Starting phenix.real_space_refine on Fri Sep 11 04:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.cif" model { file = "/net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c99_30309/09_2026/7c99_30309.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 27 5.49 5 S 33 5.16 5 C 4755 2.51 5 N 1341 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s 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: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.21 Number of scatterers: 7656 At special positions: 0 Unit cell: (107.52, 78.12, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 27 15.00 O 1497 8.00 N 1341 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 357.3 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 40.2% alpha, 11.9% beta 8 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.269A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.503A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.697A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.500A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.023A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.560A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.934A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 4.269A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.502A pdb=" N ILE B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.697A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.500A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.024A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.562A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.934A pdb=" N LEU B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 removed outlier: 4.270A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.503A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.698A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.501A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 4.023A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.561A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.933A pdb=" N LEU C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.835A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR A 122 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN A 268 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA A 124 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS A 218 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE A 265 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 220 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR A 267 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 222 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS A 155 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 219 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 327 removed outlier: 3.835A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR B 122 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN B 268 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 124 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 218 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE B 265 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 220 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 222 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 155 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 219 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.372A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS C 155 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 219 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 218 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE C 265 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 220 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR C 267 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE C 222 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR C 122 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN C 268 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA C 124 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AA9, first strand: chain 'C' and resid 330 through 331 203 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2021 1.33 - 1.45: 1371 1.45 - 1.57: 4313 1.57 - 1.69: 51 1.69 - 1.81: 57 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 10525 4.51 - 9.02: 67 9.02 - 13.53: 5 13.53 - 18.04: 0 18.04 - 22.55: 3 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 104.40 22.55 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 104.41 22.54 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 105.31 21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" N VAL A 184 " pdb=" CA VAL A 184 " pdb=" C VAL A 184 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 angle pdb=" N VAL B 184 " pdb=" CA VAL B 184 " pdb=" C VAL B 184 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.06e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4346 25.94 - 51.89: 273 51.89 - 77.83: 31 77.83 - 103.78: 12 103.78 - 129.72: 3 Dihedral angle restraints: 4665 sinusoidal: 2031 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASN A 163 " pdb=" C ASN A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN B 163 " pdb=" C ASN