Starting phenix.real_space_refine on Tue Mar 3 17:56:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6knf_0730/03_2026/6knf_0730.cif Found real_map, /net/cci-nas-00/data/ceres_data/6knf_0730/03_2026/6knf_0730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_2026/6knf_0730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_2026/6knf_0730.map" model { file = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_2026/6knf_0730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_2026/6knf_0730.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 30 5.16 5 C 4935 2.51 5 N 1326 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1005 SG CYS A 136 25.198 25.320 32.458 1.00 57.62 S ATOM 3586 SG CYS B 136 40.865 66.428 32.465 1.00 58.29 S ATOM 6167 SG CYS C 136 68.598 32.343 32.554 1.00 57.18 S Time building chain proxies: 1.67, per 1000 atoms: 0.22 Number of scatterers: 7749 At special positions: 0 Unit cell: (94.16, 94.16, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 30 16.00 O 1452 8.00 N 1326 7.00 C 4935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 307.6 milliseconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 15 sheets defined 14.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.930A pdb=" N HIS A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.519A pdb=" N GLY A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.931A pdb=" N HIS B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 232 " --> pdb=" O GLY B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'B' and resid 307 through 315 removed outlier: 3.519A pdb=" N GLY B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.930A pdb=" N HIS C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 232 " --> pdb=" O GLY C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 232' Processing helix chain 'C' and resid 307 through 315 removed outlier: 3.520A pdb=" N GLY C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 6.364A pdb=" N VAL A 39 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG A 84 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE A 41 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE A 86 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 43 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 79 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU A 119 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 336 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR A 121 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 334 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.121A pdb=" N MET A 73 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 157 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 75 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR A 294 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLY A 261 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP A 262 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 277 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.824A pdb=" N ALA A 302 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 331 through 338 removed outlier: 3.843A pdb=" N VAL A 334 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 121 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 336 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 119 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 79 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 338 removed outlier: 3.843A pdb=" N VAL A 334 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 121 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 336 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 119 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 79 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.123A pdb=" N MET B 73 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 157 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 75 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR B 294 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY B 261 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 262 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 277 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 233 through 236 removed outlier: 3.823A pdb=" N ALA B 302 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 338 removed outlier: 3.779A pdb=" N VAL B 334 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 121 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 336 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 119 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 79 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 331 through 338 removed outlier: 3.779A pdb=" N VAL B 334 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 121 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 336 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 119 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 79 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.122A pdb=" N MET C 73 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 157 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 75 