Starting phenix.real_space_refine on Sat Aug 23 11:29:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ef6_28069/08_2025/8ef6_28069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef6_28069/08_2025/8ef6_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_28069/08_2025/8ef6_28069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef6_28069/08_2025/8ef6_28069.map" model { file = "/net/cci-nas-00/data/ceres_data/8ef6_28069/08_2025/8ef6_28069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef6_28069/08_2025/8ef6_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-2.0-5787/lib/python3.9/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: 2.58, per 1000 atoms: 0.22 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: 0.75 Conformation dependent library (CDL) restraints added in 474.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 1.91 Time building geometry restraints manager: 1.06 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 - 10.93: 6932 10.93 - 21.87: 585 21.87 - 32.80: 85 32.80 - 43.73: 26 43.73 - 54.67: 6 Dihedral angle restraints: 7634 sinusoidal: 3427 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 7631 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: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 8.207 54.668 4905 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 aren 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 covalent geometry : bond 0.00467 (11970) covalent geometry : angle 0.86645 (16303) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.94387 ( 6) hydrogen bonds : bond 0.16802 ( 664) hydrogen bonds : angle 6.26208 ( 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 : 0.439 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: 0.0969 time to fit residues: 38.8865 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 : 0.272 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: R 111 ASN R 190 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.173827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133526 restraints weight = 12485.039| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.49 r_work: 0.3042 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11973 Z= 0.187 Angle : 0.600 6.880 16309 Z= 0.315 Chirality : 0.043 0.163 1910 Planarity : 0.005 0.059 1958 Dihedral : 5.706 59.963 2305 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.38 % Allowed : 6.28 % Favored : 91.34 % 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 aren not related in a simple way. whole: 1.33 (0.21), residues: 1421 helix: 2.33 (0.18), residues: 663 sheet: 0.34 (0.30), residues: 284 loop : -0.88 (0.25), residues: 474 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 0.018 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 covalent geometry : bond 0.00436 (11970) covalent geometry : angle 0.59987 (16303) SS BOND : bond 0.00599 ( 3) SS BOND : angle 1.14930 ( 6) hydrogen bonds : bond 0.05109 ( 664) hydrogen bonds : angle 4.74119 ( 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 223 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8617 (m-40) cc_final: 0.8306 (m-40) REVERT: R 260 ARG cc_start: 0.7574 (tpt90) cc_final: 0.6569 (tpp80) REVERT: R 283 MET cc_start: 0.8373 (tpt) cc_final: 0.7442 (mtp) REVERT: A 29 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7624 (mttt) REVERT: A 209 LYS cc_start: 0.8626 (ttpp) cc_final: 0.7991 (ttmt) REVERT: A 316 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 197 ARG cc_start: 0.7045 (mmt90) cc_final: 0.6147 (mmt180) REVERT: B 283 ARG cc_start: 0.6807 (ttm170) cc_final: 0.6291 (tpt-90) REVERT: C 21 MET cc_start: 0.5372 (ttm) cc_final: 0.4526 (tpp) REVERT: E 187 GLN cc_start: 0.7435 (pt0) cc_final: 0.6913 (pt0) REVERT: E 231 MET cc_start: 0.8305 (ttt) cc_final: 0.7458 (ttt) REVERT: M 67 MET cc_start: 0.6187 (tmm) cc_final: 0.5243 (tpp) REVERT: M 77 TYR cc_start: 0.7496 (m-10) cc_final: 0.7249 (m-80) REVERT: M 132 MET cc_start: 0.7926 (mtm) cc_final: 0.7673 (mtm) REVERT: M 147 SER cc_start: 0.8776 (t) cc_final: 0.8548 (m) REVERT: M 206 PHE cc_start: 0.7889 (m-80) cc_final: 0.7649 (m-80) REVERT: M 241 PHE cc_start: 0.8648 (m-10) cc_final: 0.8357 (m-80) REVERT: M 257 MET cc_start: 0.8787 (ttp) cc_final: 0.8545 (ttt) outliers