Starting phenix.real_space_refine on Sat Sep 12 11:27:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rld_4919/09_2026/6rld_4919.map" } resolution = 2.9 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 42 5.16 5 C 10045 2.51 5 N 2492 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15309 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "B" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "C" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "D" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "E" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "F" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2025 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 5, 'TRANS': 259} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.93, per 1000 atoms: 0.19 Number of scatterers: 15309 At special positions: 0 Unit cell: (97.842, 98.9055, 145.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 21 15.00 O 2709 8.00 N 2492 7.00 C 10045 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: 1.31 Conformation dependent library (CDL) restraints added in 661.8 milliseconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 54.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 22 through 58 removed outlier: 3.742A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 264 Processing helix chain 'B' and resid 22 through 58 removed outlier: 3.742A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 264 Processing helix chain 'C' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 264 Processing helix chain 'D' and resid 22 through 58 removed outlier: 3.742A pdb=" N SER D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 111 through 127 Processing helix chain 'D' and resid 167 through 172 removed outlier: 3.557A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 264 Processing helix chain 'E' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 111 through 127 Processing helix chain 'E' and resid 167 through 172 removed outlier: 3.557A pdb=" N ALA E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 264 Processing helix chain 'F' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 111 through 127 Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 264 Processing helix chain 'G' and resid 22 through 58 removed outlier: 3.741A pdb=" N SER G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 167 through 172 removed outlier: 3.558A pdb=" N ALA G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 264 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.925A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 164 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 164 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 164 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 164 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 8.463A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.142A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.141A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2925 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: 1.97 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2359 1.31 - 1.43: 3688 1.43 - 1.56: 9291 1.56 - 1.68: 55 1.68 - 1.81: 84 Bond restraints: 15477 Sorted by residual: bond pdb=" C11 PCW F 602 " pdb=" O3 PCW F 602 " ideal model delta sigma weight residual 1.326 1.400 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 PCW G 602 " pdb=" O3 PCW G 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 PCW B 602 " pdb=" O3 PCW B 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 PCW E 602 " pdb=" O3 PCW E 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 PCW A 602 " pdb=" O3 PCW A 602 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 15472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 19474 2.65 - 5.31: 1036 5.31 - 7.96: 175 7.96 - 10.62: 49 10.62 - 13.27: 42 Bond angle restraints: 20776 Sorted by residual: angle pdb=" O3P PCW D 603 " pdb=" P PCW D 603 " pdb=" O4P PCW D 603 " ideal model delta sigma weight residual 96.85 110.12 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" O3P PCW E 603 " pdb=" P PCW E 603 " pdb=" O4P PCW E 603 " ideal model delta sigma weight residual 96.85 110.09 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW B 603 " pdb=" P PCW B 603 " pdb=" O4P PCW B 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW F 603 " pdb=" P PCW F 603 " pdb=" O4P PCW F 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" O3P PCW G 603 " pdb=" P PCW G 603 " pdb=" O4P PCW G 603 " ideal model delta sigma weight residual 96.85 110.08 -13.23 3.00e+00 1.11e-01 1.94e+01 ... (remaining 20771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 8988 32.01 - 64.02: 308 64.02 - 96.03: 14 96.03 - 128.05: 21 128.05 - 160.06: 14 Dihedral angle restraints: 9345 sinusoidal: 4025 harmonic: 5320 Sorted by residual: dihedral pdb=" CA ILE E 61 " pdb=" C ILE E 61 " pdb=" N ASP E 62 " pdb=" CA ASP E 62 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE G 61 " pdb=" C ILE G 61 " pdb=" N ASP G 62 " pdb=" CA ASP G 62 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ILE A 61 " pdb=" C ILE A 61 " pdb=" N ASP A 62 " pdb=" CA ASP A 62 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 9342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1520 0.045 - 0.089: 643 0.089 - 0.134: 158 0.134 - 0.179: 49 0.179 - 0.224: 45 Chirality restraints: 2415 Sorted by residual: chirality pdb=" C2 PCW G 601 " pdb=" C1 PCW G 601 " pdb=" C3 PCW G 601 " pdb=" O2 PCW G 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 PCW D 601 " pdb=" C1 PCW D 601 " pdb=" C3 PCW D 601 " pdb=" O2 