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR C 294 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 261 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 262 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 277 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 233 through 236 removed outlier: 3.823A pdb=" N ALA C 302 " --> pdb=" O ILE C 257 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 705 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: 1.23 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2561 1.34 - 1.45: 1233 1.45 - 1.57: 4102 1.57 - 1.69: 0 1.69 - 1.80: 57 Bond restraints: 7953 Sorted by residual: bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.506 1.455 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CB PRO C 23 " pdb=" CG PRO C 23 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CB PRO A 23 " pdb=" CG PRO A 23 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" CG PRO C 254 " pdb=" CD PRO C 254 " ideal model delta sigma weight residual 1.503 1.467 0.036 3.40e-02 8.65e+02 1.12e+00 bond pdb=" CG PRO A 254 " pdb=" CD PRO A 254 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.09e+00 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10161 1.18 - 2.37: 557 2.37 - 3.55: 112 3.55 - 4.73: 12 4.73 - 5.91: 3 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASN C 305 " pdb=" N HIS C 306 " pdb=" CA HIS C 306 " ideal model delta sigma weight residual 122.55 118.75 3.80 2.03e+00 2.43e-01 3.51e+00 angle pdb=" N ASN A 307 " pdb=" CA ASN A 307 " pdb=" C ASN A 307 " ideal model delta sigma weight residual 108.17 104.74 3.43 1.85e+00 2.92e-01 3.44e+00 angle pdb=" N ASN C 307 " pdb=" CA ASN C 307 " pdb=" C ASN C 307 " ideal model delta sigma weight residual 108.17 104.75 3.42 1.85e+00 2.92e-01 3.43e+00 angle pdb=" C ASN A 305 " pdb=" N HIS A 306 " pdb=" CA HIS A 306 " ideal model delta sigma weight residual 122.55 118.81 3.74 2.03e+00 2.43e-01 3.39e+00 angle pdb=" N ASN B 307 " pdb=" CA ASN B 307 " pdb=" C ASN B 307 " ideal model delta sigma weight residual 108.17 104.77 3.40 1.85e+00 2.92e-01 3.39e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4144 17.02 - 34.05: 383 34.05 - 51.07: 84 51.07 - 68.10: 39 68.10 - 85.12: 6 Dihedral angle restraints: 4656 sinusoidal: 1812 harmonic: 2844 Sorted by residual: dihedral pdb=" CA HIS B 306 " pdb=" C HIS B 306 " pdb=" N ASN B 307 " pdb=" CA ASN B 307 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA HIS C 306 " pdb=" C HIS C 306 " pdb=" N ASN C 307 " pdb=" CA ASN C 307 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA HIS A 306 " pdb=" C HIS A 306 " pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 684 0.034 - 0.067: 298 0.067 - 0.101: 166 0.101 - 0.134: 42 0.134 - 0.168: 7 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CA HIS A 306 " pdb=" N HIS A 306 " pdb=" C HIS A 306 " pdb=" CB HIS A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA HIS B 306 " pdb=" N HIS B 306 " pdb=" C HIS B 306 " pdb=" CB HIS B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA HIS C 306 " pdb=" N HIS C 306 " pdb=" C HIS C 306 " pdb=" CB HIS C 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1194 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 336 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO C 337 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 336 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 337 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 336 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO B 337 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.020 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 122 2.59 - 3.17: 6302 3.17 - 3.75: 11208 3.75 - 4.32: 16624 4.32 - 4.90: 29170 Nonbonded interactions: 63426 Sorted by model distance: nonbonded pdb=" NE2 HIS B 100 " pdb="CU CU B 501 " model vdw 2.015 2.320 nonbonded pdb=" NE2 HIS A 100 " pdb="CU CU A 501 " model vdw 2.016 2.320 nonbonded pdb=" NE2 HIS C 100 " pdb="CU CU C 501 " model vdw 2.016 2.320 nonbonded pdb=" NE2 HIS C 306 " pdb="CU CU A 501 " model vdw 2.053 2.320 nonbonded pdb=" ND1 HIS A 145 " pdb="CU CU A 500 " model vdw 2.054 2.320 ... (remaining 63421 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.680 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.600 Find NCS groups from input model: 0.060 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 7953 Z= 0.312 Angle : 0.634 5.914 10845 Z= 0.353 Chirality : 0.048 0.168 1197 Planarity : 0.005 0.037 1422 Dihedral : 15.036 85.119 2850 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 8.82 % Allowed : 15.44 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.23), residues: 996 helix: -1.79 (0.48), residues: 78 sheet: -0.73 (0.29), residues: 288 loop : -2.16 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.013 0.002 TYR B 134 PHE 0.011 0.002 PHE B 292 TRP 0.005 0.001 TRP A 281 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 7953) covalent geometry : angle 0.63392 (10845) hydrogen bonds : bond 0.09353 ( 249) hydrogen bonds : angle 6.95148 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 75 time to evaluate : 0.310 Fit side-chains