start: 30 outliers final: 22 residues processed: 216 average time/residue: 0.0991 time to fit residues: 30.3115 Evaluate side-chains 190 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 331 SER 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 217 ILE 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: 5.9990 chunk 16 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 138 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 195 ASN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.176134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.137271 restraints weight = 12566.766| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.17 r_work: 0.3089 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11973 Z= 0.107 Angle : 0.489 5.836 16309 Z= 0.257 Chirality : 0.039 0.141 1910 Planarity : 0.004 0.054 1958 Dihedral : 5.246 55.400 2305 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.15 % Allowed : 8.90 % Favored : 88.95 % 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 aren not related in a simple way. whole: 1.86 (0.22), residues: 1421 helix: 2.88 (0.18), residues: 670 sheet: 0.35 (0.30), residues: 286 loop : -0.69 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.019 0.001 TYR E 191 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00228 (11970) covalent geometry : angle 0.48898 (16303) SS BOND : bond 0.00375 ( 3) SS BOND : angle 0.89095 ( 6) hydrogen bonds : bond 0.03992 ( 664) hydrogen bonds : angle 4.37755 ( 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: 27 poor density : 171 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8620 (m-40) cc_final: 0.8354 (m-40) REVERT: R 260 ARG cc_start: 0.7412 (tpt90) cc_final: 0.6497 (tpp80) REVERT: R 283 MET cc_start: 0.8223 (tpt) cc_final: 0.7773 (mmt) REVERT: R 340 PHE cc_start: 0.7857 (m-10) cc_final: 0.7613 (m-10) REVERT: A 33 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: A 209 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8036 (ttpt) REVERT: A 253 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7529 (mm) REVERT: A 316 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8273 (p) REVERT: B 52 ARG cc_start: 0.7803 (mtt-85) cc_final: 0.7362 (mtt90) REVERT: B 197 ARG cc_start: 0.6959 (mmt90) cc_final: 0.6456 (mpt180) REVERT: B 262 MET cc_start: 0.6583 (tpp) cc_final: 0.6181 (tpp) REVERT: B 283 ARG cc_start: 0.6837 (ttm170) cc_final: 0.6229 (mmm-85) REVERT: C 21 MET cc_start: 0.5572 (ttm) cc_final: 0.4721 (tpp) REVERT: E 113 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7426 (tp40) REVERT: E 187 GLN cc_start: 0.7476 (pt0) cc_final: 0.6982 (pt0) REVERT: E 216 THR cc_start: 0.7559 (m) cc_final: 0.7052 (t) REVERT: E 231 MET cc_start: 0.8339 (ttt) cc_final: 0.8089 (ttt) REVERT: M 67 MET cc_start: 0.5919 (tmm) cc_final: 0.5091 (tpp) REVERT: M 102 LYS cc_start: 0.6566 (ptpt) cc_final: 0.6292 (mmtt) REVERT: M 206 PHE cc_start: 0.7911 (m-80) cc_final: 0.7599 (m-80) REVERT: M 241 PHE cc_start: 0.8651 (m-10) cc_final: 0.8369 (m-80) outliers start: 27 outliers final: 15 residues processed: 187 average time/residue: 0.1002 time to fit residues: 26.6958 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 : 0.361 ------------------------------------------------------------------------------- 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 253 ILE 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 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 157 SER 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 217 ILE 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: 1.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** 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 = 0.3834 r_free = 0.3834 target = 0.172285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.132680 restraints weight = 12508.794| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.43 r_work: 0.3037 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11973 Z= 0.131 Angle : 0.496 5.661 16309 Z= 0.260 Chirality : 0.039 0.146 1910 Planarity : 0.004 0.051 1958 Dihedral : 5.182 58.743 2305 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.07 % Allowed : 10.02 % Favored : 87.92 % 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 aren not related in a simple