B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 4662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 915 0.060 - 0.120: 243 0.120 - 0.180: 32 0.180 - 0.241: 1 0.241 - 0.301: 3 Chirality restraints: 1194 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 317 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASP B 317 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP B 317 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 317 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASP C 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP C 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 317 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C ASP A 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 318 " -0.014 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 29 2.40 - 3.03: 3868 3.03 - 3.65: 10308 3.65 - 4.28: 16421 4.28 - 4.90: 27920 Nonbonded interactions: 58546 Sorted by model distance: nonbonded pdb=" OD1 ASP A 168 " pdb=" NH2 ARG A 171 " model vdw 1.776 3.120 nonbonded pdb=" OD1 ASP B 168 " pdb=" NH2 ARG B 171 " model vdw 1.777 3.120 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.084 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.084 2.510 nonbonded pdb=" O2G ANP C 401 " pdb="CA CA C 402 " model vdw 2.099 2.510 ... (remaining 58541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.008 0.149 7813 Z= 0.423 Angle : 1.065 22.547 10600 Z= 0.593 Chirality : 0.054 0.301 1194 Planarity : 0.004 0.028 1290 Dihedral : 16.529 129.722 2973 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -5.91 (0.18), residues: 915 helix: -4.79 (0.09), residues: 384 sheet: -1.97 (0.34), residues: 162 loop : -3.63 (0.23), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 192 TYR 0.008 0.002 TYR B 260 PHE 0.028 0.003 PHE C 128 HIS 0.007 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.42 ( 7813) covalent geometry : angle 1.06508 / 0.59 (10600) hydrogen bonds : bond 0.32240 / 20.75 ( 219) hydrogen bonds : angle 9.96492 / 6.75 ( 590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8728 (m) cc_final: 0.8486 (t) REVERT: A 244 GLN cc_start: 0.8191 (mt0) cc_final: 0.7938 (mt0) REVERT: A 273 ASP cc_start: 0.7986 (t0) cc_final: 0.7747 (t70) REVERT: A 331 THR cc_start: 0.9030 (p) cc_final: 0.8795 (t) REVERT: B 94 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7987 (mmtp) REVERT: B 119 MET cc_start: 0.8618 (mtt) cc_final: 0.8339 (mtm) REVERT: B 202 LEU cc_start: 0.9130 (tp) cc_final: 0.8626 (tt) REVERT: B 314 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8577 (tttt) REVERT: C 123 GLU cc_start: 0.7574 (tt0) cc_final: 0.7350 (tt0) REVERT: C 155 LYS cc_start: 0.8574 (mttt) cc_final: 0.8241 (mtpt) REVERT: C 335 ILE cc_start: 0.8922 (mm) cc_final: 0.8561 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1020 time to fit residues: 32.4677 Evaluate side-chains 153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 30 HIS A 261 ASN B 22 GLN B 30 HIS B 199 GLN B 243 GLN C 22 GLN C 30 HIS C 199 GLN C 243 GLN C 244 GLN C 291 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118994 restraints weight = 10494.110| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.07 r_work: 0.3121 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7813 Z= 0.137 Angle : 0.614 6.452 10600 Z= 0.342 Chirality : 0.046 0.174 1194 Planarity : 0.004 0.022 1290 Dihedral : 16.581 155.296 1215 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.71 % Allowed : 11.46 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.21), residues: 915 helix: -3.39 (0.18), residues: 387 sheet: -1.59 (0.35), residues: 159 loop : -3.06 (0.25), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 192 TYR 0.010 0.001 TYR B 194 PHE 0.017 0.002 PHE B 128 HIS 0.003 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 7813) covalent geometry : angle 0.61370 / 0.34 (10600) hydrogen bonds : bond 0.06148 / 3.72 ( 219) hydrogen bonds : angle 5.27687 / 3.45 ( 590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8768 (m) cc_final: 0.8524 (m) REVERT: A 93 GLU cc_start: 0.8301 (mp0) cc_final: 0.7683 (mm-30) REVERT: A 151 TYR cc_start: 0.8694 (t80) cc_final: 0.8479 (t80) REVERT: A 194 TYR cc_start: 0.9086 (m-80) cc_final: 0.8623 (m-80) REVERT: A 268 ASN cc_start: 0.9166 (p0) cc_final: 0.8910 (p0) REVERT: A 324 ASN cc_start: 0.8664 (m-40) cc_final: 0.8443 (m110) REVERT: A 331 THR cc_start: 0.8980 (p) cc_final: 0.8771 (t) REVERT: B 119 MET cc_start: 0.9045 (mtt) cc_final: 0.8825 (mtm) REVERT: B 180 ASP cc_start: 0.8132 (m-30) cc_final: 0.7591 (t0) REVERT: C 155 LYS cc_start: 0.8728 (mttt) cc_final: 0.8301 (mtpt) REVERT: C 335 ILE cc_start: 0.8961 (mm) cc_final: 0.8664 (mm) outliers start: 13 outliers final: 9 residues processed: 177 average time/residue: 0.0849 time to fit residues: 20.0575 Evaluate side-chains 167 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 72 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.4771 > 50:) chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 243 GLN A 244 GLN C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.153360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120489 restraints weight = 10484.556| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.06 