PCW D 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C2 PCW C 601 " pdb=" C1 PCW C 601 " pdb=" C3 PCW C 601 " pdb=" O2 PCW C 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2412 not shown) Planarity restraints: 2548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO D 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 270 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO G 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 271 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO C 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.039 5.00e-02 4.00e+02 ... (remaining 2545 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 4180 2.82 - 3.34: 13201 3.34 - 3.86: 24952 3.86 - 4.38: 27209 4.38 - 4.90: 49780 Nonbonded interactions: 119322 Sorted by model distance: nonbonded pdb=" NH2 ARG D 224 " pdb=" OD1 ASP E 252 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG E 224 " pdb=" OD1 ASP F 252 " model vdw 2.326 3.120 nonbonded pdb=" NE2 GLN A 272 " pdb=" OD2 ASP G 274 " model vdw 2.330 3.120 nonbonded pdb=" NH2 ARG B 224 " pdb=" OD1 ASP C 252 " model vdw 2.350 3.120 nonbonded pdb=" NH2 ARG F 224 " pdb=" OD1 ASP G 252 " model vdw 2.357 3.120 ... (remaining 119317 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.960 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.009 0.087 15477 Z= 0.415 Angle : 1.376 13.269 20776 Z= 0.602 Chirality : 0.059 0.224 2415 Planarity : 0.006 0.071 2548 Dihedral : 17.574 160.058 5915 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.47 % Allowed : 3.72 % Favored : 95.81 % 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: -3.38 (0.15), residues: 1841 helix: -2.06 (0.12), residues: 987 sheet: -1.77 (0.24), residues: 308 loop : -2.40 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.035 0.004 TYR D 75 PHE 0.040 0.005 PHE C 235 TRP 0.018 0.003 TRP F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00920 / 0.42 (15477) covalent geometry : angle 1.37606 / 0.60 (20776) hydrogen bonds : bond 0.15341 / 10.57 ( 996) hydrogen bonds : angle 6.32347 / 4.45 ( 2925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 322 time to evaluate : 0.512 Fit side-chains REVERT: A 35 LEU cc_start: 0.8480 (mt) cc_final: 0.8165 (mp) REVERT: A 47 MET cc_start: 0.6802 (mmp) cc_final: 0.6016 (tmm) REVERT: B 227 GLU cc_start: 0.8054 (tt0) cc_final: 0.7779 (tt0) REVERT: C 47 MET cc_start: 0.6811 (mmp) cc_final: 0.6305 (tmm) REVERT: C 273 MET cc_start: 0.8123 (ttm) cc_final: 0.7918 (ttp) REVERT: D 47 MET cc_start: 0.6751 (mmp) cc_final: 0.6133 (tmm) REVERT: D 278 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8136 (mtpt) REVERT: E 47 MET cc_start: 0.6967 (mmp) cc_final: 0.6318 (tmm) REVERT: E 227 GLU cc_start: 0.8119 (tt0) cc_final: 0.7860 (tt0) REVERT: F 47 MET cc_start: 0.7138 (mmp) cc_final: 0.6509 (tmm) REVERT: F 92 GLN cc_start: 0.8455 (tt0) cc_final: 0.8163 (tt0) REVERT: F 149 GLN cc_start: 0.8214 (mt0) cc_final: 0.7998 (mt0) REVERT: G 47 MET cc_start: 0.6976 (mmp) cc_final: 0.6401 (tmm) REVERT: G 135 TYR cc_start: 0.8504 (t80) cc_final: 0.8220 (t80) REVERT: G 247 GLN cc_start: 0.8321 (tp40) cc_final: 0.8064 (tp-100) outliers start: 7 outliers final: 2 residues processed: 322 average time/residue: 0.6873 time to fit residues: 240.5247 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain B residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.0020 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 149 GLN B 149 GLN B 210 GLN C 50 ASN D 50 ASN D 92 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.131925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094317 restraints weight = 21201.892| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.21 r_work: 0.3055 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15477 Z= 0.123 Angle : 0.526 8.343 20776 Z= 0.278 Chirality : 0.043 0.150 2415 Planarity : 0.005 0.068 2548 Dihedral : 18.573 142.846 2757 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.39 % Allowed : 12.03 % Favored : 84.58 % 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: -0.97 (0.18), residues: 1841 helix: 0.48 (0.15), residues: 994 sheet: -1.35 (0.25), residues: 294 loop : -2.21 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 279 TYR 0.008 0.001 TYR G 75 PHE 0.034 0.002 PHE D 68 TRP 0.005 0.001 TRP E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15477) covalent geometry : angle 0.52639 / 0.28 (20776) hydrogen bonds : bond 0.03755 / 2.54 ( 996) hydrogen bonds : angle 4.20070 / 2.97 ( 2925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6609 (mmp) cc_final: 0.5846 (tmm) REVERT: B 181 GLU cc_start: 0.8292 (tp30) cc_final: 0.7936 (tt0) REVERT: B 227 GLU cc_start: 0.8727 (tt0) cc_final: 0.8513 (tt0) REVERT: B 278 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8042 (mttt) REVERT: C 47 MET cc_start: 0.6752 (mmp) cc_final: 0.6139 (tmm) REVERT: C 149 GLN cc_start: 0.8525 (mt0) cc_final: 0.8297 (mp10) REVERT: C 273 MET cc_start: 0.8592 (ttm) cc_final: 0.8304 (ttp) REVERT: D 35 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8326 (mp) REVERT: D 47 MET cc_start: 0.6593 (mmp) cc_final: 0.5910 (tmm) REVERT: D 181 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: D 210 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: D 227 GLU cc_start: 0.8570 (tt0) cc_final: 0.8348 (tt0) REVERT: D 278 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7788 (mtpt) REVERT: E 47 MET cc_start: 0.6736 (mmp) cc_final: 0.6122 (tmm) REVERT: E 181 GLU cc_start: 0.8520 (tp30) cc_final: 0.7901 (tt0) REVERT: E 210 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (mt0) REVERT: E 227 GLU cc_start: 0.8725 (tt0) cc_final: 0.8410 (tt0) REVERT: F 47 MET cc_start: 0.6870 (mmp) cc_final: 0.6310 (tmm) REVERT: F 92 GLN cc_start: 0.8269 (tt0) cc_final: 0.7934 (tt0) REVERT: F 149 GLN cc_start: 0.8563 (mt0) cc_final: 0.8307 (mt0) REVERT: F 227 GLU cc_start: 0.8626 (tt0) cc_final: 0.8392 (tt0) REVERT: G 47 MET cc_start: 0.6891 (mmp) cc_final: 0.6163 (tmm) REVERT: G 72 LEU cc_start: 0.7391 (tp) cc_final: 0.7188 (tt) REVERT: G 135 TYR cc_start: 0.8783 (t80) cc_final: 0.8488 (t80) REVERT: G 221 MET cc_start: 0.8825 (mtm) cc_final: 0.8595 (mtm) REVERT: G 278 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8014 (mtmt) outliers start: 51 outliers final: 11 residues processed: 286 average time/residue: 0.6407 time to fit residues: 200.8765 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 82 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 149 GLN B 53 ASN B 92 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 92 GLN E 92 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 92 GLN G 149 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090860 restraints weight = 21340.202| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.19 r_work: 0.2996 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15477 Z= 0.154 Angle : 0.507 8.577 20776 Z= 0.270 Chirality : 0.042 0.154 2415 Planarity : 0.004 0.062 2548 Dihedral : 17.036 132.539 2751 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.85 % Allowed : 16.41 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.25 (0.19), residues: 1841 helix: 1.59 (0.16), residues: 987 sheet: -0.83 (0.25), residues: 308 loop : -1.90 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.009 0.001 TYR B 75 PHE 0.029 0.002 PHE G 68 TRP 0.003 0.001 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (15477) covalent geometry : angle 0.50693 / 0.27 (20776) hydrogen bonds : bond 0.03697 / 2.49 ( 996) hydrogen bonds : angle 4.06288 / 2.88 ( 2925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6656 (mmp) cc_final: 0.5790 (tmt) REVERT: A 60 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6922 (ptpp) REVERT: A 181 GLU cc_start: 0.8275 (tp30) cc_final: 0.7643 (tt0) REVERT: B 134 GLU cc_start: 0.8585 (tt0) cc_final: 0.8347 (tt0) REVERT: B 181 GLU cc_start: 0.8239 (tp30) cc_final: 0.7837 (tt0) REVERT: B 220 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8419 (pt0) REVERT: B 227 GLU cc_start: 0.8678 (tt0) cc_final: 0.8444 (tt0) REVERT: B 278 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8049 (mttt) REVERT: C 47 MET cc_start: 0.6814 (mmp) cc_final: 0.6077 (tmm) REVERT: C 273 MET cc_start: 0.8571 (ttm) cc_final: 0.8343 (ttp) REVERT: D 47 MET cc_start: 0.6598 (mmp) cc_final: 0.5993 (tmm) REVERT: D 126 MET cc_start: 0.7891 (tmt) cc_final: 0.7660 (tmt) REVERT: D 169 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9127 (ttmm) REVERT: D 210 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: E 47 MET cc_start: 0.6723 (mmp) cc_final: 0.6104 (tmm) REVERT: E 60 LYS cc_start: 0.7374 (ptmm) cc_final: 0.7079 (ptpp) REVERT: E 210 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: E 227 GLU cc_start: 0.8659 (tt0) cc_final: 0.8354 (tt0) REVERT: F 47 MET cc_start: 0.6849 (mmp) cc_final: 0.6178 (tmm) REVERT: F 92 GLN cc_start: 0.8371 (tt0) cc_final: 0.8063 (tt0) REVERT: F 181 GLU cc_start: 0.8325 (tp30) cc_final: 0.7679 (mp0) REVERT: F 227 GLU cc_start: 0.8636 (tt0) cc_final: 0.8394 (tt0) REVERT: F 273 MET cc_start: 0.8443 (ttm) cc_final: 0.8101 (ttp) REVERT: G 47 MET cc_start: 0.6896 (mmp) cc_final: 0.6164 (tmm) REVERT: G 72 LEU cc_start: 0.7416 (tp) cc_final: 0.7161 (tt) REVERT: G 221 MET cc_start: 0.8942 (mtm) cc_final: 0.8742 (mtm) outliers start: 58 outliers final: 17 residues processed: 245 average time/residue: 0.6447 time to fit residues: 173.3139 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.0870 chunk 148 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 149 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 92 GLN E 92 GLN F 53 ASN G 92 GLN G 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094504 restraints weight = 21319.724| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.19 r_work: 0.3054 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15477 Z= 0.099 Angle : 0.463 9.511 20776 Z= 0.242 Chirality : 0.040 0.148 2415 Planarity : 0.004 0.063 2548 Dihedral : 15.180 121.108 2751 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.59 % Allowed : 18.01 % Favored : 78.41 % 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: 0.99 (0.19), residues: 1841 helix: 2.23 (0.16), residues: 987 sheet: -0.66 (0.25), residues: 294 loop : -1.51 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.005 0.001 TYR G 75 PHE 0.023 0.001 PHE E 68 TRP 0.003 0.000 TRP D 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (15477) covalent geometry : angle 0.46298 / 0.24 (20776) hydrogen bonds : bond 0.03177 / 2.14 ( 996) hydrogen bonds : angle 3.76811 / 2.68 ( 2925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6492 (mmp) cc_final: 0.5804 (tmt) REVERT: A 159 ASP cc_start: 0.8373 (t0) cc_final: 0.8160 (t0) REVERT: A 181 GLU cc_start: 0.8375 (tp30) cc_final: 0.7739 (tt0) REVERT: A 277 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7787 (t80) REVERT: B 68 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.5894 (OUTLIER) REVERT: B 134 GLU cc_start: 0.8477 (tt0) cc_final: 0.8245 (tt0) REVERT: B 159 ASP cc_start: 0.8221 (t0) cc_final: 0.7977 (t0) REVERT: B 171 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 181 GLU cc_start: 0.8287 (tp30) cc_final: 0.7898 (tt0) REVERT: B 227 