Starting phenix.real_space_refine on Fri Jul 3 03:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2026/8ef6_28069.cif" } resolution = 3.2 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 7605 2.51 5 N 1895 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11686 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 161 Unusual residues: {'CLR': 5, 'MOI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 161 Unusual residues: {'CLR': 5, 'MOI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.42, per 1000 atoms: 0.21 Number of scatterers: 11686 At special positions: 0 Unit cell: (113.526, 112.455, 152.082, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2088 8.00 N 1895 7.00 C 7605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 509.1 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 49.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 removed outlier: 4.055A pdb=" N THR R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.571A pdb=" N PHE R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.879A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 3.661A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.616A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 4.031A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.854A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.706A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.552A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.368A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.511A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.635A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.548A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.200A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.161A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 98 Processing helix chain 'M' and resid 103 through 122 removed outlier: 4.054A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.572A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.878A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.660A pdb=" N ALA M 199 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.617A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 339 removed outlier: 4.031A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'F' and resid 337 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 removed outlier: 3.658A pdb=" N THR R 220 " --> pdb=" O THR R 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.116A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.728A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.768A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.694A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.870A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.577A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.798A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.577A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.729A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.729A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.584A pdb=" N VAL E 148 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 removed outlier: 3.659A pdb=" N THR M 220 " --> pdb=" O THR M 209 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3533 1.34 - 1.46: 2481 1.46 - 1.58: 5811 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 11970 Sorted by residual: bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.26e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.11e+00 bond pdb=" CA THR R 296 " pdb=" C THR R 296 " ideal model delta sigma weight residual 1.522 1.545 -0.024 1.26e-02 6.30e+03 3.50e+00 bond pdb=" CA THR M 296 " pdb=" C THR M 296 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.26e-02 6.30e+03 3.37e+00 bond pdb=" C MET M 245 " pdb=" N PRO M 246 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.26e+00 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 15661 2.08 - 4.15: 553 4.15 - 6.23: 70 6.23 - 8.30: 17 8.30 - 10.38: 2 Bond angle restraints: 16303 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" NE ARG B 314 " pdb=" CZ ARG B 314 " pdb=" NH2 ARG B 314 " ideal model delta sigma weight residual 119.20 122.35 -3.15 9.00e-01 1.23e+00 1.22e+01 angle pdb=" NE ARG B 314 " pdb=" CZ ARG B 314 " pdb=" NH1 ARG B 314 " ideal model delta sigma weight residual 121.50 118.39 3.11 1.00e+00 1.00e+00 9.70e+00 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 125.02 130.40 -5.38 1.76e+00 3.23e-01 9.34e+00 ... (remaining 16298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.85: 6274 9.85 - 19.69: 604 19.69 - 29.53: 79 29.53 - 39.38: 26 39.38 - 49.22: 5 Dihedral angle restraints: 6988 sinusoidal: 2781 harmonic: 4207 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 163.57 16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 67.23 25.77 1 1.00e+01 1.00e-02 9.55e+00 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1705 0.089 - 0.177: 169 0.177 - 0.266: 16 0.266 - 0.354: 10 0.354 - 0.443: 10 Chirality restraints: 1910 Sorted by residual: chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 1907 not shown) Planarity restraints: 1958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 236 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 240 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ILE M 240 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE M 240 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE M 241 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 240 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ILE R 240 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE R 240 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE R 241 " 0.014 2.00e-02 2.50e+03 ... (remaining 1955 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2467 2.79 - 3.32: 10483 3.32 - 3.85: 18938 3.85 - 4.37: 21349 4.37 - 4.90: 38562 Nonbonded interactions: 91799 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.267 3.040 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.268 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.308 3.040 ... (remaining 91794 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 'M' selection = chain 'R' } 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: 0.010 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.005 0.055 11973 Z= 0.247 Angle : 0.866 10.377 16309 Z= 0.458 Chirality : 0.066 0.443 1910 Planarity : 0.007 0.071 1958 Dihedral : 7.715 44.170 4259 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 1421 helix: 0.80 (0.16), residues: 656 sheet: 0.33 (0.30), residues: 274 loop : -1.22 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.023 0.002 TYR M 108 PHE 0.024 0.002 PHE M 349 TRP 0.027 0.003 TRP B 332 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.25 (11970) covalent geometry : angle 0.86645 / 0.46 (16303) SS BOND : bond 0.00230 / 0.12 ( 3) SS BOND : angle 0.94387 / 0.48 ( 6) hydrogen bonds : bond 0.16802 / 10.96 ( 664) hydrogen bonds : angle 6.26208 / 4.53 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: R 166 ASP cc_start: 0.7706 (t0) cc_final: 0.7482 (t0) REVERT: R 211 LYS cc_start: 0.7415 (pttt) cc_final: 0.6989 (ptmm) REVERT: R 260 ARG cc_start: 0.7276 (tpt90) cc_final: 0.6575 (tpp80) REVERT: R 283 MET cc_start: 0.7108 (tpt) cc_final: 0.6799 (mtt) REVERT: R 304 ILE cc_start: 0.8048 (mt) cc_final: 0.7848 (mt) REVERT: A 195 HIS cc_start: 0.7890 (m-70) cc_final: 0.7590 (m-70) REVERT: C 21 MET cc_start: 0.4985 (ttm) cc_final: 0.4435 (tpp) REVERT: E 187 GLN cc_start: 0.7090 (pt0) cc_final: 0.6826 (pt0) REVERT: E 216 THR cc_start: 0.7095 (p) cc_final: 0.6831 (t) REVERT: M 164 SER cc_start: 0.8499 (t) cc_final: 0.8189 (p) REVERT: M 206 PHE cc_start: 0.7636 (m-80) cc_final: 0.7394 (m-80) REVERT: M 232 ASN cc_start: 0.7650 (m110) cc_final: 0.7352 (m-40) REVERT: M 241 PHE cc_start: 0.8172 (m-10) cc_final: 0.7903 (m-80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.0982 time to fit residues: 39.6542 Evaluate side-chains 189 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 111 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 331 ASN B 91 HIS B 183 HIS B 220 GLN B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 ASN M 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.173698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133641 restraints weight = 12486.449| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.43 r_work: 0.3041 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11973 Z= 0.184 Angle : 0.600 7.124 16309 Z= 0.315 Chirality : 0.042 0.163 1910 Planarity : 0.005 0.061 1958 Dihedral : 4.618 23.660 1659 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.46 % Allowed : 6.36 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.31 (0.21), residues: 1421 helix: 2.28 (0.18), residues: 665 sheet: 0.35 (0.30), residues: 284 loop : -0.88 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 67 TYR 0.025 0.002 TYR E 191 PHE 0.017 0.002 PHE A 189 TRP 0.017 0.002 TRP B 99 HIS 0.010 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (11970) covalent geometry : angle 0.59961 / 0.31 (16303) SS BOND : bond 0.00521 / 0.26 ( 3) SS BOND : angle 1.32838 / 0.68 ( 6) hydrogen bonds : bond 0.05112 / 3.34 ( 664) hydrogen bonds : angle 4.74322 / 3.40 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8620 (m-40) cc_final: 0.8312 (m-40) REVERT: R 260 ARG cc_start: 0.7564 (tpt90) cc_final: 0.6559 (tpp80) REVERT: R 283 MET cc_start: 0.8366 (tpt) cc_final: 0.7439 (mtp) REVERT: A 29 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7620 (mttt) REVERT: A 209 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8004 (ttmt) REVERT: A 316 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 197 ARG cc_start: 0.7051 (mmt90) cc_final: 0.6180 (mmt180) REVERT: B 283 ARG cc_start: 0.6810 (ttm170) cc_final: 0.6294 (tpt-90) REVERT: C 21 MET cc_start: 0.5375 (ttm) cc_final: 0.4528 (tpp) REVERT: E 187 GLN cc_start: 0.7443 (pt0) cc_final: 0.6927 (pt0) REVERT: E 231 MET cc_start: 0.8324 (ttt) cc_final: 0.7530 (ttt) REVERT: M 67 MET cc_start: 0.6189 (tmm) cc_final: 0.5242 (tpp) REVERT: M 77 TYR cc_start: 0.7501 (m-10) cc_final: 0.7239 (m-80) REVERT: M 132 MET cc_start: 0.7931 (mtm) cc_final: 0.7630 (mtm) REVERT: M 147 SER cc_start: 0.8780 (t) cc_final: 0.8557 (m) REVERT: M 206 PHE cc_start: 0.7890 (m-80) cc_final: 0.7653 (m-80) REVERT: M 241 PHE cc_start: 0.8643 (m-10) cc_final: 0.8355 (m-80) REVERT: M 257 MET cc_start: 0.8808 (ttp) cc_final: 0.8572 (ttt) outliers start: 31 outliers final: 21 residues processed: 217 average time/residue: 0.0955 time to fit residues: 29.7949 Evaluate side-chains 189 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 135 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 138 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.179983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.144302 restraints weight = 12562.149| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.49 r_work: 0.3182 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11973 Z= 0.102 Angle : 0.483 5.731 16309 Z= 0.254 Chirality : 0.038 0.149 1910 Planarity : 0.004 0.052 1958 Dihedral : 4.162 24.116 1659 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.91 % Allowed : 8.74 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.89 (0.22), residues: 1421 helix: 2.90 (0.18), residues: 670 sheet: 0.41 (0.30), residues: 284 loop : -0.69 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.018 0.001 TYR E 191 PHE 0.012 0.001 PHE B 151 TRP 0.009 0.001 TRP B 99 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (11970) covalent geometry : angle 0.48252 / 0.25 (16303) SS BOND : bond 0.00441 / 0.22 ( 3) SS BOND : angle 0.76393 / 0.39 ( 6) hydrogen bonds : bond 0.03897 / 2.54 ( 664) hydrogen bonds : angle 4.35654 / 3.12 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.399 Fit side-chains REVERT: R 88 ASN cc_start: 0.8550 (m-40) cc_final: 0.8277 (m-40) REVERT: R 260 ARG cc_start: 0.7313 (tpt90) cc_final: 0.6417 (tpp80) REVERT: R 283 MET cc_start: 0.8012 (tpt) cc_final: 0.7175 (mtp) REVERT: A 33 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: A 209 LYS cc_start: 0.8469 (ttpp) cc_final: 0.7973 (ttpt) REVERT: A 298 GLU cc_start: 0.6921 (tp30) cc_final: 0.6653 (mt-10) REVERT: A 316 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 52 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7211 (mtt90) REVERT: B 197 ARG cc_start: 0.6938 (mmt90) cc_final: 0.6479 (mpt180) REVERT: B 262 MET cc_start: 0.6473 (tpp) cc_final: 0.6084 (tpp) REVERT: B 283 ARG cc_start: 0.6716 (ttm170) cc_final: 0.6192 (mmm-85) REVERT: C 21 MET cc_start: 0.5530 (ttm) cc_final: 0.4700 (tpp) REVERT: E 113 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7383 (tp40) REVERT: E 187 GLN cc_start: 0.7378 (pt0) cc_final: 0.6883 (pt0) REVERT: E 216 THR cc_start: 0.7540 (m) cc_final: 0.7032 (t) REVERT: E 231 MET cc_start: 0.8143 (ttt) cc_final: 0.7802 (ttt) REVERT: M 67 MET cc_start: 0.5932 (tmm) cc_final: 0.5127 (tpp) REVERT: M 102 LYS cc_start: 0.6474 (ptpt) cc_final: 0.6273 (mmtt) REVERT: M 164 SER cc_start: 0.9027 (t) cc_final: 0.8671 (p) REVERT: M 206 PHE cc_start: 0.7854 (m-80) cc_final: 0.7550 (m-80) REVERT: M 241 PHE cc_start: 0.8570 (m-10) cc_final: 0.8283 (m-80) outliers start: 24 outliers final: 15 residues processed: 189 average time/residue: 0.1014 time to fit residues: 27.3784 Evaluate side-chains 181 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 131 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 190 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.175147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.136398 restraints weight = 12498.226| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.24 r_work: 0.3075 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11973 Z= 0.107 Angle : 0.471 5.684 16309 Z= 0.247 Chirality : 0.038 0.139 1910 Planarity : 0.003 0.050 1958 Dihedral : 4.085 24.264 1659 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.83 % Allowed : 10.10 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 2.08 (0.22), residues: 1421 helix: 3.11 (0.18), residues: 670 sheet: 0.46 (0.30), residues: 283 loop : -0.67 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 181 TYR 0.015 0.001 TYR E 191 PHE 0.011 0.001 PHE A 189 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11970) covalent geometry : angle 0.47132 / 0.25 (16303) SS BOND : bond 0.00409 / 0.20 ( 3) SS BOND : angle 0.66952 / 0.34 ( 6) hydrogen bonds : bond 0.03742 / 2.44 ( 664) hydrogen bonds : angle 4.22583 / 3.02 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8654 (m-40) cc_final: 0.8389 (m-40) REVERT: R 207 MET cc_start: 0.8677 (mtm) cc_final: 0.8473 (mtm) REVERT: R 260 ARG cc_start: 0.7422 (tpt90) cc_final: 0.6513 (tpp80) REVERT: R 283 MET cc_start: 0.8231 (tpt) cc_final: 0.7800 (mmp) REVERT: R 305 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8100 (ttpp) REVERT: A 33 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: A 209 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8142 (ttmt) REVERT: A 316 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 52 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7370 (mtt90) REVERT: B 197 ARG cc_start: 0.6859 (mmt90) cc_final: 0.6356 (mpt180) REVERT: B 283 ARG cc_start: 0.6810 (ttm170) cc_final: 0.6235 (tpt-90) REVERT: C 21 MET cc_start: 0.5628 (ttm) cc_final: 0.4767 (tpp) REVERT: E 83 MET cc_start: 0.6386 (mtt) cc_final: 0.6173 (mtt) REVERT: E 87 ARG cc_start: 0.5991 (mtt180) cc_final: 0.5668 (ttm110) REVERT: E 187 GLN cc_start: 0.7450 (pt0) cc_final: 0.6976 (pt0) REVERT: E 216 THR cc_start: 0.7585 (m) cc_final: 0.6986 (t) REVERT: E 231 MET cc_start: 