r_work: 0.3119 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7813 Z= 0.125 Angle : 0.553 7.882 10600 Z= 0.305 Chirality : 0.045 0.157 1194 Planarity : 0.003 0.031 1290 Dihedral : 16.624 156.573 1215 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.43 % Allowed : 11.99 % 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: -3.89 (0.23), residues: 915 helix: -2.63 (0.21), residues: 396 sheet: -1.37 (0.37), residues: 159 loop : -2.92 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.008 0.001 TYR A 194 PHE 0.024 0.002 PHE B 108 HIS 0.010 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7813) covalent geometry : angle 0.55299 / 0.30 (10600) hydrogen bonds : bond 0.04647 / 2.83 ( 219) hydrogen bonds : angle 4.63201 / 3.00 ( 590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: A 194 TYR cc_start: 0.9108 (m-80) cc_final: 0.8810 (m-80) REVERT: A 252 ARG cc_start: 0.8430 (ttt90) cc_final: 0.8189 (ttm-80) REVERT: A 268 ASN cc_start: 0.9167 (p0) cc_final: 0.8905 (p0) REVERT: A 331 THR cc_start: 0.9014 (p) cc_final: 0.8770 (t) REVERT: B 93 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: B 107 GLU cc_start: 0.8371 (tp30) cc_final: 0.7796 (tp30) REVERT: C 119 MET cc_start: 0.8890 (mtt) cc_final: 0.8592 (mtt) REVERT: C 155 LYS cc_start: 0.8769 (mttt) cc_final: 0.8337 (mtpt) REVERT: C 335 ILE cc_start: 0.8881 (mm) cc_final: 0.8638 (mm) outliers start: 26 outliers final: 15 residues processed: 169 average time/residue: 0.0791 time to fit residues: 18.1571 Evaluate side-chains 147 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118576 restraints weight = 10670.826| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.09 r_work: 0.3052 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7813 Z= 0.211 Angle : 0.607 7.568 10600 Z= 0.327 Chirality : 0.047 0.199 1194 Planarity : 0.004 0.041 1290 Dihedral : 16.591 156.216 1215 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.29 % Allowed : 14.10 % Favored : 82.61 % 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: -3.47 (0.24), residues: 915 helix: -2.16 (0.23), residues: 393 sheet: -1.06 (0.39), residues: 153 loop : -2.90 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 252 TYR 0.015 0.002 TYR A 260 PHE 0.025 0.002 PHE C 128 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 7813) covalent geometry : angle 0.60739 / 0.33 (10600) hydrogen bonds : bond 0.04816 / 2.92 ( 219) hydrogen bonds : angle 4.33631 / 2.85 ( 590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: A 194 TYR cc_start: 0.9236 (m-80) cc_final: 0.8857 (m-80) REVERT: A 232 ASP cc_start: 0.8315 (m-30) cc_final: 0.8061 (m-30) REVERT: A 331 THR cc_start: 0.8987 (p) cc_final: 0.8776 (t) REVERT: B 107 GLU cc_start: 0.8414 (tp30) cc_final: 0.7817 (tp30) REVERT: C 117 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 155 LYS cc_start: 0.8752 (mttt) cc_final: 0.8287 (mtpt) REVERT: C 192 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7504 (ttt180) REVERT: C 238 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8378 (mt-10) REVERT: C 335 ILE cc_start: 0.9037 (mm) cc_final: 0.8803 (mm) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.0906 time to fit residues: 16.5214 Evaluate side-chains 138 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.0020 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119794 restraints weight = 10594.623| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.09 r_work: 0.3099 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7813 Z= 0.123 Angle : 0.529 6.797 10600 Z= 0.288 Chirality : 0.045 0.170 1194 Planarity : 0.003 0.020 1290 Dihedral : 16.570 157.718 1215 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.03 % Allowed : 15.42 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.24), residues: 915 helix: -1.68 (0.24), residues: 393 sheet: -0.83 (0.39), residues: 147 loop : -2.86 (0.25), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.020 0.002 TYR B 260 PHE 0.020 0.002 PHE C 128 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7813) covalent geometry : angle 0.52911 / 0.29 (10600) hydrogen bonds : bond 0.03766 / 2.29 ( 219) hydrogen bonds : angle 4.11703 / 2.67 ( 590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: A 192 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.6715 (ttt180) REVERT: A 232 ASP cc_start: 0.8087 (m-30) cc_final: 0.7861 (m-30) REVERT: A 252 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7950 (ttm-80) REVERT: A 258 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8459 (mt-10) REVERT: A 331 THR cc_start: 0.8998 (p) cc_final: 0.8785 (t) REVERT: B 93 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 107 GLU cc_start: 0.8147 (tp30) cc_final: 0.7623 (tp30) REVERT: B 180 ASP cc_start: 0.7909 (m-30) cc_final: 0.7542 (t0) REVERT: B 258 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8478 (mt-10) REVERT: B 260 TYR cc_start: 0.8594 (m-10) cc_final: 0.8120 (m-10) REVERT: C 117 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7464 (mt-10) REVERT: C 155 LYS cc_start: 0.8687 (mttt) cc_final: 0.8245 (mtpt) REVERT: C 192 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7321 (ttt180) REVERT: C 238 