way. whole: 2.01 (0.22), residues: 1421 helix: 3.02 (0.18), residues: 668 sheet: 0.39 (0.29), residues: 285 loop : -0.60 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.016 0.001 TYR E 191 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.001 TRP R 320 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00300 (11970) covalent geometry : angle 0.49611 (16303) SS BOND : bond 0.00489 ( 3) SS BOND : angle 0.93705 ( 6) hydrogen bonds : bond 0.04052 ( 664) hydrogen bonds : angle 4.35127 ( 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 193 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8706 (m-40) cc_final: 0.8429 (m-40) REVERT: R 260 ARG cc_start: 0.7505 (tpt90) cc_final: 0.6570 (tpp80) REVERT: R 283 MET cc_start: 0.8282 (tpt) cc_final: 0.7880 (mmp) REVERT: R 305 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8015 (ttpp) REVERT: R 340 PHE cc_start: 0.7836 (m-10) cc_final: 0.7608 (m-10) REVERT: A 33 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: A 209 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8170 (ttpt) REVERT: A 316 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8254 (p) REVERT: B 120 ILE cc_start: 0.8730 (mm) cc_final: 0.8496 (mt) REVERT: B 262 MET cc_start: 0.6661 (tpp) cc_final: 0.6450 (tpp) REVERT: B 283 ARG cc_start: 0.6914 (ttm170) cc_final: 0.6263 (tpt-90) REVERT: C 21 MET cc_start: 0.5612 (ttm) cc_final: 0.4701 (tpp) REVERT: E 87 ARG cc_start: 0.6038 (mtt180) cc_final: 0.5679 (ttm110) REVERT: E 113 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7502 (tp40) REVERT: E 187 GLN cc_start: 0.7547 (pt0) cc_final: 0.7034 (pt0) REVERT: M 67 MET cc_start: 0.5873 (tmm) cc_final: 0.5062 (tpp) REVERT: M 102 LYS cc_start: 0.6705 (ptpt) cc_final: 0.6419 (mttm) REVERT: M 206 PHE cc_start: 0.7927 (m-80) cc_final: 0.7625 (m-80) REVERT: M 241 PHE cc_start: 0.8709 (m-10) cc_final: 0.8410 (m-80) REVERT: M 245 MET cc_start: 0.8447 (mmp) cc_final: 0.8180 (mmp) outliers start: 26 outliers final: 17 residues processed: 186 average time/residue: 0.0915 time to fit residues: 24.3835 Evaluate side-chains 179 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 260 THR 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 100 VAL Chi-restraints excluded: chain B residue 318 LEU 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 157 SER Chi-restraints excluded: chain E residue 198 SER 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 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: 1.9990 chunk 108 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.169227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129811 restraints weight = 12490.683| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.32 r_work: 0.3000 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11973 Z= 0.140 Angle : 0.510 6.127 16309 Z= 0.267 Chirality : 0.040 0.147 1910 Planarity : 0.004 0.050 1958 Dihedral : 5.104 58.887 2305 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.15 % Allowed : 10.49 % 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 aren not related in a simple way. whole: 1.97 (0.22), residues: 1421 helix: 2.96 (0.19), residues: 668 sheet: 0.28 (0.29), residues: 285 loop : -0.52 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 97 TYR 0.015 0.001 TYR E 191 PHE 0.012 0.001 PHE A 189 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00325 (11970) covalent geometry : angle 0.51001 (16303) SS BOND : bond 0.00405 ( 3) SS BOND : angle 0.86394 ( 6) hydrogen bonds : bond 0.04173 ( 664) hydrogen bonds : angle 4.38277 ( 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 201 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.272 Fit side-chains REVERT: R 88 ASN cc_start: 0.8775 (m-40) cc_final: 0.8531 (m-40) REVERT: R 260 ARG cc_start: 0.7558 (tpt90) cc_final: 0.6633 (tpp80) REVERT: R 283 MET cc_start: 0.8296 (tpt) cc_final: 0.7956 (mmp) REVERT: R 340 PHE cc_start: 0.7922 (m-10) cc_final: 0.7670 (m-10) REVERT: A 33 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: A 209 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8112 (ttpt) REVERT: A 298 GLU cc_start: 0.6822 (tp30) cc_final: 0.6445 (pt0) REVERT: A 316 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 262 MET cc_start: 0.6811 (tpp) cc_final: 