Starting phenix.real_space_refine on Tue Mar 3 17:56:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c99_30309/03_2026/7c99_30309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c99_30309/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7c99_30309/03_2026/7c99_30309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c99_30309/03_2026/7c99_30309.map" model { file = "/net/cci-nas-00/data/ceres_data/7c99_30309/03_2026/7c99_30309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c99_30309/03_2026/7c99_30309.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.80, per 1000 atoms: 0.24 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: 0.60 Conformation dependent library (CDL) restraints added in 232.6 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: 0.77 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: 0.91 Time building geometry restraints manager: 0.75 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: 4363 25.94 - 51.89: 301 51.89 - 77.83: 64 77.83 - 103.78: 18 103.78 - 129.72: 3 Dihedral angle restraints: 4749 sinusoidal: 2115 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 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 928 0.060 - 0.120: 231 0.120 - 0.180: 31 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: 5.300 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.380 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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= 0.371 Angle : 1.051 22.547 10600 Z= 0.544 Chirality : 0.053 0.301 1194 Planarity : 0.004 0.028 1290 Dihedral : 18.459 129.722 3057 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 covalent geometry : bond 0.00791 ( 7813) covalent geometry : angle 1.05148 (10600) hydrogen bonds : bond 0.32240 ( 219) hydrogen bonds : angle 9.96492 ( 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 : 0.208 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: 0.1085 time to fit residues: 34.3506 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 : 0.269 ------------------------------------------------------------------------------- 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 30 HIS A 243 GLN 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.121839 restraints weight = 10472.138| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.07 r_work: 0.3125 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7813 Z= 0.128 Angle : 0.578 6.296 10600 Z= 0.313 Chirality : 0.045 0.159 1194 Planarity : 0.003 0.024 1290 Dihedral : 17.940 153.170 1299 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.32 % Allowed : 11.33 % Favored : 87.35 % 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: -4.76 (0.20), residues: 915 helix: -3.44 (0.17), residues: 399 sheet: -1.76 (0.35), residues: 159 loop : -3.27 (0.24), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 252 TYR 0.006 0.001 TYR A 194 PHE 0.018 0.001 PHE B 128 HIS 0.002 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7813) covalent geometry : angle 0.57806 (10600) hydrogen bonds : bond 0.05204 ( 219) hydrogen bonds : angle 4.88121 ( 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 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8751 (m) cc_final: 0.8529 (m) REVERT: A 93 GLU cc_start: 0.8301 (mp0) cc_final: 0.7687 (mm-30) REVERT: A 194 TYR cc_start: 0.9054 (m-80) cc_final: 0.8699 (m-80) REVERT: A 252 ARG cc_start: 0.8479 (ttt90) cc_final: 0.8263 (ttm-80) REVERT: A 268 ASN cc_start: 0.9147 (p0) cc_final: 0.8894 (p0) REVERT: A 331 THR cc_start: 0.8973 (p) cc_final: 0.8755 (t) REVERT: B 119 MET cc_start: 0.9029 (mtt) cc_final: 0.8797 (mtm) REVERT: B 180 ASP cc_start: 0.8073 (m-30) cc_final: 0.7517 (t0) REVERT: B 210 PHE cc_start: 0.8847 (m-10) cc_final: 0.8468 (m-80) REVERT: C 90 GLU cc_start: 0.7834 (mp0) cc_final: 0.7589 (mp0) REVERT: C 108 PHE cc_start: 0.8985 (t80) cc_final: 0.8699 (t80) REVERT: C 155 LYS cc_start: 0.8711 (mttt) cc_final: 0.8256 (mtpt) REVERT: C 335 ILE cc_start: 0.8848 (mm) cc_final: 0.8623 (mm) outliers start: 10 outliers final: 6 residues processed: 178 average time/residue: 0.0961 time to fit residues: 22.3549 Evaluate side-chains 140 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 THR Chi-restraints excluded: chain B residue 327 THR 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: 0.9980 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3661 r_free = 0.3661 target = 0.150486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118294 restraints weight = 10530.406| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.05 r_work: 0.3099 rms_B_bonded: 2.96 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: 0.8579 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7813 Z= 0.142 Angle : 0.540 5.725 10600 Z= 0.291 Chirality : 0.045 0.171 1194 Planarity : 0.003 0.025 1290 Dihedral : 16.894 148.915 1299 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.50 % Allowed : 13.18 % Favored : 84.32 % 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: -3.84 (0.23), residues: 915 helix: -2.40 (0.22), residues: 399 sheet: -1.51 (0.35), residues: 171 loop : -3.07 (0.26), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.009 0.001 TYR