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 335 ILE cc_start: 0.8855 (mm) cc_final: 0.8650 (mm) outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 0.0921 time to fit residues: 18.4320 Evaluate side-chains 150 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115781 restraints weight = 10666.076| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.07 r_work: 0.3043 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7813 Z= 0.240 Angle : 0.635 7.270 10600 Z= 0.338 Chirality : 0.048 0.214 1194 Planarity : 0.004 0.046 1290 Dihedral : 16.510 154.692 1215 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.43 % Allowed : 16.07 % Favored : 80.50 % 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: -3.03 (0.25), residues: 915 helix: -1.58 (0.25), residues: 393 sheet: -0.78 (0.40), residues: 147 loop : -2.95 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 176 TYR 0.011 0.002 TYR B 260 PHE 0.027 0.003 PHE C 128 HIS 0.003 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 ( 7813) covalent geometry : angle 0.63520 / 0.34 (10600) hydrogen bonds : bond 0.04818 / 2.94 ( 219) hydrogen bonds : angle 4.21278 / 2.77 ( 590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 192 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.6725 (ttt180) REVERT: A 232 ASP cc_start: 0.8284 (m-30) cc_final: 0.8023 (m-30) REVERT: A 331 THR cc_start: 0.8988 (p) cc_final: 0.8784 (t) REVERT: B 93 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: B 260 TYR cc_start: 0.8741 (m-10) cc_final: 0.8416 (m-10) REVERT: C 93 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: C 117 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7815 (mt-10) REVERT: C 155 LYS cc_start: 0.8736 (mttt) cc_final: 0.8375 (mtpt) REVERT: C 192 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7604 (ttt180) REVERT: C 238 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8384 (mt-10) REVERT: C 335 ILE cc_start: 0.9088 (mm) cc_final: 0.8859 (mm) outliers start: 26 outliers final: 13 residues processed: 140 average time/residue: 0.1037 time to fit residues: 19.1645 Evaluate side-chains 139 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115105 restraints weight = 10684.932| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.06 r_work: 0.3065 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7813 Z= 0.195 Angle : 0.590 7.931 10600 Z= 0.317 Chirality : 0.047 0.204 1194 Planarity : 0.003 0.042 1290 Dihedral : 16.551 155.738 1215 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.90 % Allowed : 17.39 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.25), residues: 915 helix: -1.26 (0.26), residues: 378 sheet: -0.98 (0.40), residues: 153 loop : -2.76 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 252 TYR 0.014 0.002 TYR B 260 PHE 0.023 0.002 PHE C 128 HIS 0.003 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 7813) covalent geometry : angle 0.59001 / 0.32 (10600) hydrogen bonds : bond 0.04197 / 2.55 ( 219) hydrogen bonds : angle 4.14729 / 2.71 ( 590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 192 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.6732 (ttt180) REVERT: A 232 ASP cc_start: 0.8271 (m-30) cc_final: 0.8016 (m-30) REVERT: A 252 ARG cc_start: 0.8609 (ttt90) cc_final: 0.8375 (ttm-80) REVERT: B 93 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: B 180 ASP cc_start: 0.8097 (m-30) cc_final: 0.7608 (t0) REVERT: B 260 TYR cc_start: 0.8790 (m-10) cc_final: 0.8571 (m-10) REVERT: C 93 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 117 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 155 LYS cc_start: 0.8696 (mttt) cc_final: 0.8362 (mtpt) REVERT: C 192 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: C 238 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8416 (mt-10) REVERT: C 335 ILE cc_start: 0.9090 (mm) cc_final: 0.8876 (mm) outliers start: 22 outliers final: 11 residues processed: 131 average time/residue: 0.0948 time to fit residues: 16.5033 Evaluate side-chains 131 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100 HIS C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118826 restraints weight = 10594.757| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.05 r_work: 0.3101 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7813 Z= 0.149 Angle : 0.539 6.744 10600 Z= 0.293 Chirality : 0.045 0.192 1194 Planarity : 0.003 0.031 1290 Dihedral : 16.556 156.783 1215 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.90 % Allowed : 17.65 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.26), residues: 915 helix: -1.04 (0.26), residues: 378 sheet: -0.95 (0.39), residues: 153 loop : -2.67 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 252 TYR 0.012 0.001 TYR B 260 PHE 0.023 0.002 PHE C 128 HIS 0.002 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7813) covalent geometry : angle 0.53935 / 0.29 (10600) hydrogen bonds : bond 0.03812 / 2.31 ( 219) hydrogen bonds : angle 4.03609 / 2.62 ( 590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.6782 (ttt180) REVERT: A 232 ASP cc_start: 0.8261 (m-30) cc_final: 0.8019 (m-30) REVERT: A 252 ARG cc_start: 0.8558 (ttt90) cc_final: 0.8340 (ttm-80) REVERT: B 93 