometry : angle 0.88178 (24836) SS BOND : bond 0.00251 ( 14) SS BOND : angle 1.22978 ( 28) hydrogen bonds : bond 0.05009 ( 1208) hydrogen bonds : angle 5.55818 ( 3582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 376 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4391 (tmt) cc_final: 0.3154 (tpt) REVERT: A 210 MET cc_start: 0.8357 (mmm) cc_final: 0.7914 (mmm) REVERT: B 1 MET cc_start: 0.4017 (tmt) cc_final: 0.2782 (tpt) REVERT: B 210 MET cc_start: 0.8422 (mmm) cc_final: 0.7971 (mmm) REVERT: B 233 TYR cc_start: 0.8200 (t80) cc_final: 0.7921 (t80) REVERT: C 1 MET cc_start: 0.3909 (tmt) cc_final: 0.2825 (tpt) REVERT: C 283 TYR cc_start: 0.9680 (m-10) cc_final: 0.9312 (m-10) REVERT: D 1 MET cc_start: 0.3804 (tmt) cc_final: 0.2758 (tpt) REVERT: E 1 MET cc_start: 0.4103 (tmt) cc_final: 0.3001 (tpt) REVERT: E 111 TYR cc_start: 0.8529 (m-10) cc_final: 0.8296 (m-10) REVERT: E 115 LEU cc_start: 0.9685 (tp) cc_final: 0.9351 (mt) REVERT: F 1 MET cc_start: 0.3917 (tmt) cc_final: 0.2792 (tpt) REVERT: F 37 MET cc_start: 0.9368 (tpp) cc_final: 0.9112 (ppp) REVERT: G 1 MET cc_start: 0.3883 (tmt) cc_final: 0.2690 (tpt) outliers start: 54 outliers final: 38 residues processed: 403 average time/residue: 0.1144 time to fit residues: 73.8507 Evaluate side-chains 378 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 167 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 0.1980 chunk 89 optimal weight: 30.0000 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.081387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063308 restraints weight = 74495.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065507 restraints weight = 41000.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.067008 restraints weight = 27451.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.067986 restraints weight = 20702.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.068629 restraints weight = 17013.945| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18340 Z= 0.168 Angle : 0.912 15.754 24864 Z= 0.424 Chirality : 0.055 0.486 2961 Planarity : 0.004 0.069 2975 Dihedral : 5.448 23.242 2366 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.32 % Allowed : 24.83 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2170 helix: 0.81 (0.13), residues: 1638 sheet: 3.26 (0.75), residues: 42 loop : -0.59 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 29 TYR 0.029 0.002 TYR G 283 PHE 0.028 0.002 PHE A 54 TRP 0.010 0.001 TRP G 85 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00371 (18326) covalent geometry : angle 0.91121 (24836) SS BOND : bond 0.00213 ( 14) SS BOND : angle 1.19899 ( 28) hydrogen bonds : bond 0.05038 ( 1208) hydrogen bonds : angle 5.54002 ( 3582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 0.582 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4440 (tmt) cc_final: 0.3287 (tpt) REVERT: A 210 MET cc_start: 0.8329 (mmm) cc_final: 0.7865 (mmm) REVERT: B 1 MET cc_start: 0.3895 (tmt) cc_final: 0.2673 (tpt) REVERT: B 210 MET cc_start: 0.8383 (mmm) cc_final: 0.7916 (mmm) REVERT: B 280 LEU cc_start: 0.9119 (tt) cc_final: 0.8819 (tp) REVERT: C 1 MET cc_start: 0.3840 (tmt) cc_final: 0.2844 (tpt) REVERT: C 283 TYR cc_start: 0.9664 (m-10) cc_final: 0.9339 (m-10) REVERT: D 1 MET cc_start: 0.3736 (tmt) cc_final: 0.2624 (tpt) REVERT: D 210 MET cc_start: 0.8820 (mmm) cc_final: 0.8511 (mmm) REVERT: E 1 MET cc_start: 0.4040 (tmt) cc_final: 0.2874 (tpt) REVERT: E 111 TYR cc_start: 0.8501 (m-10) cc_final: 0.8289 (m-10) REVERT: E 115 LEU cc_start: 0.9695 (tp) cc_final: 0.9356 (mt) REVERT: E 332 LEU cc_start: 0.9703 (pp) cc_final: 0.9487 (mt) REVERT: F 1 MET cc_start: 0.3937 (tmt) cc_final: 0.2828 (tpt) REVERT: G 1 MET cc_start: 0.3942 (tmt) cc_final: 0.2792 (tpt) REVERT: G 210 MET cc_start: 0.8739 (mmm) cc_final: 0.8218 (mmm) REVERT: G 225 LEU cc_start: 0.9400 (mt) cc_final: 0.9199 (mt) outliers start: 47 outliers final: 40 residues processed: 397 average time/residue: 0.1137 time to fit residues: 72.7750 Evaluate side-chains 398 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 113 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 194 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.079784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.062094 restraints weight = 76106.