0.8461 (ttt) cc_final: 0.8204 (ttt) REVERT: M 67 MET cc_start: 0.5846 (tmm) cc_final: 0.5059 (tpp) REVERT: M 102 LYS cc_start: 0.6560 (ptpt) cc_final: 0.6252 (mmtt) REVERT: M 147 SER cc_start: 0.8743 (t) cc_final: 0.8535 (m) REVERT: M 206 PHE cc_start: 0.7898 (m-80) cc_final: 0.7519 (m-80) REVERT: M 241 PHE cc_start: 0.8735 (m-10) cc_final: 0.8445 (m-80) REVERT: M 245 MET cc_start: 0.8396 (mmp) cc_final: 0.7975 (mmp) outliers start: 23 outliers final: 16 residues processed: 187 average time/residue: 0.0965 time to fit residues: 26.0469 Evaluate side-chains 181 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN M 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.164657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.125941 restraints weight = 12536.395| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.18 r_work: 0.2948 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11973 Z= 0.241 Angle : 0.622 6.629 16309 Z= 0.320 Chirality : 0.043 0.189 1910 Planarity : 0.005 0.051 1958 Dihedral : 5.188 34.645 1659 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.54 % Allowed : 10.10 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.63 (0.22), residues: 1421 helix: 2.66 (0.19), residues: 665 sheet: 0.17 (0.29), residues: 292 loop : -0.68 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 181 TYR 0.013 0.002 TYR E 103 PHE 0.018 0.002 PHE A 189 TRP 0.017 0.002 TRP B 169 HIS 0.007 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (11970) covalent geometry : angle 0.62152 / 0.32 (16303) SS BOND : bond 0.00415 / 0.20 ( 3) SS BOND : angle 0.87871 / 0.46 ( 6) hydrogen bonds : bond 0.05221 / 3.45 ( 664) hydrogen bonds : angle 4.72700 / 3.36 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.362 Fit side-chains REVERT: R 88 ASN cc_start: 0.8856 (m-40) cc_final: 0.8567 (m-40) REVERT: R 260 ARG cc_start: 0.7678 (tpt90) cc_final: 0.6673 (tpp80) REVERT: R 283 MET cc_start: 0.8423 (tpt) cc_final: 0.8081 (mmp) REVERT: A 33 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: A 209 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8197 (ttmt) REVERT: A 298 GLU cc_start: 0.6844 (tp30) cc_final: 0.6474 (pt0) REVERT: A 316 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 283 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6245 (tpt-90) REVERT: C 21 MET cc_start: 0.5585 (ttm) cc_final: 0.4766 (tpp) REVERT: E 63 THR cc_start: 0.7569 (p) cc_final: 0.7295 (p) REVERT: E 87 ARG cc_start: 0.6301 (mtt180) cc_final: 0.5843 (ttm110) REVERT: E 187 GLN cc_start: 0.7752 (pt0) cc_final: 0.7210 (pt0) REVERT: M 67 MET cc_start: 0.6069 (tmm) cc_final: 0.5305 (tpp) REVERT: M 102 LYS cc_start: 0.7001 (ptpt) cc_final: 0.6478 (pttm) REVERT: M 206 PHE cc_start: 0.7961 (m-80) cc_final: 0.7683 (m-80) REVERT: M 245 MET cc_start: 0.8312 (mmp) cc_final: 0.7999 (mmt) outliers start: 32 outliers final: 21 residues processed: 191 average time/residue: 0.0970 time to fit residues: 26.7003 Evaluate side-chains 182 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.168669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.128877 restraints weight = 12537.345| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.27 r_work: 0.3005 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11973 Z= 0.123 Angle : 0.502 6.861 16309 Z= 0.263 Chirality : 0.039 0.138 1910 Planarity : 0.004 0.047 1958 Dihedral : 4.675 32.115 1659 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.91 % Allowed : 12.40 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.88 (0.22), residues: 1421 helix: 2.89 (0.19), residues: 667 sheet: 0.19 (0.29), residues: 288 loop : -0.51 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 181 TYR 0.017 0.001 TYR E 94 PHE 0.016 0.001 PHE A 189 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11970) covalent geometry : angle 0.50073 / 0.26 (16303) SS BOND : bond 0.00404 / 0.20 ( 3) SS BOND : angle 2.07935 / 1.27 ( 