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: B 180 ASP cc_start: 0.8072 (m-30) cc_final: 0.7605 (t0) REVERT: B 258 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8647 (mt-10) REVERT: B 260 TYR cc_start: 0.8721 (m-80) cc_final: 0.8500 (m-10) REVERT: C 93 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 117 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 192 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7536 (ttt180) REVERT: C 335 ILE cc_start: 0.9018 (mm) cc_final: 0.8816 (mm) outliers start: 22 outliers final: 16 residues processed: 148 average time/residue: 0.0922 time to fit residues: 18.0469 Evaluate side-chains 148 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118701 restraints weight = 10499.009| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.05 r_work: 0.3101 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 0.068 7813 Z= 0.107 Angle : 0.522 8.536 10600 Z= 0.282 Chirality : 0.044 0.175 1194 Planarity : 0.003 0.026 1290 Dihedral : 16.577 157.853 1215 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.24 % Allowed : 18.58 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.26), residues: 915 helix: -0.79 (0.27), residues: 378 sheet: -0.95 (0.38), residues: 153 loop : -2.54 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.011 0.001 TYR B 260 PHE 0.021 0.001 PHE C 128 HIS 0.007 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7813) covalent geometry : angle 0.52245 / 0.28 (10600) hydrogen bonds : bond 0.03317 / 2.01 ( 219) hydrogen bonds : angle 3.88177 / 2.50 ( 590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8455 (t0) cc_final: 0.8173 (t0) REVERT: A 252 ARG cc_start: 0.8547 (ttt90) cc_final: 0.8334 (ttm-80) REVERT: A 273 ASP cc_start: 0.8591 (t0) cc_final: 0.8153 (t70) REVERT: B 93 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: B 180 ASP cc_start: 0.8009 (m-30) cc_final: 0.7549 (t0) REVERT: B 260 TYR cc_start: 0.8616 (m-80) cc_final: 0.8370 (m-10) REVERT: C 72 LYS cc_start: 0.8600 (mttp) cc_final: 0.7761 (tptt) REVERT: C 93 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: C 117 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 192 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7494 (ttt180) outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 0.0880 time to fit residues: 18.5799 Evaluate side-chains 151 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118047 restraints weight = 10583.233| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.07 r_work: 0.3066 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7813 Z= 0.193 Angle : 0.580 7.807 10600 Z= 0.310 Chirality : 0.047 0.201 1194 Planarity : 0.003 0.035 1290 Dihedral : 16.530 156.111 1215 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.24 % Allowed : 18.84 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.26), residues: 915 helix: -1.09 (0.26), residues: 396 sheet: -0.91 (0.39), residues: 153 loop : -2.61 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 129 TYR 0.013 0.002 TYR B 260 PHE 0.026 0.002 PHE C 128 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 7813) covalent geometry : angle 0.58035 / 0.31 (10600) hydrogen bonds : bond 0.04033 / 2.46 ( 219) hydrogen bonds : angle 4.00378 / 2.61 ( 590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 252 ARG cc_start: 0.8538 (ttt90) cc_final: 0.8311 (ttm-80) REVERT: A 273 ASP cc_start: 0.8646 (t0) cc_final: 0.8192 (t70) REVERT: B 93 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: B 180 ASP cc_start: 0.8028 (m-30) cc_final: 0.7555 (t0) REVERT: B 260 TYR cc_start: 0.8740 (m-80) cc_final: 0.8373 (m-10) REVERT: C 72 LYS cc_start: 0.8625 (mttp) cc_final: 0.7767 (tptt) REVERT: C 93 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: C 117 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 192 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7576 (ttt180) REVERT: C 238 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8446 (mt-10) outliers start: 17 outliers final: 12 residues processed: 146 average time/residue: 0.0905 time to fit residues: 17.8977 Evaluate side-chains 149 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS A 211 HIS C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117795 restraints weight = 10528.631| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.04 r_work: 0.3090 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7813 Z= 0.150 Angle : 0.563 8.459 10600 Z= 0.300 Chirality : 0.045 0.191 1194 Planarity : 0.003 0.028 1290 Dihedral : 16.549 156.967 1215 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.24 % Allowed : 19.37 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.26), residues: 915 helix: -0.97 (0.26), residues: 396 sheet: -0.90 (0.39), residues: 153 loop : -2.55 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 129 TYR 0.013 0.001 TYR B 260 PHE 0.023 0.002 PHE C 128 HIS 0.007 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7813) covalent geometry : angle 0.56279 / 0.30 (10600) hydrogen bonds : bond 0.03678 / 2.23 ( 219) hydrogen bonds : angle 3.94412 / 2.56 ( 590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.59 seconds wall clock time: 35 minutes 39.35 seconds (2139.35 seconds total)