GLU cc_start: 0.8696 (tt0) cc_final: 0.8460 (tt0) REVERT: B 253 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8333 (t) REVERT: B 278 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8126 (mttt) REVERT: C 47 MET cc_start: 0.6830 (mmp) cc_final: 0.6099 (tmm) REVERT: C 149 GLN cc_start: 0.8538 (mt0) cc_final: 0.7994 (mm110) REVERT: C 155 MET cc_start: 0.8958 (ptt) cc_final: 0.8679 (ptt) REVERT: C 273 MET cc_start: 0.8585 (ttm) cc_final: 0.8304 (ttp) REVERT: D 47 MET cc_start: 0.6641 (mmp) cc_final: 0.5948 (tmm) REVERT: D 126 MET cc_start: 0.7898 (tmt) cc_final: 0.7654 (tmt) REVERT: D 253 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8379 (t) REVERT: E 47 MET cc_start: 0.6710 (mmp) cc_final: 0.6115 (tmt) REVERT: E 60 LYS cc_start: 0.7515 (ptmm) cc_final: 0.7056 (ptpp) REVERT: E 181 GLU cc_start: 0.8439 (tp30) cc_final: 0.7836 (tt0) REVERT: E 227 GLU cc_start: 0.8678 (tt0) cc_final: 0.8386 (tt0) REVERT: E 278 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7515 (mtmt) REVERT: F 47 MET cc_start: 0.7006 (mmp) cc_final: 0.6286 (tmm) REVERT: F 92 GLN cc_start: 0.8233 (tt0) cc_final: 0.7884 (tt0) REVERT: F 227 GLU cc_start: 0.8614 (tt0) cc_final: 0.8382 (tt0) REVERT: F 273 MET cc_start: 0.8439 (ttm) cc_final: 0.8096 (ttp) REVERT: G 47 MET cc_start: 0.6875 (mmp) cc_final: 0.6265 (tmm) REVERT: G 72 LEU cc_start: 0.7435 (tp) cc_final: 0.7165 (tt) REVERT: G 221 MET cc_start: 0.8750 (mtm) cc_final: 0.8512 (mtm) REVERT: G 278 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7924 (mtmt) outliers start: 54 outliers final: 16 residues processed: 269 average time/residue: 0.5910 time to fit residues: 175.2971 Evaluate side-chains 217 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 149 GLN B 92 GLN B 203 GLN C 53 ASN C 92 GLN D 53 ASN D 92 GLN E 92 GLN G 92 GLN G 149 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092302 restraints weight = 21262.498| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.18 r_work: 0.3018 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15477 Z= 0.118 Angle : 0.471 8.225 20776 Z= 0.245 Chirality : 0.040 0.146 2415 Planarity : 0.004 0.058 2548 Dihedral : 14.720 117.728 2751 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 19.27 % Favored : 77.21 % 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: 1.25 (0.19), residues: 1841 helix: 2.46 (0.16), residues: 987 sheet: -0.41 (0.26), residues: 308 loop : -1.56 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 279 TYR 0.006 0.001 TYR F 27 PHE 0.022 0.002 PHE A 68 TRP 0.002 0.000 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15477) covalent geometry : angle 0.47143 / 0.24 (20776) hydrogen bonds : bond 0.03304 / 2.22 ( 996) hydrogen bonds : angle 3.76652 / 2.68 ( 2925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6532 (mmp) cc_final: 0.5823 (tmm) REVERT: A 149 GLN cc_start: 0.8373 (mt0) cc_final: 0.7909 (mm110) REVERT: A 203 GLN cc_start: 0.8064 (tt0) cc_final: 0.7796 (tp40) REVERT: A 277 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7945 (t80) REVERT: B 68 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5861 (OUTLIER) REVERT: B 159 ASP cc_start: 0.8260 (t0) cc_final: 0.7991 (t0) REVERT: B 181 GLU cc_start: 0.8237 (tp30) cc_final: 0.7751 (tt0) REVERT: B 227 GLU cc_start: 0.8694 (tt0) cc_final: 0.8482 (tt0) REVERT: B 253 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8350 (t) REVERT: B 278 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8173 (mttt) REVERT: C 47 MET cc_start: 0.6807 (mmp) cc_final: 0.6107 (tmm) REVERT: C 149 GLN cc_start: 0.8493 (mt0) cc_final: 0.8015 (mm110) REVERT: C 155 MET cc_start: 0.8992 (ptt) cc_final: 0.8754 (ptt) REVERT: C 181 GLU cc_start: 0.8427 (tp30) cc_final: 0.7723 (mp0) REVERT: C 273 MET cc_start: 0.8612 (ttm) cc_final: 0.8347 (ttp) REVERT: D 47 MET cc_start: 0.6839 (mmp) cc_final: 0.6134 (tmm) REVERT: D 126 MET cc_start: 0.7970 (tmt) cc_final: 0.7706 (tmt) REVERT: D 253 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8453 (t) REVERT: E 47 MET cc_start: 0.6688 (mmp) cc_final: 0.6128 (tmt) REVERT: E 60 LYS cc_start: 0.7363 (ptmm) cc_final: 0.6970 (ptpp) REVERT: E 181 GLU cc_start: 0.8437 (tp30) cc_final: 0.7840 (tt0) REVERT: E 210 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: E 227 GLU cc_start: 0.8667 (tt0) cc_final: 0.8359 (tt0) REVERT: F 47 MET cc_start: 0.7018 (mmp) cc_final: 0.6289 (tmm) REVERT: F 92 GLN cc_start: 0.8336 (tt0) cc_final: 0.8066 (tt0) REVERT: F 105 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8168 (tt) REVERT: F 181 GLU cc_start: 0.8328 (tp30) cc_final: 0.7744 (mp0) REVERT: F 227 GLU cc_start: 0.8625 (tt0) cc_final: 0.8402 (tt0) REVERT: F 273 MET cc_start: 0.8405 (ttm) cc_final: 0.8052 (ttp) REVERT: G 47 MET cc_start: 0.6798 (mmp) cc_final: 0.6221 (tmm) REVERT: G 221 MET cc_start: 0.8777 (mtm) cc_final: 0.8548 (mtm) REVERT: G 278 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7982 (mtmt) outliers start: 53 outliers final: 21 residues processed: 242 average time/residue: 0.6147 time to fit residues: 163.3273 Evaluate side-chains 221 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 203 GLN C 92 GLN C 149 GLN D 92 GLN E 92 GLN E 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086308 restraints weight = 21428.739| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.17 r_work: 0.2922 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15477 Z= 0.267 Angle : 0.573 11.547 20776 Z= 0.302 Chirality : 0.044 0.166 2415 Planarity : 0.005 0.063 2548 Dihedral : 14.882 110.601 2751 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.39 % Allowed : 20.33 % Favored : 75.28 % 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: 1.08 (0.19), residues: 1841 helix: 2.21 (0.16), residues: 987 sheet: -0.44 (0.26), residues: 308 loop : -1.44 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 184 TYR 0.008 0.002 TYR D 270 PHE 0.020 0.003 PHE E 68 TRP 0.004 0.001 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.27 (15477) covalent geometry : angle 0.57258 / 0.30 (20776) hydrogen bonds : bond 0.04171 / 2.81 ( 996) hydrogen bonds : angle 4.08770 / 2.90 ( 2925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6708 (mmp) cc_final: 0.5803 (tmm) REVERT: A 60 LYS cc_start: 0.7403 (ptmm) cc_final: 0.7015 (ptpp) REVERT: A 149 GLN cc_start: 0.8378 (mt0) cc_final: 0.7925 (mm110) REVERT: A 161 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8606 (mtmm) REVERT: A 203 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8108 (tp40) REVERT: B 25 LEU cc_start: 0.8252 (pp) cc_final: 0.7646 (tt) REVERT: B 47 MET cc_start: 0.7011 (mmp) cc_final: 0.6342 (tmm) REVERT: B 68 PHE cc_start: 0.6110 (OUTLIER) cc_final: 0.5851 (p90) REVERT: B 159 ASP cc_start: 0.8570 (t0) cc_final: 0.8314 (t0) REVERT: B 171 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8767 (mp) REVERT: B 227 GLU cc_start: 0.8927 (tt0) cc_final: 0.8715 (tt0) REVERT: B 253 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 278 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: C 47 MET cc_start: 0.6834 (mmp) cc_final: 0.5897 (tmt) REVERT: C 149 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8049 (mm-40) REVERT: C 155 MET cc_start: 0.9211 (ptt) cc_final: 0.8971 (ptt) REVERT: C 181 GLU cc_start: 0.8661 (tp30) cc_final: 0.7853 (mp0) REVERT: C 273 MET cc_start: 0.8767 (ttm) cc_final: 0.8503 (ttp) REVERT: D 35 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 47 MET cc_start: 0.6823 (mmp) cc_final: 0.5884 (tmm) REVERT: D 126 MET cc_start: 0.8233 (tmt) cc_final: 0.7938 (tmt) REVERT: D 149 GLN cc_start: 0.8503 (mt0) cc_final: 0.8076 (mm110) REVERT: D 181 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8349 (tp30) REVERT: D 210 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: E 47 MET cc_start: 0.6661 (mmp) cc_final: 0.6004 (tmt) REVERT: E 60 LYS cc_start: 0.7415 (ptmm) cc_final: 0.7006 (ptpp) REVERT: E 149 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7965 (mm-40) REVERT: E 203 GLN cc_start: 0.8406 (tt0) cc_final: 0.8194 (tp-100) REVERT: E 210 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: E 227 GLU cc_start: 0.8951 (tt0) cc_final: 0.8689 (tt0) REVERT: F 47 MET cc_start: 0.7151 (mmp) cc_final: 0.6336 (tmm) REVERT: F 92 GLN cc_start: 0.8576 (tt0) cc_final: 0.8302 (tt0) REVERT: F 105 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8277 (tt) REVERT: F 149 GLN cc_start: 0.8507 (mt0) cc_final: 0.8119 (mm110) REVERT: F 155 MET cc_start: 0.8970 (ptt) cc_final: 0.8644 (ptm) REVERT: F 203 GLN cc_start: 0.8446 (tt0) cc_final: 0.8175 (tp40) REVERT: F 210 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8618 (mt0) REVERT: F 227 GLU cc_start: 0.8862 (tt0) cc_final: 0.8648 (tt0) REVERT: F 273 MET cc_start: 0.8642 (ttm) cc_final: 0.8373 (ttp) REVERT: G 47 MET cc_start: 0.6883 (mmp) cc_final: 0.6133 (tmm) REVERT: G 60 LYS cc_start: 0.7621 (ptmm) cc_final: 0.7213 (ptpp) REVERT: G 149 GLN cc_start: 0.8548 (mt0) cc_final: 0.8053 (mm110) REVERT: G 181 GLU cc_start: 0.8510 (tp30) cc_final: 0.7886 (mp0) REVERT: G 203 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8202 (tp40) REVERT: G 247 GLN cc_start: 0.8844 (tp40) cc_final: 0.8584 (tp-100) REVERT: G 278 LYS cc_start: 0.8416 (mtpt) cc_final: 0.7924 (mtmt) outliers start: 66 outliers final: 19 residues processed: 249 average time/residue: 0.5957 time to fit residues: 163.3265 Evaluate side-chains 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 168 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 179 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 0.0970 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN C 92 GLN C 149 GLN D 92 GLN E 92 GLN E 149 GLN G 53 ASN G 149 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091461 restraints weight = 21099.914| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.16 r_work: 0.3004 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15477 Z= 0.109 Angle : 0.489 11.081 20776 Z= 0.252 Chirality : 0.040 0.147 2415 Planarity : 0.004 0.061 2548 Dihedral : 14.098 117.835 2751 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.59 % Allowed : 21.79 % Favored : 75.61 % 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: 1.53 (0.20), residues: 1841 helix: 2.62 (0.16), residues: 987 sheet: -0.40 (0.26), residues: 294 loop : -1.18 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 279 TYR 0.008 0.001 TYR D 194 PHE 0.017 0.002 PHE E 68 TRP 0.003 0.000 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15477) covalent geometry : angle 0.48944 / 0.25 (20776) hydrogen bonds : bond 0.03327 / 2.24 ( 996) hydrogen bonds : angle 3.79777 / 2.69 ( 2925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6683 (mmp) cc_final: 0.5791 (tmt) REVERT: A 60 LYS cc_start: 0.7355 (ptmm) cc_final: 0.6939 (ptpp) REVERT: A 149 GLN cc_start: 0.8422 (mt0) cc_final: 0.7972 (mm110) REVERT: A 161 LYS cc_start: 0.9064 (ptpt) cc_final: 0.8648 (mtmm) REVERT: A 181 GLU cc_start: 0.8620 (tp30) cc_final: 0.7943 (tt0) REVERT: A 203 GLN cc_start: 0.8274 (tt0) cc_final: 0.8038 (tp40) REVERT: B 47 MET cc_start: 0.6935 (mmp) cc_final: 0.6259 (tmm) REVERT: B 68 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5901 (p90) REVERT: B 159 ASP cc_start: 0.8499 (t0) cc_final: 