REVERT: A 18 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7141 (p0) REVERT: B 340 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6267 (mtt) REVERT: C 340 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5947 (mtt) outliers start: 72 outliers final: 29 residues processed: 140 average time/residue: 0.4624 time to fit residues: 69.4702 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 340 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS B 221 ASN C 76 HIS C 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.078636 restraints weight = 11749.079| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.29 r_work: 0.2792 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7953 Z= 0.138 Angle : 0.548 5.669 10845 Z= 0.296 Chirality : 0.046 0.135 1197 Planarity : 0.004 0.035 1422 Dihedral : 6.514 59.371 1117 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 5.51 % Allowed : 18.26 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.65 (0.24), residues: 996 helix: -2.05 (0.39), residues: 93 sheet: -0.23 (0.29), residues: 273 loop : -1.39 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 250 TYR 0.009 0.001 TYR C 184 PHE 0.009 0.001 PHE C 124 TRP 0.003 0.001 TRP A 281 HIS 0.004 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7953) covalent geometry : angle 0.54782 (10845) hydrogen bonds : bond 0.03986 ( 249) hydrogen bonds : angle 5.87275 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 0.330 Fit side-chains REVERT: A 18 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7641 (p0) REVERT: B 92 THR cc_start: 0.9289 (p) cc_final: 0.9077 (t) REVERT: B 340 MET cc_start: 0.7073 (mtt) cc_final: 0.6593 (mtt) REVERT: C 340 MET cc_start: 0.6773 (mtt) cc_final: 0.6359 (mtt) outliers start: 45 outliers final: 14 residues processed: 96 average time/residue: 0.4780 time to fit residues: 49.2833 Evaluate side-chains 67 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.077503 restraints weight = 11515.690| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.19 r_work: 0.2768 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7953 Z= 0.244 Angle : 0.582 5.860 10845 Z= 0.314 Chirality : 0.048 0.155 1197 Planarity : 0.005 0.037 1422 Dihedral : 6.497 52.162 1089 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.27 % Allowed : 19.12 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.30 (0.25), residues: 996 helix: -1.68 (0.42), residues: 93 sheet: 0.04 (0.27), residues: 306 loop : -1.23 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 159 TYR 0.014 0.002 TYR B 134 PHE 0.009 0.002 PHE C 124 TRP 0.004 0.001 TRP A 281 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 7953) covalent geometry : angle 0.58157 (10845) hydrogen bonds : bond 0.04574 ( 249) hydrogen bonds : angle 5.94599 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 53 time to evaluate : 0.281 Fit side-chains REVERT: A 18 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7678 (p0) REVERT: B 253 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8748 (ptp90) REVERT: B 340 MET cc_start: 0.7100 (mtt) cc_final: 0.6572 (mtt) outliers start: 43 outliers final: 26 residues processed: 85 average time/residue: 0.4931 time to fit residues: 44.9781 Evaluate side-chains 76 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.078951 restraints weight = 11708.669| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.29 r_work: 0.2793 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7953 Z= 0.143 Angle : 0.518 5.650 10845 Z= 0.280 Chirality : 0.046 0.132 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.272 50.767 1089 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 6.62 % Allowed : 17.52 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.03 (0.25), residues: 996 helix: -1.42 (0.43), residues: 93 sheet: 0.32 (0.29), residues: 273 loop : -1.05 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.009 0.001 TYR C 184 PHE 0.009 0.001 PHE C 124 TRP 0.003 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7953) covalent geometry : angle 0.51850 (10845) hydrogen bonds : bond 0.03751 ( 249) hydrogen bonds : angle 5.66068 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 56 time to evaluate : 0.322 Fit side-chains REVERT: A 18 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7637 (p0) REVERT: A 253 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8722 (ptp90) REVERT: B 18 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7690 (p0) REVERT: B 29 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8339 (t0) REVERT: B 253 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8650 (ptp90) REVERT: B 340 MET cc_start: 0.6984 (mtt) cc_final: 0.6463 (mtt) outliers start: 54 outliers final: 25 residues processed: 100 average time/residue: 0.4465 time to fit residues: 48.1156 Evaluate side-chains 81 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.080385 restraints weight = 11570.119| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.30 r_work: 0.2817 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7953 Z= 0.127 Angle : 0.506 5.626 10845 Z= 0.272 Chirality : 0.046 0.130 