A 194 PHE 0.020 0.002 PHE C 128 HIS 0.011 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7813) covalent geometry : angle 0.53969 (10600) hydrogen bonds : bond 0.04017 ( 219) hydrogen bonds : angle 4.09406 ( 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 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: A 194 TYR cc_start: 0.9227 (m-80) cc_final: 0.8864 (m-80) REVERT: A 252 ARG cc_start: 0.8492 (ttt90) cc_final: 0.8268 (ttm-80) REVERT: B 93 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 107 GLU cc_start: 0.8306 (tp30) cc_final: 0.7770 (tp30) REVERT: B 180 ASP cc_start: 0.8050 (m-30) cc_final: 0.7524 (t0) REVERT: B 210 PHE cc_start: 0.8791 (m-10) cc_final: 0.8340 (m-80) REVERT: C 117 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7754 (mt-10) REVERT: C 119 MET cc_start: 0.8920 (mtt) cc_final: 0.8704 (mtt) REVERT: C 155 LYS cc_start: 0.8727 (mttt) cc_final: 0.8317 (mtpt) REVERT: C 238 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8462 (mt-10) outliers start: 19 outliers final: 8 residues processed: 150 average time/residue: 0.0864 time to fit residues: 17.2514 Evaluate side-chains 144 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET 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 202 LEU 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: 7.9990 chunk 2 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.0000 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.156063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124084 restraints weight = 10602.228| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.07 r_work: 0.3130 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7813 Z= 0.097 Angle : 0.484 6.025 10600 Z= 0.262 Chirality : 0.043 0.155 1194 Planarity : 0.003 0.020 1290 Dihedral : 16.618 147.912 1299 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.37 % Allowed : 14.49 % Favored : 83.14 % 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: -3.19 (0.25), residues: 915 helix: -1.68 (0.25), residues: 396 sheet: -1.35 (0.36), residues: 171 loop : -2.90 (0.27), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 252 TYR 0.011 0.001 TYR B 260 PHE 0.019 0.001 PHE C 128 HIS 0.002 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7813) covalent geometry : angle 0.48407 (10600) hydrogen bonds : bond 0.03087 ( 219) hydrogen bonds : angle 3.81442 ( 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 158 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: A 260 TYR cc_start: 0.8387 (m-80) cc_final: 0.8100 (m-80) REVERT: B 180 ASP cc_start: 0.8014 (m-30) cc_final: 0.7476 (t0) REVERT: B 210 PHE cc_start: 0.8722 (m-10) cc_final: 0.8198 (m-80) REVERT: C 117 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7756 (mt-10) REVERT: C 155 LYS cc_start: 0.8644 (mttt) cc_final: 0.8293 (mtpt) REVERT: C 192 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7269 (ttt180) REVERT: C 238 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8525 (mt-10) outliers start: 18 outliers final: 10 residues processed: 151 average time/residue: 0.0891 time to fit residues: 17.9436 Evaluate side-chains 138 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain B residue 92 SER 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 323 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 211 HIS C 100 HIS C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115371 restraints weight = 10765.911| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.04 r_work: 0.3032 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7813 Z= 0.242 Angle : 0.625 6.975 10600 Z= 0.331 Chirality : 0.048 0.209 1194 Planarity : 0.004 0.044 1290 Dihedral : 16.577 148.617 1299 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.03 % Allowed : 16.07 % Favored : 80.90 % 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: -3.11 (0.25), residues: 915 helix: -1.63 (0.25), residues: 396 sheet: -1.11 (0.39), residues: 153 loop : -2.89 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 129 TYR 0.018 0.002 TYR B 260 PHE 0.024 0.002 PHE C 128 HIS 0.006 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 7813) covalent geometry : angle 0.62500 (10600) hydrogen bonds : bond 0.04589 ( 219) hydrogen bonds : angle 4.12224 ( 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 146 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.257 Fit side-chains REVERT: B 93 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 94 LYS cc_start: 0.8510 (tppt) cc_final: 0.8307 (mmtm) REVERT: B 180 ASP cc_start: 0.8072 (m-30) cc_final: 0.7602 (t0) REVERT: C 117 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 155 LYS cc_start: 0.8693 (mttt) cc_final: 0.8333 (mtpt) REVERT: C 192 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7597 (ttt180) REVERT: C 238 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8414 (mt-10) REVERT: C 335 ILE cc_start: 0.9116 (mm) cc_final: 0.8883 (mm) outliers start: 23 outliers final: 11 residues processed: 136 average time/residue: 0.0917 time to fit residues: 16.7542 Evaluate side-chains 136 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU 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 96 