0.8229 (t0) REVERT: B 181 GLU cc_start: 0.8547 (tp30) cc_final: 0.7889 (tt0) REVERT: B 203 GLN cc_start: 0.8376 (tp40) cc_final: 0.8059 (tm-30) REVERT: B 278 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8114 (mttt) REVERT: C 47 MET cc_start: 0.6818 (mmp) cc_final: 0.5972 (tmm) REVERT: C 149 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: C 155 MET cc_start: 0.9100 (ptt) cc_final: 0.8882 (ptt) REVERT: C 159 ASP cc_start: 0.8674 (t0) cc_final: 0.8473 (t0) REVERT: C 181 GLU cc_start: 0.8671 (tp30) cc_final: 0.7878 (mp0) REVERT: C 273 MET cc_start: 0.8739 (ttm) cc_final: 0.8491 (ttp) REVERT: D 47 MET cc_start: 0.6900 (mmp) cc_final: 0.6121 (tmm) REVERT: D 126 MET cc_start: 0.8099 (tmt) cc_final: 0.7806 (tmt) REVERT: D 149 GLN cc_start: 0.8553 (mt0) cc_final: 0.8119 (mm110) REVERT: D 227 GLU cc_start: 0.8936 (tt0) cc_final: 0.8725 (tt0) REVERT: E 47 MET cc_start: 0.6660 (mmp) cc_final: 0.6047 (tmt) REVERT: E 60 LYS cc_start: 0.7336 (ptmm) cc_final: 0.6991 (ptpp) REVERT: E 149 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8038 (mm110) REVERT: E 181 GLU cc_start: 0.8645 (tp30) cc_final: 0.8010 (tt0) REVERT: E 227 GLU cc_start: 0.8905 (tt0) cc_final: 0.8658 (tt0) REVERT: F 47 MET cc_start: 0.7064 (mmp) cc_final: 0.6249 (tmm) REVERT: F 92 GLN cc_start: 0.8410 (tt0) cc_final: 0.8134 (tt0) REVERT: F 126 MET cc_start: 0.8686 (ttm) cc_final: 0.8453 (ttm) REVERT: F 149 GLN cc_start: 0.8590 (mt0) cc_final: 0.8320 (mm110) REVERT: F 181 GLU cc_start: 0.8529 (tp30) cc_final: 0.7875 (mp0) REVERT: F 203 GLN cc_start: 0.8315 (tt0) cc_final: 0.8034 (tp40) REVERT: F 227 GLU cc_start: 0.8870 (tt0) cc_final: 0.8644 (tt0) REVERT: F 273 MET cc_start: 0.8629 (ttm) cc_final: 0.8372 (ttp) REVERT: G 47 MET cc_start: 0.6865 (mmp) cc_final: 0.6142 (tmm) REVERT: G 60 LYS cc_start: 0.7554 (ptmm) cc_final: 0.7139 (ptpp) REVERT: G 149 GLN cc_start: 0.8553 (mt0) cc_final: 0.8078 (mm110) REVERT: G 181 GLU cc_start: 0.8508 (tp30) cc_final: 0.7893 (mp0) REVERT: G 203 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8136 (tp40) REVERT: G 221 MET cc_start: 0.8967 (mtm) cc_final: 0.8565 (mtm) REVERT: G 247 GLN cc_start: 0.8764 (tp40) cc_final: 0.8499 (tp-100) REVERT: G 278 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7945 (mtmt) outliers start: 39 outliers final: 14 residues processed: 230 average time/residue: 0.6405 time to fit residues: 161.1985 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 92 GLN A 203 GLN B 234 ASN D 92 GLN E 92 GLN G 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088317 restraints weight = 21423.368| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.18 r_work: 0.2951 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15477 Z= 0.175 Angle : 0.519 12.329 20776 Z= 0.269 Chirality : 0.041 0.145 2415 Planarity : 0.004 0.060 2548 Dihedral : 14.092 122.730 2751 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.59 % Allowed : 22.13 % Favored : 75.28 % 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: 1.53 (0.20), residues: 1841 helix: 2.55 (0.16), residues: 994 sheet: -0.34 (0.26), residues: 294 loop : -1.12 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 46 TYR 0.013 0.001 TYR D 194 PHE 0.019 0.002 PHE C 68 TRP 0.002 0.000 TRP D 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (15477) covalent geometry : angle 0.51921 / 0.27 (20776) hydrogen bonds : bond 0.03679 / 2.48 ( 996) hydrogen bonds : angle 3.89033 / 2.76 ( 2925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6691 (mmp) cc_final: 0.5787 (tmt) REVERT: A 56 MET cc_start: 0.0842 (ptt) cc_final: 0.0583 (ptt) REVERT: A 60 LYS cc_start: 0.7385 (ptmm) cc_final: 0.7014 (ptpp) REVERT: A 149 GLN cc_start: 0.8441 (mt0) cc_final: 0.7980 (mm110) REVERT: A 161 LYS cc_start: 0.9084 (ptpt) cc_final: 0.8632 (mtmm) REVERT: A 181 GLU cc_start: 0.8654 (tp30) cc_final: 0.8028 (tt0) REVERT: A 203 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8061 (tp40) REVERT: A 278 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8141 (mtpt) REVERT: B 25 LEU cc_start: 0.8030 (pp) cc_final: 0.7406 (tt) REVERT: B 47 MET cc_start: 0.6974 (mmp) cc_final: 0.6330 (tmm) REVERT: B 68 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5937 (p90) REVERT: B 126 MET cc_start: 0.8384 (tpt) cc_final: 0.8170 (ttp) REVERT: B 159 ASP cc_start: 0.8564 (t0) cc_final: 0.8306 (t0) REVERT: B 171 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 181 GLU cc_start: 0.8556 (tp30) cc_final: 0.7965 (tt0) REVERT: B 278 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8095 (mttt) REVERT: C 47 MET cc_start: 0.6893 (mmp) cc_final: 0.5964 (tmt) REVERT: C 149 GLN cc_start: 0.8499 (mt0) cc_final: 0.8105 (mm-40) REVERT: C 155 MET cc_start: 0.9164 (ptt) cc_final: 0.8957 (ptt) REVERT: C 181 GLU cc_start: 0.8682 (tp30) cc_final: 0.7842 (mp0) REVERT: C 203 GLN cc_start: 0.8478 (tt0) cc_final: 0.8136 (tp40) REVERT: C 273 MET cc_start: 0.8748 (ttm) cc_final: 0.8495 (ttp) REVERT: D 47 MET cc_start: 0.6820 (mmp) cc_final: 0.5917 (tmm) REVERT: D 60 LYS cc_start: 0.7555 (ptmm) cc_final: 0.7131 (ptpp) REVERT: D 126 MET cc_start: 0.8208 (tmt) cc_final: 0.7919 (tmt) REVERT: D 149 GLN cc_start: 0.8591 (mt0) cc_final: 0.8183 (mm110) REVERT: D 203 GLN cc_start: 0.8319 (tm-30) cc_final: 0.8006 (tp40) REVERT: D 210 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: E 47 MET cc_start: 0.6692 (mmp) cc_final: 0.6020 (tmt) REVERT: E 60 LYS cc_start: 0.7344 (ptmm) cc_final: 0.7044 (ptpp) REVERT: E 149 GLN cc_start: 0.8356 (mt0) cc_final: 0.8031 (mm-40) REVERT: E 181 GLU cc_start: 0.8621 (tp30) cc_final: 0.7911 (tt0) REVERT: E 203 GLN