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064000 restraints weight = 44201.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065515 restraints weight = 30247.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066418 restraints weight = 23634.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.067008 restraints weight = 19899.289| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18340 Z= 0.176 Angle : 0.934 15.489 24864 Z= 0.433 Chirality : 0.056 0.485 2961 Planarity : 0.004 0.056 2975 Dihedral : 5.358 24.001 2366 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 24.83 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2170 helix: 0.88 (0.13), residues: 1631 sheet: 3.52 (0.75), residues: 42 loop : -0.64 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 29 TYR 0.017 0.002 TYR G 233 PHE 0.030 0.002 PHE D 294 TRP 0.010 0.001 TRP E 85 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00387 (18326) covalent geometry : angle 0.93355 (24836) SS BOND : bond 0.00309 ( 14) SS BOND : angle 1.37140 ( 28) hydrogen bonds : bond 0.05011 ( 1208) hydrogen bonds : angle 5.58716 ( 3582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 0.477 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 revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4235 (tmt) cc_final: 0.3079 (tpt) REVERT: A 210 MET cc_start: 0.8324 (mmm) cc_final: 0.7848 (mmm) REVERT: A 241 ASP cc_start: 0.8672 (p0) cc_final: 0.8314 (p0) REVERT: B 1 MET cc_start: 0.3730 (tmt) cc_final: 0.2527 (tpt) REVERT: B 210 MET cc_start: 0.8384 (mmm) cc_final: 0.7947 (mmm) REVERT: B 280 LEU cc_start: 0.9183 (tt) cc_final: 0.8885 (tp) REVERT: C 1 MET cc_start: 0.3842 (tmt) cc_final: 0.2879 (tpt) REVERT: C 283 TYR cc_start: 0.9676 (m-10) cc_final: 0.9334 (m-10) REVERT: D 1 MET cc_start: 0.3923 (tmt) cc_final: 0.2806 (tpt) REVERT: D 37 MET cc_start: 0.9287 (tpp) cc_final: 0.9053 (ppp) REVERT: D 210 MET cc_start: 0.8755 (mmm) cc_final: 0.8407 (mmm) REVERT: D 241 ASP cc_start: 0.8573 (p0) cc_final: 0.8337 (p0) REVERT: E 1 MET cc_start: 0.4018 (tmt) cc_final: 0.2884 (tpt) REVERT: F 1 MET cc_start: 0.4006 (tmt) cc_final: 0.2962 (tpt) REVERT: G 1 MET cc_start: 0.3956 (tmt) cc_final: 0.2814 (tpt) REVERT: G 81 ASP cc_start: 0.8952 (p0) cc_final: 0.8631 (p0) REVERT: G 225 LEU cc_start: 0.9389 (mt) cc_final: 0.9176 (mt) outliers start: 47 outliers final: 39 residues processed: 396 average time/residue: 0.1159 time to fit residues: 74.0651 Evaluate side-chains 387 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 348 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 159 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 118 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.081065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.063262 restraints weight = 75078.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065356 restraints weight = 43462.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.066809 restraints weight = 29743.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.067743 restraints weight = 22803.