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.152753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120770 restraints weight = 10543.493| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.05 r_work: 0.3102 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7813 Z= 0.116 Angle : 0.505 6.347 10600 Z= 0.272 Chirality : 0.044 0.171 1194 Planarity : 0.003 0.019 1290 Dihedral : 16.463 149.549 1299 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.98 % Allowed : 17.65 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.26), residues: 915 helix: -1.25 (0.26), residues: 399 sheet: -1.17 (0.36), residues: 171 loop : -2.73 (0.28), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.021 0.001 TYR B 260 PHE 0.021 0.001 PHE C 128 HIS 0.003 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7813) covalent geometry : angle 0.50505 (10600) hydrogen bonds : bond 0.03309 ( 219) hydrogen bonds : angle 3.80051 ( 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 147 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 180 ASP cc_start: 0.8043 (m-30) cc_final: 0.7573 (t0) REVERT: B 210 PHE cc_start: 0.8802 (m-10) cc_final: 0.8546 (m-80) REVERT: C 93 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 117 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7876 (mt-10) REVERT: C 192 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7469 (ttt180) outliers start: 15 outliers final: 10 residues processed: 140 average time/residue: 0.0912 time to fit residues: 17.0818 Evaluate side-chains 143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 219 LEU 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 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: 0.9980 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 211 HIS ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.149854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118226 restraints weight = 10660.574| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.03 r_work: 0.3106 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7813 Z= 0.125 Angle : 0.510 6.146 10600 Z= 0.274 Chirality : 0.044 0.178 1194 Planarity : 0.003 0.022 1290 Dihedral : 16.387 150.163 1299 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.24 % Allowed : 17.92 % Favored : 79.84 % 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: -2.52 (0.26), residues: 915 helix: -1.03 (0.26), residues: 399 sheet: -1.12 (0.36), residues: 171 loop : -2.62 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.026 0.002 TYR B 260 PHE 0.021 0.002 PHE C 128 HIS 0.007 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7813) covalent geometry : angle 0.50986 (10600) hydrogen bonds : bond 0.03326 ( 219) hydrogen bonds : angle 3.78712 ( 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 148 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: B 41 LYS cc_start: 0.6029 (mtpt) cc_final: 0.5818 (mmmt) REVERT: B 93 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 180 ASP cc_start: 0.7957 (m-30) cc_final: 0.7522 (t0) REVERT: B 210 PHE cc_start: 0.8738 (m-10) cc_final: 0.8165 (m-80) REVERT: B 260 TYR cc_start: 0.8280 (m-10) cc_final: 0.8061 (m-10) REVERT: C 72 LYS cc_start: 0.8613 (mttp) cc_final: 0.7756 (tptt) REVERT: C 93 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 117 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 192 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7478 (ttt180) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 0.0820 time to fit residues: 15.2051 Evaluate side-chains 143 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 LEU 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 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: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.151465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119942 restraints weight = 10607.951| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.05 r_work: 0.3106 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7813 Z= 0.118 Angle : 0.507 6.114 10600 Z= 0.273 Chirality : 0.044 0.174 1194 Planarity : 0.003 0.020 1290 Dihedral : 16.343 150.128 1299 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.37 % Allowed : 18.58 % Favored : 79.05 % 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: -2.32 (0.26), residues: 915 helix: -0.86 (0.26), residues: 399 sheet: -1.05 (0.37), residues: 171 loop : -2.50 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.023 0.001 TYR B 260 PHE 0.021 0.002 PHE C 128 HIS 0.003 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7813) covalent geometry : angle 0.50701 (10600) hydrogen bonds : bond 0.03199 ( 219) hydrogen bonds : angle 3.78798 ( 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 149 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: B 180 ASP cc_start: 0.7924 (m-30) cc_final: 0.7497 (t0) REVERT: B 210 PHE cc_start: 0.8728 (m-10) cc_final: 0.8168 (m-80) REVERT: C 38 LYS cc_start: 0.7357 (pttm) cc_final: 0.6364 (ptmm) REVERT: C 72 LYS cc_start: 0.8557 (mttp) cc_final: 0.7714 (tptt) REVERT: C 117 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7901 (mt-10) REVERT: C 119 MET cc_start: 0.8868 (mtt) cc_final: 0.8660 (mtt) REVERT: C 192 