0.6507 (tpp) REVERT: B 283 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6235 (tpt-90) REVERT: C 21 MET cc_start: 0.5820 (ttm) cc_final: 0.4905 (tpp) REVERT: E 87 ARG cc_start: 0.6064 (mtt180) cc_final: 0.5619 (ttm110) REVERT: E 187 GLN cc_start: 0.7693 (pt0) cc_final: 0.7184 (pt0) REVERT: M 67 MET cc_start: 0.6029 (tmm) cc_final: 0.5265 (tpp) REVERT: M 102 LYS cc_start: 0.6862 (ptpt) cc_final: 0.6489 (mttm) REVERT: M 206 PHE cc_start: 0.7897 (m-80) cc_final: 0.7597 (m-80) REVERT: M 245 MET cc_start: 0.8348 (mmp) cc_final: 0.8091 (mmt) REVERT: M 262 LYS cc_start: 0.6915 (mptt) cc_final: 0.6701 (mptt) outliers start: 27 outliers final: 21 residues processed: 190 average time/residue: 0.0967 time to fit residues: 26.1620 Evaluate side-chains 184 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 TRP 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 156 VAL Chi-restraints excluded: chain E residue 157 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 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: 0.9990 chunk 128 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.172017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.134583 restraints weight = 12500.051| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.07 r_work: 0.3072 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11973 Z= 0.111 Angle : 0.476 5.837 16309 Z= 0.250 Chirality : 0.038 0.137 1910 Planarity : 0.003 0.048 1958 Dihedral : 4.926 58.151 2305 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.15 % Allowed : 11.61 % Favored : 86.25 % 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 aren not related in a simple way. whole: 2.09 (0.22), residues: 1421 helix: 3.08 (0.19), residues: 668 sheet: 0.25 (0.29), residues: 286 loop : -0.42 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.015 0.001 TYR E 191 PHE 0.012 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 Details of bonding type rmsd covalent geometry : bond 0.00247 (11970) covalent geometry : angle 0.47518 (16303) SS BOND : bond 0.00427 ( 3) SS BOND : angle 1.78362 ( 6) hydrogen bonds : bond 0.03740 ( 664) hydrogen bonds : angle 4.25589 ( 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 191 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: R 260 ARG cc_start: 0.7487 (tpt90) cc_final: 0.6591 (tpp80) REVERT: R 283 MET cc_start: 0.8148 (tpt) cc_final: 0.7840 (mmp) REVERT: A 18 MET cc_start: 0.8616 (mtp) cc_final: 0.8343 (mtp) REVERT: A 33 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: A 209 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8048 (ttmt) REVERT: A 316 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8182 (p) REVERT: B 52 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7358 (mtt90) REVERT: B 262 MET cc_start: 0.6698 (tpp) cc_final: 0.6400 (tpp) REVERT: B 283 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6204 (tpt-90) REVERT: C 21 MET cc_start: 0.5803 (ttm) cc_final: 0.4910 (tpp) REVERT: E 87 ARG cc_start: 0.5986 (mtt180) cc_final: 0.5575 (ttm110) REVERT: E 187 GLN cc_start: 0.7670 (pt0) cc_final: 0.7129 (pt0) REVERT: M 67 MET cc_start: 0.5977 (tmm) cc_final: 0.5299 (tpp) REVERT: M 72 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7127 (p) REVERT: M 102 LYS cc_start: 0.6840 (ptpt) cc_final: 0.6460 (mmtt) REVERT: M 206 PHE cc_start: 0.7839 (m-80) cc_final: 0.7415 (m-80) REVERT: M 245 MET cc_start: 0.8195 (mmp) cc_final: 0.7857 (mmt) REVERT: M 262 LYS cc_start: 0.6834 (mptt) cc_final: 0.6463 (mptt) outliers start: 27 outliers final: 19 residues processed: 181 average time/residue: 0.0898 time to fit residues: 23.3157 Evaluate side-chains 181 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE 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 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 157 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 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: 4.