Starting phenix.real_space_refine on Tue Jul 29 22:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ef6_28069/07_2025/8ef6_28069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef6_28069/07_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_28069/07_2025/8ef6_28069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2025/8ef6_28069.map" model { file = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2025/8ef6_28069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef6_28069/07_2025/8ef6_28069.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.27, per 1000 atoms: 0.62 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.39 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: 3.70 Time building geometry restraints manager: 3.45 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: 0.560 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.460 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.003 TRP B 332 HIS 0.007 0.001 HIS E 35 PHE 0.024 0.002 PHE M 349 TYR 0.023 0.002 TYR M 108 ARG 0.008 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.16802 ( 664) hydrogen bonds : angle 6.26208 ( 1920) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.94387 ( 6) covalent geometry : bond 0.00467 (11970) covalent geometry : angle 0.86645 (16303) *********************** 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 : 1.238 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: 0.2340 time to fit residues: 92.9478 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 : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.9744 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 183 HIS B 220 GLN B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 ASN M 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.172245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.132528 restraints weight = 12410.087| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.34 r_work: 0.3020 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11973 Z= 0.197 Angle : 0.621 7.394 16309 Z= 0.325 Chirality : 0.043 0.168 1910 Planarity : 0.005 0.061 1958 Dihedral : 5.769 58.863 2305 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.54 % Allowed : 6.20 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1421 helix: 2.19 (0.18), residues: 665 sheet: 0.27 (0.29), residues: 291 loop : -0.87 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.011 0.002 HIS B 54 PHE 0.019 0.002 PHE A 189 TYR 0.026 0.002 TYR E 191 ARG 0.005 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 664) hydrogen bonds : angle 4.77546 ( 1920) SS BOND : bond 0.00706 ( 3) SS BOND : angle 1.34447 ( 6) covalent geometry : bond 0.00468 (11970) covalent geometry : angle 0.62090 (16303) *********************** 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 227 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8657 (m-40) cc_final: 0.8357 (m-40) REVERT: R 102 LYS cc_start: 0.7178 (ptpt) cc_final: 0.6825 (mtmm) REVERT: R 155 THR cc_start: 0.8895 (m) cc_final: 0.8650 (p) REVERT: R 260 ARG cc_start: 0.7582 (tpt90) cc_final: 0.6591 (tpp80) REVERT: R 283 MET cc_start: 0.8346 (tpt) cc_final: 0.7592 (mtt) REVERT: A 29 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7633 (mttt) REVERT: A 316 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 197 ARG cc_start: 0.7039 (mmt90) cc_final: 0.6173 (mmt180) REVERT: B 283 ARG cc_start: 0.6839 (ttm170) cc_final: 0.6315 (tpt-90) REVERT: C 21 MET cc_start: 0.5379 (ttm) cc_final: 0.4530 (tpp) REVERT: E 187 GLN cc_start: 0.7456 (pt0) cc_final: 0.6937 (pt0) REVERT: E 231 MET cc_start: 0.8406 (ttt) cc_final: 0.7632 (ttt) REVERT: E 240 PHE cc_start: 0.8148 (m-10) cc_final: 0.7917 (m-10) REVERT: M 67 MET cc_start: 0.6172 (tmm) cc_final: 0.5249 (tpp) REVERT: M 132 MET cc_start: 0.8013 (mtm) cc_final: 0.7609 (mtm) REVERT: M 147 SER cc_start: 0.8785 (t) cc_final: 0.8552 (m) REVERT: M 206 PHE cc_start: 0.7901 (m-80) cc_final: 0.7670 (m-80) REVERT: M 241 PHE cc_start: 0.8668 (m-10) cc_final: 0.8437 (m-80) REVERT: M 257 MET cc_start: 0.8807 (ttp) cc_final: 0.8574 (ttt) outliers start: 32 outliers final: 22 residues processed: 220 average time/residue: 0.2752 time to fit residues: 85.9273 Evaluate side-chains 189 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 72 SER 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 