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7453 (ttt180) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.0804 time to fit residues: 15.3992 Evaluate side-chains 142 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 LEU 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 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 323 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119552 restraints weight = 10571.248| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.02 r_work: 0.3106 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7813 Z= 0.119 Angle : 0.512 6.077 10600 Z= 0.276 Chirality : 0.044 0.173 1194 Planarity : 0.003 0.020 1290 Dihedral : 16.297 150.152 1299 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.71 % Allowed : 19.50 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.27), residues: 915 helix: -0.75 (0.27), residues: 399 sheet: -1.04 (0.36), residues: 171 loop : -2.38 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.033 0.002 TYR B 260 PHE 0.021 0.002 PHE C 128 HIS 0.003 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7813) covalent geometry : angle 0.51162 (10600) hydrogen bonds : bond 0.03226 ( 219) hydrogen bonds : angle 3.79133 ( 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 142 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.291 Fit side-chains REVERT: B 93 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 180 ASP cc_start: 0.7892 (m-30) cc_final: 0.7487 (t0) REVERT: B 210 PHE cc_start: 0.8595 (m-10) cc_final: 0.7969 (m-80) REVERT: C 38 LYS cc_start: 0.7301 (pttm) cc_final: 0.6333 (ptmm) REVERT: C 72 LYS cc_start: 0.8555 (mttp) cc_final: 0.7710 (tptt) REVERT: C 117 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8036 (mt-10) REVERT: C 192 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7455 (ttt180) REVERT: C 238 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8582 (mt-10) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.0771 time to fit residues: 14.0714 Evaluate side-chains 139 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 LEU 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 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 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.153852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122712 restraints weight = 10537.212| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.04 r_work: 0.3183 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7813 Z= 0.106 Angle : 0.503 5.994 10600 Z= 0.271 Chirality : 0.043 0.167 1194 Planarity : 0.003 0.019 1290 Dihedral : 16.240 149.973 1299 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.71 % Allowed : 19.50 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.27), residues: 915 helix: -0.60 (0.27), residues: 396 sheet: -1.03 (0.36), residues: 171 loop : -2.28 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.026 0.001 TYR B 260 PHE 0.021 0.002 PHE C 128 HIS 0.003 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7813) covalent geometry : angle 0.50275 (10600) hydrogen bonds : bond 0.02976 ( 219) hydrogen bonds : angle 3.72112 ( 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 147 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: B 180 ASP cc_start: 0.7870 (m-30) cc_final: 0.7497 (t0) REVERT: B 210 PHE cc_start: 0.8466 (m-10) cc_final: 0.7766 (m-80) REVERT: C 38 LYS cc_start: 0.7270 (pttm) cc_final: 0.6289 (ptmm) REVERT: C 72 LYS cc_start: 0.8545 (mttp) cc_final: 0.7688 (tptt) REVERT: C 117 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7974 (mt-10) REVERT: C 192 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8176 (tpt-90) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 0.0808 time to fit residues: 15.3590 Evaluate side-chains 142 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 LEU 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 323 GLU Chi-restraints excluded: chain B residue 327 THR 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: 0.1980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 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 = 0.3684 r_free = 0.3684 target = 0.152638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121509 restraints weight = 10518.914| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.04 r_work: 0.3178 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7813 Z= 0.124 Angle : 0.525 6.469 10600 Z= 0.281 Chirality : 0.044 0.174 1194 Planarity : 0.003 0.058 1290 Dihedral : 16.226 149.974 1299 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.71 % Allowed : 20.03 % Favored : 78.26 % 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: -1.99 (0.27), residues: 915 helix: -0.60 (0.27), residues: 396 sheet: -1.09 (0.36), residues: 174 loop : -2.18 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.027 0.002 TYR B 260 PHE 0.021 0.002 PHE C 128 HIS 0.003 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7813) covalent geometry : angle 0.52547 (10600) hydrogen bonds : bond 0.03214 ( 219) hydrogen bonds : angle 3.73045 ( 590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.34 seconds wall clock time: 35 minutes 38.57 seconds (2138.57 seconds total)