6) hydrogen bonds : bond 0.04007 / 2.62 ( 664) hydrogen bonds : angle 4.39534 / 3.14 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.351 Fit side-chains REVERT: R 88 ASN cc_start: 0.8784 (m-40) cc_final: 0.8580 (m-40) REVERT: R 260 ARG cc_start: 0.7551 (tpt90) cc_final: 0.6584 (tpp80) REVERT: R 283 MET cc_start: 0.8300 (tpt) cc_final: 0.7993 (mmp) REVERT: A 29 LYS cc_start: 0.8089 (mttt) cc_final: 0.7546 (mttt) REVERT: A 33 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: A 209 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8153 (ttmt) REVERT: A 298 GLU cc_start: 0.6770 (tp30) cc_final: 0.6413 (pt0) REVERT: A 316 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8179 (p) REVERT: B 283 ARG cc_start: 0.7049 (ttm170) cc_final: 0.6194 (tpt-90) REVERT: C 21 MET cc_start: 0.5800 (ttm) cc_final: 0.4908 (tpp) REVERT: E 63 THR cc_start: 0.7575 (p) cc_final: 0.7303 (p) REVERT: E 87 ARG cc_start: 0.6050 (mtt180) cc_final: 0.5581 (ttm110) REVERT: E 141 MET cc_start: 0.8653 (mmm) cc_final: 0.8109 (mmm) REVERT: E 187 GLN cc_start: 0.7811 (pt0) cc_final: 0.7291 (pt0) REVERT: M 67 MET cc_start: 0.6094 (tmm) cc_final: 0.5327 (tpp) REVERT: M 72 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.6996 (p) REVERT: M 102 LYS cc_start: 0.6913 (ptpt) cc_final: 0.6406 (pttm) REVERT: M 206 PHE cc_start: 0.7884 (m-80) cc_final: 0.7575 (m-80) REVERT: M 245 MET cc_start: 0.8259 (mmp) cc_final: 0.8027 (mmt) outliers start: 24 outliers final: 21 residues processed: 182 average time/residue: 0.1029 time to fit residues: 26.6475 Evaluate side-chains 183 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.165123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125495 restraints weight = 12534.126| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.22 r_work: 0.2967 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11973 Z= 0.179 Angle : 0.558 8.071 16309 Z= 0.289 Chirality : 0.041 0.151 1910 Planarity : 0.004 0.050 1958 Dihedral : 5.088 47.165 1659 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.86 % Allowed : 11.84 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.72 (0.22), residues: 1421 helix: 2.80 (0.19), residues: 665 sheet: 0.03 (0.29), residues: 287 loop : -0.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 181 TYR 0.021 0.002 TYR E 94 PHE 0.019 0.002 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (11970) covalent geometry : angle 0.55635 / 0.29 (16303) SS BOND : bond 0.00373 / 0.18 ( 3) SS BOND : angle 2.12741 / 1.30 ( 6) hydrogen bonds : bond 0.04592 / 3.02 ( 664) hydrogen bonds : angle 4.52535 / 3.22 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.440 Fit side-chains REVERT: R 88 ASN cc_start: 0.8839 (m-40) cc_final: 0.8604 (m-40) REVERT: R 283 MET cc_start: 0.8353 (tpt) cc_final: 0.7708 (mtt) REVERT: A 33 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: A 209 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8128 (ttmt) REVERT: A 298 GLU cc_start: 0.6577 (tp30) cc_final: 0.6247 (pt0) REVERT: A 316 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8145 (p) REVERT: C 21 MET cc_start: 0.5666 (ttm) cc_final: 0.4763 (tpp) REVERT: E 63 THR cc_start: 0.7617 (p) cc_final: 0.7354 (p) REVERT: E 87 ARG cc_start: 0.6056 (mtt180) cc_final: 0.5662 (ttm110) REVERT: E 187 GLN cc_start: 0.7734 (pt0) cc_final: 0.7169 (pt0) REVERT: M 67 MET cc_start: 0.6123 (tmm) cc_final: 0.5361 (tpp) REVERT: M 102 LYS cc_start: 0.6944 (ptpt) cc_final: 0.6401 (pttm) REVERT: M 206 PHE cc_start: 0.7915 (m-80) cc_final: 0.7610 (m-80) REVERT: M 245 MET cc_start: 0.8254 (mmp) cc_final: 0.8008 (mmt) outliers start: 36 outliers final: 25 residues processed: 180 average time/residue: 0.0965 time to fit residues: 25.4959 Evaluate side-chains 180 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.166184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.128095 restraints weight = 