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 106 ASN ** 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 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.164214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.124968 restraints weight = 12543.638| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.16 r_work: 0.2959 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11973 Z= 0.206 Angle : 0.581 7.106 16309 Z= 0.300 Chirality : 0.042 0.146 1910 Planarity : 0.004 0.049 1958 Dihedral : 5.577 56.476 2305 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.70 % Allowed : 11.53 % Favored : 85.77 % 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 aren not related in a simple way. whole: 1.74 (0.22), residues: 1421 helix: 2.80 (0.19), residues: 665 sheet: 0.12 (0.29), residues: 290 loop : -0.60 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 181 TYR 0.025 0.002 TYR R 301 PHE 0.019 0.002 PHE A 189 TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS M 321 Details of bonding type rmsd covalent geometry : bond 0.00501 (11970) covalent geometry : angle 0.57957 (16303) SS BOND : bond 0.00394 ( 3) SS BOND : angle 2.21108 ( 6) hydrogen bonds : bond 0.04872 ( 664) hydrogen bonds : angle 4.62264 ( 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 204 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.439 Fit side-chains REVERT: R 283 MET cc_start: 0.8376 (tpt) cc_final: 0.7738 (mtt) REVERT: A 33 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: A 209 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8171 (ttmt) REVERT: A 298 GLU cc_start: 0.6598 (tp30) cc_final: 0.6263 (pt0) REVERT: A 316 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8109 (p) REVERT: B 52 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7349 (mtt90) REVERT: B 214 ARG cc_start: 0.7666 (mpt-90) cc_final: 0.7459 (mmt-90) REVERT: B 262 MET cc_start: 0.6761 (tpp) cc_final: 0.6531 (tpp) REVERT: B 283 ARG cc_start: 0.6948 (ttm170) cc_final: 0.6089 (tpt-90) REVERT: C 21 MET cc_start: 0.5736 (ttm) cc_final: 0.4849 (tpp) REVERT: E 63 THR cc_start: 0.7641 (p) cc_final: 0.7363 (p) REVERT: E 87 ARG cc_start: 0.6123 (mtt180) cc_final: 0.5723 (ttm110) REVERT: E 187 GLN cc_start: 0.7775 (pt0) cc_final: 0.7202 (pt0) REVERT: M 67 MET cc_start: 0.6139 (tmm) cc_final: 0.5422 (tpp) REVERT: M 102 LYS cc_start: 0.6965 (ptpt) cc_final: 0.6450 (pttm) REVERT: M 206 PHE cc_start: 0.7986 (m-80) cc_final: 0.7687 (m-80) REVERT: M 245 MET cc_start: 0.8271 (mmp) cc_final: 0.8027 (mmt) outliers start: 34 outliers final: 26 residues processed: 189 average time/residue: 0.1049 time to fit residues: 28.9319 Evaluate side-chains 189 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL 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 213 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 157 SER 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 217 ILE 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 Chi-restraints excluded: chain M residue 336 VAL 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: 5.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 chunk 121 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3773 r_free = 0.3773 target = 0.166553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128640 restraints weight = 12581.244| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.17 r_work: 0.3009 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4402 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= 0.121 Angle : 0.497 6.504 16309 Z= 0.259 Chirality : 0.039 0.140 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.196 59.536 2305 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.07 % Allowed : 13.04 % 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 aren not related in a simple way. whole: 1.93 (0.22), residues: 1421 helix: 2.99 (0.19), residues: 665 sheet: 0.17 (0.29), residues: 284 loop : -0.55 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.018 0.001 TYR E 94 PHE 0.017 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 Details of bonding type rmsd covalent geometry : bond 0.00274 (11970) covalent geometry : angle 0.49576 (16303) SS BOND : bond 0.00387 ( 3) SS BOND : angle 1.63815 ( 6) hydrogen bonds : bond 0.03931 ( 664) hydrogen bonds : angle 4.34974 ( 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 183 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.285 Fit side-chains REVERT: R 283 MET cc_start: 0.8265 (tpt) cc_final: 0.7696 (mtt) REVERT: A 18 MET cc_start: 0.8612 (mtp) cc_final: 0.8353 (mtp) REVERT: A 33 