cc_start: 0.8403 (tt0) cc_final: 0.8174 (tp40) REVERT: E 227 GLU cc_start: 0.8923 (tt0) cc_final: 0.8661 (tt0) REVERT: F 47 MET cc_start: 0.7142 (mmp) cc_final: 0.6329 (tmm) REVERT: F 92 GLN cc_start: 0.8472 (tt0) cc_final: 0.8215 (tt0) REVERT: F 149 GLN cc_start: 0.8596 (mt0) cc_final: 0.8273 (mm110) REVERT: F 155 MET cc_start: 0.8964 (ptt) cc_final: 0.8666 (ptm) REVERT: F 181 GLU cc_start: 0.8541 (tp30) cc_final: 0.7874 (mp0) REVERT: F 203 GLN cc_start: 0.8375 (tt0) cc_final: 0.8129 (tp40) REVERT: F 210 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: F 227 GLU cc_start: 0.8865 (tt0) cc_final: 0.8644 (tt0) REVERT: F 273 MET cc_start: 0.8642 (ttm) cc_final: 0.8373 (ttp) REVERT: F 277 PHE cc_start: 0.8251 (t80) cc_final: 0.7715 (m-80) REVERT: G 47 MET cc_start: 0.6877 (mmp) cc_final: 0.6137 (tmm) REVERT: G 60 LYS cc_start: 0.7566 (ptmm) cc_final: 0.7157 (ptpp) REVERT: G 149 GLN cc_start: 0.8544 (mt0) cc_final: 0.8061 (mm110) REVERT: G 181 GLU cc_start: 0.8566 (tp30) cc_final: 0.7812 (mp0) REVERT: G 221 MET cc_start: 0.9098 (mtm) cc_final: 0.8731 (mtm) REVERT: G 247 GLN cc_start: 0.8830 (tp40) cc_final: 0.8580 (tp-100) REVERT: G 278 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7914 (mtmt) outliers start: 39 outliers final: 18 residues processed: 220 average time/residue: 0.6924 time to fit residues: 166.3703 Evaluate side-chains 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN C 92 GLN D 92 GLN E 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091367 restraints weight = 21338.567| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.18 r_work: 0.3004 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15477 Z= 0.109 Angle : 0.482 11.594 20776 Z= 0.247 Chirality : 0.040 0.145 2415 Planarity : 0.004 0.060 2548 Dihedral : 13.656 125.247 2751 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.79 % Allowed : 22.72 % Favored : 75.48 % 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: 1.77 (0.20), residues: 1841 helix: 2.75 (0.16), residues: 994 sheet: -0.26 (0.27), residues: 294 loop : -1.01 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 46 TYR 0.009 0.001 TYR D 194 PHE 0.017 0.002 PHE C 68 TRP 0.003 0.000 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15477) covalent geometry : angle 0.48164 / 0.25 (20776) hydrogen bonds : bond 0.03277 / 2.21 ( 996) hydrogen bonds : angle 3.76656 / 2.67 ( 2925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6680 (mmp) cc_final: 0.5790 (tmt) REVERT: A 60 LYS cc_start: 0.7317 (ptmm) cc_final: 0.6968 (ptpp) REVERT: A 149 GLN cc_start: 0.8428 (mt0) cc_final: 0.7975 (mm110) REVERT: A 155 MET cc_start: 0.9059 (ptt) cc_final: 0.8779 (ptt) REVERT: A 161 LYS cc_start: 0.9083 (ptpt) cc_final: 0.8697 (mtmp) REVERT: A 181 GLU cc_start: 0.8601 (tp30) cc_final: 0.7965 (tt0) REVERT: A 278 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8101 (mtpt) REVERT: B 47 MET cc_start: 0.7013 (mmp) cc_final: 0.6345 (tmm) REVERT: B 68 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.6017 (p90) REVERT: B 159 ASP cc_start: 0.8515 (t0) cc_final: 0.8244 (t0) REVERT: B 181 GLU cc_start: 0.8514 (tp30) cc_final: 0.7935 (tt0) REVERT: B 278 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8166 (mttt) REVERT: C 47 MET cc_start: 0.6882 (mmp) cc_final: 0.6037 (tmm) REVERT: C 149 GLN cc_start: 0.8527 (mt0) cc_final: 0.8180 (mm-40) REVERT: C 155 MET cc_start: 0.9108 (ptt) cc_final: 0.8906 (ptt) REVERT: C 181 GLU cc_start: 0.8693 (tp30) cc_final: 0.7883 (mp0) REVERT: C 203 GLN cc_start: 0.8411 (tt0) cc_final: 0.8076 (tp40) REVERT: C 273 MET cc_start: 0.8766 (ttm) cc_final: 0.8515 (ttp) REVERT: D 47 MET cc_start: 0.6956 (mmp) cc_final: 0.6101 (tmm) REVERT: D 60 LYS cc_start: 0.7487 (ptmm) cc_final: 0.7070 (ptpp) REVERT: D 126 MET cc_start: 0.8144 (tmt) cc_final: 0.7859 (tmt) REVERT: D 149 GLN cc_start: 0.8597 (mt0) cc_final: 0.8183 (mm110) REVERT: D 203 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8107 (tp-100) REVERT: D 210 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: D 227 GLU cc_start: 0.8897 (tt0) cc_final: 0.8687 (tt0) REVERT: E 47 MET cc_start: 0.6681 (mmp) cc_final: 0.6016 (tmt) REVERT: E 60 LYS cc_start: 0.7295 (ptmm) cc_final: 0.6982 (ptpp) REVERT: E 149 GLN cc_start: 0.8264 (mt0) cc_final: 0.7958 (mm110) REVERT: E 181 GLU cc_start: 0.8606 (tp30) cc_final: 0.7903 (tt0) REVERT: E 203 GLN cc_start: 0.8373 (tt0) cc_final: 0.8161 (tp-100) REVERT: E 227 GLU cc_start: 0.8877 (tt0) cc_final: 0.8631 (tt0) REVERT: E 278 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7580 (mtpt) REVERT: F 47 MET cc_start: 0.7143 (mmp) cc_final: 0.6333 (tmm) REVERT: F 92 GLN cc_start: 0.8411 (tt0) cc_final: 0.8139 (tt0) REVERT: F 105 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8171 (tt) REVERT: F 126 MET cc_start: 0.8644 (ttm) cc_final: 0.8391 (ttm) REVERT: F 149 GLN cc_start: 0.8650 (mt0) cc_final: 0.8336 (mm110) REVERT: F 155 MET cc_start: 0.8910 (ptt) cc_final: 0.8569 (ptm) REVERT: F 181 GLU cc_start: 0.8503 (tp30) cc_final: 0.7863 (mp0) REVERT: F 203 GLN cc_start: 0.8319 (tt0) cc_final: 0.8055 (tp40) REVERT: F 227 GLU cc_start: 0.8855 (tt0) cc_final: 0.8630 (tt0) REVERT: F 273 MET cc_start: 0.8633 (ttm) cc_final: 0.8357 (ttp) REVERT: G 47 MET cc_start: 0.6868 (mmp) cc_final: 0.6141 (tmm) REVERT: G 60 LYS cc_start: 0.7471 (ptmm) cc_final: 0.7075 (ptpp) REVERT: G 149 GLN cc_start: 0.8552 (mt0) cc_final: 0.8077 (mm110) REVERT: G 181 GLU cc_start: 0.8533 (tp30) cc_final: 0.7859 (mp0) REVERT: G 278 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7899 (mtmt) outliers start: 27 outliers final: 16 residues processed: 