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.068389 restraints weight = 18924.545| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 18340 Z= 0.167 Angle : 0.991 18.373 24864 Z= 0.450 Chirality : 0.057 0.499 2961 Planarity : 0.004 0.044 2975 Dihedral : 5.341 26.768 2366 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.92 % Allowed : 25.91 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2170 helix: 0.80 (0.13), residues: 1631 sheet: 3.81 (0.75), residues: 42 loop : -0.70 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 29 TYR 0.032 0.002 TYR E 308 PHE 0.027 0.002 PHE E 333 TRP 0.019 0.001 TRP D 85 HIS 0.004 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00370 (18326) covalent geometry : angle 0.99106 (24836) SS BOND : bond 0.00206 ( 14) SS BOND : angle 1.23110 ( 28) hydrogen bonds : bond 0.04923 ( 1208) hydrogen bonds : angle 5.53711 ( 3582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 0.754 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4062 (tmt) cc_final: 0.2915 (tpt) REVERT: A 210 MET cc_start: 0.8305 (mmm) cc_final: 0.7833 (mmm) REVERT: A 283 TYR cc_start: 0.9659 (m-10) cc_final: 0.9260 (m-10) REVERT: B 1 MET cc_start: 0.3292 (tmt) cc_final: 0.2196 (tpt) REVERT: B 210 MET cc_start: 0.8348 (mmm) cc_final: 0.7935 (mmm) REVERT: C 1 MET cc_start: 0.3721 (tmt) cc_final: 0.2892 (tpt) REVERT: C 229 TYR cc_start: 0.8981 (t80) cc_final: 0.8124 (m-80) REVERT: C 283 TYR cc_start: 0.9639 (m-10) cc_final: 0.9317 (m-10) REVERT: D 1 MET cc_start: 0.3925 (tmt) cc_final: 0.2799 (tpt) REVERT: D 210 MET cc_start: 0.8688 (mmm) cc_final: 0.8291 (mmm) REVERT: D 279 ASN cc_start: 0.9438 (t0) cc_final: 0.9112 (t0) REVERT: D 283 TYR cc_start: 0.9622 (m-10) cc_final: 0.9353 (m-10) REVERT: E 1 MET cc_start: 0.3947 (tmt) cc_final: 0.2829 (tpt) REVERT: E 241 ASP cc_start: 0.8707 (p0) cc_final: 0.8322 (p0) REVERT: F 1 MET cc_start: 0.4051 (tmt) cc_final: 0.3092 (tpt) REVERT: F 210 MET cc_start: 0.8383 (mmm) cc_final: 0.7807 (mmm) REVERT: G 1 MET cc_start: 0.3889 (tmt) cc_final: 0.2779 (tpt) REVERT: G 81 ASP cc_start: 0.8975 (p0) cc_final: 0.8646 (p0) REVERT: G 332 LEU cc_start: 0.9690 (pp) cc_final: 0.9468 (mt) outliers start: 39 outliers final: 36 residues processed: 395 average time/residue: 0.1184 time to fit residues: 75.5423 Evaluate side-chains 392 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 356 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 78 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.079818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.062109 restraints weight = 76135.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.064010 restraints weight = 43372.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.065558 restraints weight = 29595.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.066460 restraints weight = 23246.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.067061 restraints weight = 19589.703| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18340 Z= 0.186 Angle : 1.005 17.658 24864 Z= 0.456 Chirality : 0.058 0.482 2961 Planarity : 0.004 0.061 2975 Dihedral : 5.343 24.320 2366 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.92 % Allowed : 26.55 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2170 helix: 0.81 (0.13), residues: 1631 sheet: 3.68 (0.73), residues: 42 loop : -0.75 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 29 TYR 0.018 0.002 TYR D 233 PHE 0.021 0.002 PHE G 54 TRP 0.015 0.002 TRP D 85 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00410 (18326) covalent geometry : angle 1.00488 (24836) SS BOND : bond 0.00338 ( 14) SS BOND : angle 1.45426 ( 28) hydrogen bonds : bond 0.04930 ( 1208) hydrogen bonds : angle 5.63992 ( 3582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.66 seconds wall clock time: 56 minutes 42.42 seconds (3402.42 seconds total)