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.196 50.628 1089 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.76 % Allowed : 17.65 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.90 (0.25), residues: 996 helix: -1.63 (0.41), residues: 93 sheet: 0.71 (0.30), residues: 255 loop : -1.02 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 253 TYR 0.009 0.001 TYR C 184 PHE 0.009 0.001 PHE C 124 TRP 0.003 0.001 TRP B 281 HIS 0.003 0.000 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7953) covalent geometry : angle 0.50558 (10845) hydrogen bonds : bond 0.03551 ( 249) hydrogen bonds : angle 5.53680 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 59 time to evaluate : 0.309 Fit side-chains REVERT: A 18 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 253 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8759 (ptp90) REVERT: B 18 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7651 (p0) REVERT: B 29 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8364 (t0) REVERT: B 331 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8536 (ttp) REVERT: B 340 MET cc_start: 0.7023 (mtt) cc_final: 0.6529 (mtt) REVERT: C 180 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8465 (tp30) outliers start: 47 outliers final: 31 residues processed: 94 average time/residue: 0.4893 time to fit residues: 49.4486 Evaluate side-chains 93 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 56 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.077773 restraints weight = 11679.212| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.27 r_work: 0.2766 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 7953 Z= 0.275 Angle : 0.588 5.918 10845 Z= 0.318 Chirality : 0.048 0.164 1197 Planarity : 0.004 0.036 1422 Dihedral : 6.614 50.976 1089 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.51 % Allowed : 17.77 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 996 helix: -1.69 (0.43), residues: 90 sheet: 0.07 (0.28), residues: 303 loop : -0.90 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 253 TYR 0.014 0.002 TYR B 134 PHE 0.011 0.002 PHE A 292 TRP 0.004 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 7953) covalent geometry : angle 0.58828 (10845) hydrogen bonds : bond 0.04608 ( 249) hydrogen bonds : angle 5.89479 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 52 time to evaluate : 0.310 Fit side-chains REVERT: A 18 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7637 (p0) REVERT: A 331 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (ttp) REVERT: B 18 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7722 (p0) REVERT: B 331 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8634 (ttp) REVERT: B 340 MET cc_start: 0.7041 (mtt) cc_final: 0.6573 (mtt) outliers start: 45 outliers final: 29 residues processed: 87 average time/residue: 0.4688 time to fit residues: 43.9851 Evaluate side-chains 86 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 82 optimal weight: 0.0770 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.081101 restraints weight = 11523.372| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.30 r_work: 0.2836 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7953 Z= 0.115 Angle : 0.510 5.593 10845 Z= 0.275 Chirality : 0.045 0.137 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.175 51.508 1088 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.66 % Allowed : 18.26 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.79 (0.26), residues: 996 helix: -1.81 (0.42), residues: 93 sheet: 0.82 (0.30), residues: 255 loop : -0.91 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.008 0.001 TYR C 184 PHE 0.008 0.001 PHE C 124 TRP 0.003 0.001 TRP A 281 HIS 0.003 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7953) covalent geometry : angle 0.50965 (10845) hydrogen bonds : bond 0.03454 ( 249) hydrogen bonds : angle 5.49497 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.295 Fit side-chains REVERT: A 18 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 253 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8757 (ptp90) REVERT: A 340 MET cc_start: 0.6722 (mtt) cc_final: 0.6258 (mpt) REVERT: B 18 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7638 (p0) REVERT: B 331 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8470 (ttp) REVERT: B 340 MET cc_start: 0.6960 (mtt) cc_final: 0.6447 (mtt) outliers start: 38 outliers final: 25 residues processed: 89 average time/residue: 0.5215 time to fit residues: 49.6618 Evaluate side-chains 81 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.0060 chunk 33 optimal weight: 0.0980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080587 restraints weight = 11666.906| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.31 r_work: 0.2819 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7953 Z= 0.136 Angle : 0.523 5.638 10845 Z= 0.281 Chirality : 0.045 0.132 1197 Planarity : 0.004 0.036 1422 Dihedral : 6.180 52.440 1088 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.04 % Allowed : 19.12 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.26), residues: 996 helix: -1.74 (0.43), residues: 93 sheet: 0.87 (0.30), residues: 255 loop : -0.89 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.009 0.001 TYR C 184 PHE 0.009 0.001 PHE C 124 TRP 0.003 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7953) covalent geometry : angle 0.52331 (10845) hydrogen bonds : bond 0.03550 ( 249) hydrogen bonds : angle 5.48405 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.309 Fit side-chains REVERT: A 18 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7592 (p0) REVERT: A 253 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8795 (ptp90) REVERT: A 340 MET cc_start: 0.6725 (mtt) cc_final: 0.6240 (mpt) REVERT: B 18 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7659 (p0) REVERT: B 331 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8426 (ttp) REVERT: B 340 MET cc_start: 0.6981 (mtt) cc_final: 0.6456 (mtt) outliers start: 33 outliers final: 28 residues processed: 80 average time/residue: 0.5491 time to fit residues: 46.9326 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.078768 restraints weight = 11675.592| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.29 r_work: 0.2786 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7953 Z= 0.225 Angle : 0.567 5.804 10845 Z= 0.306 Chirality : 0.047 0.154 1197 Planarity : 0.004 0.036 1422 Dihedral : 6.413 53.835 1088 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.41 % Allowed : 18.38 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.87 (0.26), residues: 996 helix: -1.72 (0.43), residues: 93 sheet: 0.16 (0.28), residues: 303 loop : -0.75 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.013 0.001 TYR C 134 PHE 0.011 0.002 PHE C 99 TRP 0.003 0.001 TRP B 281 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 7953) covalent geometry : angle 0.56677 (10845) hydrogen bonds : bond 0.04193 ( 249) hydrogen bonds : angle 5.73238 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 52 time to evaluate : 0.313 Fit side-chains REVERT: A 18 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7642 (p0) REVERT: A 253 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8818 (ptp90) REVERT: A 340 MET cc_start: 0.6765 (mtt) cc_final: 0.6275 (mpt) REVERT: B 18 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7671 (p0) REVERT: B 159 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8331 (mmt180) REVERT: B 340 MET cc_start: 0.7010 (mtt) cc_final: 0.6463 (mtt) outliers start: 36 outliers final: 26 residues processed: 83 average time/residue: 0.5691 time to fit residues: 50.2841 Evaluate side-chains 83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.079705 restraints weight = 11568.125| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.29 r_work: 0.2805 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7953 Z= 0.164 Angle : 0.539 5.693 10845 Z= 0.291 Chirality : 0.046 0.151 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.319 53.804 1088 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.04 % Allowed : 18.75 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.89 (0.26), residues: 996 helix: -1.74 (0.43), residues: 93 sheet: 0.32 (0.28), residues: 285 loop : -0.84 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.010 0.001 TYR B 134 PHE 0.009 0.001 PHE C 124 TRP 0.003 0.001 TRP C 281 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7953) covalent geometry : angle 0.53922 (10845) hydrogen bonds : bond 0.03838 ( 249) hydrogen bonds : angle 5.62810 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.309 Fit side-chains REVERT: A 18 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7596 (p0) REVERT: A 253 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8799 (ptp90) REVERT: A 340 MET cc_start: 0.6670 (mtt) cc_final: 0.6214 (mpt) REVERT: B 18 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7632 (p0) REVERT: B 159 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8332 (mmt180) REVERT: B 340 MET cc_start: 0.6976 (mtt) cc_final: 0.6443 (mtt) outliers start: 33 outliers final: 28 residues processed: 84 average time/residue: 0.5773 time to fit residues: 51.6523 Evaluate side-chains 85 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.080060 restraints weight = 11555.812| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.30 r_work: 0.2809 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7953 Z= 0.150 Angle : 0.538 6.257 10845 Z= 0.290 Chirality : 0.046 0.147 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.274 53.827 1088 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.17 % Allowed : 18.87 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.74 (0.26), residues: 996 helix: -1.75 (0.43), residues: 93 sheet: 0.66 (0.30), residues: 261 loop : -0.80 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.009 0.001 TYR B 134 PHE 0.010 0.001 PHE C 124 TRP 0.002 0.001 TRP C 281 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7953) covalent geometry : angle 0.53813 (10845) hydrogen bonds : bond 0.03724 ( 249) hydrogen bonds : angle 5.58612 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.98 seconds wall clock time: 44 minutes 1.08 seconds (2641.08 seconds total)