228 average time/residue: 0.6963 time to fit residues: 173.1865 Evaluate side-chains 213 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 109 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 GLN D 92 GLN E 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092723 restraints weight = 21358.742| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.19 r_work: 0.3026 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15477 Z= 0.101 Angle : 0.481 11.257 20776 Z= 0.244 Chirality : 0.040 0.140 2415 Planarity : 0.004 0.059 2548 Dihedral : 13.255 128.220 2751 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.33 % Allowed : 23.52 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1841 helix: 2.84 (0.16), residues: 994 sheet: -0.18 (0.27), residues: 294 loop : -0.93 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 46 TYR 0.007 0.001 TYR D 135 PHE 0.017 0.001 PHE C 68 TRP 0.004 0.000 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (15477) covalent geometry : angle 0.48051 / 0.24 (20776) hydrogen bonds : bond 0.03207 / 2.17 ( 996) hydrogen bonds : angle 3.69749 / 2.62 ( 2925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6728 (mmp) cc_final: 0.5917 (tmt) REVERT: A 60 LYS cc_start: 0.7267 (ptmm) cc_final: 0.6948 (ptpp) REVERT: A 149 GLN cc_start: 0.8511 (mt0) cc_final: 0.8049 (mm110) REVERT: A 155 MET cc_start: 0.9022 (ptt) cc_final: 0.8775 (ptt) REVERT: A 161 LYS cc_start: 0.9061 (ptpt) cc_final: 0.8629 (mtmp) REVERT: A 181 GLU cc_start: 0.8583 (tp30) cc_final: 0.7939 (tt0) REVERT: A 278 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: B 47 MET cc_start: 0.6995 (mmp) cc_final: 0.6281 (tmt) REVERT: B 68 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.5983 (p90) REVERT: B 159 ASP cc_start: 0.8604 (t0) cc_final: 0.8314 (t0) REVERT: B 171 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 181 GLU cc_start: 0.8506 (tp30) cc_final: 0.7889 (tt0) REVERT: B 278 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8082 (mttt) REVERT: C 47 MET cc_start: 0.6843 (mmp) cc_final: 0.6030 (tmt) REVERT: C 126 MET cc_start: 0.8563 (ttm) cc_final: 0.8268 (tmt) REVERT: C 149 GLN cc_start: 0.8570 (mt0) cc_final: 0.8214 (mm-40) REVERT: C 161 LYS cc_start: 0.9009 (ptpt) cc_final: 0.8731 (mtmm) REVERT: C 181 GLU cc_start: 0.8642 (tp30) cc_final: 0.7848 (mp0) REVERT: C 203 GLN cc_start: 0.8423 (tt0) cc_final: 0.8104 (tp40) REVERT: C 273 MET cc_start: 0.8788 (ttm) cc_final: 0.8536 (ttp) REVERT: D 47 MET cc_start: 0.6910 (mmp) cc_final: 0.6095 (tmm) REVERT: D 60 LYS cc_start: 0.7471 (ptmm) cc_final: 0.7078 (ptpp) REVERT: D 126 MET cc_start: 0.8138 (tmt) cc_final: 0.7865 (tmt) REVERT: D 149 GLN cc_start: 0.8695 (mt0) cc_final: 0.8248 (mm110) REVERT: D 161 LYS cc_start: 0.8982 (ptpt) cc_final: 0.8731 (mtmm) REVERT: D 203 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7982 (tp-100) REVERT: D 210 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: D 227 GLU cc_start: 0.8875 (tt0) cc_final: 0.8657 (tt0) REVERT: E 47 MET cc_start: 0.6774 (mmp) cc_final: 0.6124 (tmt) REVERT: E 60 LYS cc_start: 0.7255 (ptmm) cc_final: 0.6966 (ptpp) REVERT: E 149 GLN cc_start: 0.8302 (mt0) cc_final: 0.8012 (mm-40) REVERT: E 181 GLU cc_start: 0.8591 (tp30) cc_final: 0.7888 (tt0) REVERT: E 203 GLN cc_start: 0.8370 (tt0) cc_final: 0.8155 (tp-100) REVERT: F 47 MET cc_start: 0.7090 (mmp) cc_final: 0.6344 (tmm) REVERT: F 92 GLN cc_start: 0.8424 (tt0) cc_final: 0.8138 (tt0) REVERT: F 105 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8222 (tt) REVERT: F 126 MET cc_start: 0.8585 (ttm) cc_final: 0.8350 (ttm) REVERT: F 149 GLN cc_start: 0.8702 (mt0) cc_final: 0.8341 (mm110) REVERT: F 155 MET cc_start: 0.8917 (ptt) cc_final: 0.8611 (ptm) REVERT: F 203 GLN cc_start: 0.8321 (tt0) cc_final: 0.8072 (tp40) REVERT: F 227 GLU cc_start: 0.8848 (tt0) cc_final: 0.8627 (tt0) REVERT: F 273 MET cc_start: 0.8626 (ttm) cc_final: 0.8327 (ttp) REVERT: G 47 MET cc_start: 0.6880 (mmp) cc_final: 0.6155 (tmm) REVERT: G 60 LYS cc_start: 0.7415 (ptmm) cc_final: 0.7034 (ptpp) REVERT: G 149 GLN cc_start: 0.8603 (mt0) cc_final: 0.8126 (mm110) REVERT: G 181 GLU cc_start: 0.8483 (tp30) cc_final: 0.7910 (mp0) REVERT: G 221 MET cc_start: 0.8867 (mtm) cc_final: 0.8591 (mtm) REVERT: G 278 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7916 (mtmt) outliers start: 20 outliers final: 12 residues processed: 217 average time/residue: 0.7378 time to fit residues: 173.7609 Evaluate side-chains 206 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN C 92 GLN D 92 GLN E 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092126 restraints weight = 21233.400| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.18 r_work: 0.3017 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15477 Z= 0.109 Angle : 0.496 11.671 20776 Z= 0.250 Chirality : 0.040 0.145 2415 Planarity : 0.004 0.059 2548 Dihedral : 12.970 129.215 2751 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.26 % Allowed : 24.25 % Favored : 74.49 % 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: 1.93 (0.20), residues: 1841 helix: 2.84 (0.16), residues: 994 sheet: -0.15 (0.27), residues: 294 loop : -0.87 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 46 TYR 0.008 0.001 TYR D 194 PHE 0.017 0.001 PHE C 68 TRP 0.003 0.000 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15477) covalent geometry : angle 0.49630 / 0.25 (20776) hydrogen bonds : bond 0.03231 / 2.18 ( 996) hydrogen bonds : angle 3.69744 / 2.62 ( 2925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.93 seconds wall clock time: 90 minutes 40.50 seconds (5440.50 seconds total)