12547.475| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.14 r_work: 0.2989 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11973 Z= 0.134 Angle : 0.511 7.155 16309 Z= 0.265 Chirality : 0.039 0.139 1910 Planarity : 0.004 0.048 1958 Dihedral : 4.931 50.972 1659 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.38 % Allowed : 12.80 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.85 (0.22), residues: 1421 helix: 2.94 (0.19), residues: 665 sheet: 0.09 (0.29), residues: 285 loop : -0.58 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 181 TYR 0.018 0.001 TYR E 94 PHE 0.017 0.001 PHE A 189 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11970) covalent geometry : angle 0.50979 / 0.27 (16303) SS BOND : bond 0.00370 / 0.18 ( 3) SS BOND : angle 1.64091 / 0.99 ( 6) hydrogen bonds : bond 0.04054 / 2.65 ( 664) hydrogen bonds : angle 4.36896 / 3.13 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.372 Fit side-chains REVERT: R 283 MET cc_start: 0.8268 (tpt) cc_final: 0.7673 (mtt) REVERT: A 18 MET cc_start: 0.8604 (mtp) cc_final: 0.8344 (mtp) REVERT: A 33 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: A 209 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8144 (ttmt) REVERT: A 298 GLU cc_start: 0.6534 (tp30) cc_final: 0.6169 (pt0) REVERT: B 52 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7417 (mtt90) REVERT: C 21 MET cc_start: 0.5798 (ttm) cc_final: 0.4934 (tpp) REVERT: E 87 ARG cc_start: 0.6024 (mtt180) cc_final: 0.5619 (ttm110) REVERT: E 187 GLN cc_start: 0.7802 (pt0) cc_final: 0.7265 (pt0) REVERT: M 67 MET cc_start: 0.6077 (tmm) cc_final: 0.5359 (tpp) REVERT: M 72 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7019 (p) REVERT: M 102 LYS cc_start: 0.6904 (ptpt) cc_final: 0.6382 (pttm) REVERT: M 206 PHE cc_start: 0.7910 (m-80) cc_final: 0.7596 (m-80) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.0958 time to fit residues: 24.8127 Evaluate side-chains 177 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 114 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.164420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124980 restraints weight = 12423.263| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.19 r_work: 0.2965 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11973 Z= 0.180 Angle : 0.558 8.002 16309 Z= 0.288 Chirality : 0.041 0.144 1910 Planarity : 0.004 0.051 1958 Dihedral : 5.254 55.916 1659 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.46 % Allowed : 12.56 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.71 (0.22), residues: 1421 helix: 2.79 (0.19), residues: 665 sheet: -0.03 (0.29), residues: 292 loop : -0.56 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 181 TYR 0.024 0.002 TYR E 94 PHE 0.019 0.002 PHE A 189 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (11970) covalent geometry : angle 0.55672 / 0.29 (16303) SS BOND : bond 0.00349 / 0.17 ( 3) SS BOND : angle 1.89153 / 1.14 ( 6) hydrogen bonds : bond 0.04539 / 2.98 ( 664) hydrogen bonds : angle 4.49705 / 3.21 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.408 Fit side-chains REVERT: R 98 TYR cc_start: 0.7551 (m-80) cc_final: 0.7251 (m-10) REVERT: R 211 LYS cc_start: 0.7509 (pttt) cc_final: 0.7252 (ptmm) REVERT: R 283 MET cc_start: 0.8322 (tpt) cc_final: 0.7718 (mtt) REVERT: A 18 MET cc_start: 0.8681 (mtp) cc_final: 0.8418 (mtp) REVERT: A 33 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: A 209 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8121 (ttmt) REVERT: A 298 GLU cc_start: 0.6545 (tp30) cc_final: 0.6265 (mt-10) REVERT: B 52 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7421 (mtt90) REVERT: B 234 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: C 21 MET cc_start: 0.5916 (ttm) cc_final: 0.5012 (tpp) REVERT: E 87 ARG cc_start: 0.6015 (mtt180) cc_final: 0.5644 (ttm110) REVERT: E 141 MET cc_start: 0.8687 (mmm) cc_final: 0.8388 (mmm) REVERT: E 187 GLN cc_start: 