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: A 209 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8139 (ttmt) REVERT: A 298 GLU cc_start: 0.6522 (tp30) cc_final: 0.6178 (pt0) REVERT: B 52 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7405 (mtt90) REVERT: B 259 GLN cc_start: 0.7326 (tt0) cc_final: 0.7120 (tt0) REVERT: C 21 MET cc_start: 0.5795 (ttm) cc_final: 0.4939 (tpp) REVERT: E 87 ARG cc_start: 0.5980 (mtt180) cc_final: 0.5579 (ttm110) REVERT: E 141 MET cc_start: 0.8744 (mmm) cc_final: 0.8504 (mmm) REVERT: E 187 GLN cc_start: 0.7809 (pt0) cc_final: 0.7276 (pt0) REVERT: M 67 MET cc_start: 0.5989 (tmm) cc_final: 0.5322 (tpp) REVERT: M 72 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7026 (p) REVERT: M 102 LYS cc_start: 0.6895 (ptpt) cc_final: 0.6396 (pttm) REVERT: M 206 PHE cc_start: 0.7922 (m-80) cc_final: 0.7606 (m-80) outliers start: 26 outliers final: 19 residues processed: 177 average time/residue: 0.0951 time to fit residues: 24.3765 Evaluate side-chains 175 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 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 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 157 SER 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 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: 7.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 96 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.166608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127441 restraints weight = 12453.917| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.22 r_work: 0.3001 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4489 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= 0.129 Angle : 0.502 6.179 16309 Z= 0.261 Chirality : 0.039 0.139 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.204 59.690 2305 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 13.04 % 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 aren not related in a simple way. whole: 1.98 (0.22), residues: 1421 helix: 3.02 (0.19), residues: 667 sheet: 0.19 (0.29), residues: 283 loop : -0.52 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.019 0.001 TYR E 94 PHE 0.017 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 Details of bonding type rmsd covalent geometry : bond 0.00299 (11970) covalent geometry : angle 0.50103 (16303) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.69269 ( 6) hydrogen bonds : bond 0.03981 ( 664) hydrogen bonds : angle 4.31735 ( 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 182 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.402 Fit side-chains REVERT: R 283 MET cc_start: 0.8269 (tpt) cc_final: 0.7690 (mtt) REVERT: A 18 MET cc_start: 0.8651 (mtp) cc_final: 0.8393 (mtp) REVERT: A 33 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: A 209 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8145 (ttmt) REVERT: A 298 GLU cc_start: 0.6500 (tp30) cc_final: 0.6152 (pt0) REVERT: B 52 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7435 (mtt90) REVERT: B 259 GLN cc_start: 0.7378 (tt0) cc_final: 0.7167 (tt0) REVERT: B 262 MET cc_start: 0.6674 (tpp) cc_final: 0.6330 (tpp) REVERT: B 322 ASP cc_start: 0.8233 (t0) cc_final: 0.7816 (m-30) REVERT: C 21 MET cc_start: 0.5863 (ttm) cc_final: 0.5006 (tpp) REVERT: E 87 ARG cc_start: 0.5929 (mtt180) cc_final: 0.5566 (ttm110) REVERT: E 141 MET cc_start: 0.8734 (mmm) cc_final: 0.8528 (mmm) REVERT: E 187 GLN cc_start: 0.7794 (pt0) cc_final: 0.7256 (pt0) REVERT: M 67 MET cc_start: 0.6050 (tmm) cc_final: 0.5378 (tpp) REVERT: M 72 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.6999 (p) REVERT: M 102 LYS cc_start: 0.6912 (ptpt) cc_final: 0.6418 (pttm) REVERT: M 206 PHE cc_start: 0.7880 (m-80) cc_final: 0.7553 (m-80) outliers start: 25 outliers final: 21 residues processed: 177 average time/residue: 0.0946 time to fit residues: 24.6743 Evaluate side-chains 177 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 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 186 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 318 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 205 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 308 VAL Chi-restraints excluded: chain M residue 313 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: 0.7980 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.167777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129856 restraints weight = 12594.957| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.16 r_work: 0.3009 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11973 Z= 0.115 Angle : 0.484 6.091 16309 Z= 0.254 Chirality : 0.038 0.135 1910 Planarity : 0.004 0.045 1958 Dihedral : 5.117 59.707 2305 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.75 % Allowed : 13.43 % 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 aren not related in a simple way. whole: 2.05 (0.22), residues: 1421 helix: 3.10 (0.19), residues: 667 sheet: 0.22 (0.30), residues: 283 loop : -0.52 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 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 M 321 Details of bonding type rmsd covalent geometry : bond 0.00258 (11970) covalent geometry : angle 0.48368 (16303) SS BOND : bond 0.00428 ( 3) SS BOND : angle 1.49656 ( 6) hydrogen bonds : bond 0.03759 ( 664) hydrogen bonds : angle 4.24158 ( 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 176 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.474 Fit side-chains REVERT: R 283 MET cc_start: 0.8226 (tpt) cc_final: 0.7666 (mtt) REVERT: A 18 MET cc_start: 0.8647 (mtp) cc_final: 0.8396 (mtp) REVERT: A 29 LYS cc_start: 0.8076 (mttt) cc_final: 0.7609 (mttt) REVERT: A 33 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: A 209 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8184 (ttmt) REVERT: A 298 GLU cc_start: 0.6399 (tp30) cc_final: 0.6027 (pt0) REVERT: B 52 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7433 (mtt90) REVERT: B 262 MET cc_start: 0.6681 (tpp) cc_final: 0.6300 (tpp) REVERT: C 21 MET cc_start: 0.5868 (ttm) cc_final: 0.5002 (tpp) REVERT: E 87 ARG cc_start: 0.5912 (mtt180) cc_final: 0.5562 (ttm110) REVERT: E 141 MET cc_start: 0.8733 (mmm) cc_final: 0.8523 (mmm) REVERT: E 187 GLN cc_start: 0.7779 (pt0) cc_final: 0.7482 (pt0) REVERT: M 67 MET cc_start: 0.6166 (tmm) cc_final: 0.5471 (tpp) REVERT: M 72 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7013 (p) REVERT: M 102 LYS cc_start: 0.6873 (ptpt) cc_final: 0.6394 (pttm) REVERT: M 206 PHE cc_start: 0.7882 (m-80) cc_final: 0.7444 (m-80) outliers start: 22 outliers final: 20 residues processed: 171 average time/residue: 0.1146 time to fit residues: 28.5193 Evaluate side-chains 173 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 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 186 GLU 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 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 205 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 308 VAL Chi-restraints excluded: chain M residue 313 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: 3.9990 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 152 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** 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 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.163518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127124 restraints weight = 12596.261| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.16 r_work: 0.2946 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11973 Z= 0.229 Angle : 0.605 6.608 16309 Z= 0.312 Chirality : 0.042 0.148 1910 Planarity : 0.004 0.053 1958 Dihedral : 5.730 58.727 2305 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.23 % Allowed : 13.04 % Favored : 84.74 % 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 aren not related in a simple way. whole: 1.60 (0.22), residues: 1421 helix: 2.69 (0.19), residues: 665 sheet: -0.10 (0.29), residues: 294 loop : -0.58 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 265 TYR 0.026 0.002 TYR E 94 PHE 0.022 0.002 PHE A 189 TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS E 168 Details of bonding type rmsd covalent geometry : bond 0.00556 (11970) covalent geometry : angle 0.60366 (16303) SS BOND : bond 0.00383 ( 3) SS BOND : angle 2.16891 ( 6) hydrogen bonds : bond 0.05002 ( 664) hydrogen bonds : angle 4.62553 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.23 seconds wall clock time: 45 minutes 4.52 seconds (2704.52 seconds total)