0.7765 (pt0) cc_final: 0.7207 (pt0) REVERT: M 67 MET cc_start: 0.6068 (tmm) cc_final: 0.5365 (tpp) REVERT: M 206 PHE cc_start: 0.7970 (m-80) cc_final: 0.7669 (m-80) REVERT: M 245 MET cc_start: 0.8259 (mmp) cc_final: 0.7961 (mmt) outliers start: 31 outliers final: 26 residues processed: 174 average time/residue: 0.0992 time to fit residues: 25.2642 Evaluate side-chains 178 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.167654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.140224 restraints weight = 12532.162| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.53 r_work: 0.3066 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11973 Z= 0.160 Angle : 0.538 8.282 16309 Z= 0.279 Chirality : 0.040 0.140 1910 Planarity : 0.004 0.050 1958 Dihedral : 5.230 59.889 1659 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.31 % Allowed : 12.72 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.73 (0.22), residues: 1421 helix: 2.83 (0.19), residues: 665 sheet: -0.05 (0.29), residues: 292 loop : -0.56 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 181 TYR 0.022 0.001 TYR E 94 PHE 0.018 0.001 PHE A 189 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (11970) covalent geometry : angle 0.53708 / 0.28 (16303) SS BOND : bond 0.00376 / 0.18 ( 3) SS BOND : angle 1.72358 / 1.04 ( 6) hydrogen bonds : bond 0.04322 / 2.83 ( 664) hydrogen bonds : angle 4.44419 / 3.18 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.422 Fit side-chains REVERT: R 98 TYR cc_start: 0.7548 (m-80) cc_final: 0.7263 (m-10) REVERT: R 211 LYS cc_start: 0.7501 (pttt) cc_final: 0.7233 (ptmm) REVERT: R 283 MET cc_start: 0.8344 (tpt) cc_final: 0.7720 (mtt) REVERT: A 18 MET cc_start: 0.8590 (mtp) cc_final: 0.8329 (mtp) REVERT: A 33 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: A 209 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8137 (ttmt) REVERT: A 298 GLU cc_start: 0.6553 (tp30) cc_final: 0.6251 (mt-10) REVERT: B 52 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7527 (mtt90) REVERT: B 234 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: C 21 MET cc_start: 0.5954 (ttm) cc_final: 0.5121 (tpp) REVERT: E 87 ARG cc_start: 0.6016 (mtt180) cc_final: 0.5639 (ttm110) REVERT: E 141 MET cc_start: 0.8686 (mmm) cc_final: 0.8389 (mmm) REVERT: E 187 GLN cc_start: 0.7762 (pt0) cc_final: 0.7192 (pt0) REVERT: M 67 MET cc_start: 0.6186 (tmm) cc_final: 0.5442 (tpp) REVERT: M 72 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7002 (p) REVERT: M 206 PHE cc_start: 0.7938 (m-80) cc_final: 0.7635 (m-80) outliers start: 29 outliers final: 25 residues processed: 173 average time/residue: 0.0986 time to fit residues: 24.6642 Evaluate side-chains 181 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 124 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.167873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.128860 restraints weight = 12494.604| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.18 r_work: 0.3013 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11973 Z= 0.110 Angle : 0.488 7.033 16309 Z= 0.255 Chirality : 0.038 0.136 1910 Planarity : 0.004 0.046 1958 Dihedral : 4.931 57.319 1659 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.91 % Allowed : 13.20 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.94 (0.22), residues: 1421 helix: 3.04 (0.19), residues: 667 sheet: 0.03 (0.29), residues: 291 loop : -0.51 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 181 TYR 0.017 0.001 TYR E 94 PHE 0.015 0.001 PHE A 189 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11970) covalent geometry : angle 0.48733 / 0.25 (16303) SS BOND : bond 0.00362 / 0.18 ( 3) SS BOND : angle 1.53165 / 0.92 ( 6) hydrogen bonds : bond 0.03737 / 2.43 ( 664) hydrogen bonds : angle 4.25640 / 3.05 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.97 seconds wall clock time: 48 minutes 17.28 seconds (2897.28 seconds total)