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 155 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 A 331 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.172477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133040 restraints weight = 12570.798| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.36 r_work: 0.3061 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11973 Z= 0.127 Angle : 0.514 6.490 16309 Z= 0.270 Chirality : 0.040 0.169 1910 Planarity : 0.004 0.054 1958 Dihedral : 5.413 57.306 2305 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.07 % Allowed : 8.90 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.22), residues: 1421 helix: 2.80 (0.18), residues: 665 sheet: 0.28 (0.29), residues: 292 loop : -0.67 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 320 HIS 0.005 0.001 HIS B 54 PHE 0.012 0.001 PHE A 189 TYR 0.017 0.001 TYR E 191 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 664) hydrogen bonds : angle 4.45608 ( 1920) SS BOND : bond 0.00499 ( 3) SS BOND : angle 0.89416 ( 6) covalent geometry : bond 0.00286 (11970) covalent geometry : angle 0.51420 (16303) *********************** 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: 26 poor density : 172 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8677 (m-40) cc_final: 0.8437 (m-40) REVERT: R 260 ARG cc_start: 0.7488 (tpt90) cc_final: 0.6539 (tpp80) REVERT: R 283 MET cc_start: 0.8277 (tpt) cc_final: 0.7813 (mmp) REVERT: R 305 LYS cc_start: 0.8313 (ttpp) cc_final: 0.8047 (ttpp) REVERT: A 33 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: A 209 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8073 (ttmt) REVERT: A 316 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 120 ILE cc_start: 0.8744 (mm) cc_final: 0.8481 (mt) REVERT: B 197 ARG cc_start: 0.6966 (mmt90) cc_final: 0.6462 (mpt180) REVERT: B 212 ASP cc_start: 0.7990 (t0) cc_final: 0.7780 (t0) REVERT: B 283 ARG cc_start: 0.6866 (ttm170) cc_final: 0.6158 (mmm-85) REVERT: C 21 MET cc_start: 0.5589 (ttm) cc_final: 0.4727 (tpp) REVERT: E 113 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7450 (tp40) REVERT: E 187 GLN cc_start: 0.7556 (pt0) cc_final: 0.7018 (pt0) REVERT: E 231 MET cc_start: 0.8424 (ttt) cc_final: 0.7706 (ttt) REVERT: E 240 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: M 67 MET cc_start: 0.5912 (tmm) cc_final: 0.5039 (tpp) REVERT: M 102 LYS cc_start: 0.6687 (ptpt) cc_final: 0.6347 (mttm) REVERT: M 147 SER cc_start: 0.8739 (t) cc_final: 0.8509 (m) REVERT: M 206 PHE cc_start: 0.7885 (m-80) cc_final: 0.7615 (m-80) REVERT: M 241 PHE cc_start: 0.8652 (m-10) cc_final: 0.8367 (m-80) outliers start: 26 outliers final: 16 residues processed: 187 average time/residue: 0.2678 time to fit residues: 70.5538 Evaluate side-chains 183 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR 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 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.172554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133226 restraints weight = 12420.552| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.35 r_work: 0.3067 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3513 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= 0.112 Angle : 0.480 5.963 16309 Z= 0.251 Chirality : 0.038 0.142 1910 Planarity : 0.004 0.050 1958 Dihedral : 5.124 53.831 2305 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.46 % Allowed : 9.54 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1421 helix: 3.00 (0.19), residues: 670 sheet: 0.31 (0.29), residues: 292 loop : -0.47 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 320 HIS 0.005 0.001 HIS B 54 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR E 191 ARG 0.003 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 664) hydrogen bonds : angle 4.28281 ( 1920) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.88443 ( 6) covalent geometry : bond 0.00248 (11970) covalent geometry : angle 0.47932 (16303) *********************** 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 210 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8727 (m-40) cc_final: 0.8492 (m-40) REVERT: R 260 ARG cc_start: 0.7461 (tpt90) cc_final: 0.6550 (tpp80) REVERT: R 283 MET cc_start: 0.8289 (tpt) cc_final: 0.7867 (mmp) REVERT: R 305 LYS cc_start: 0.8300 (ttpp) cc_final: 0.8045 (ttpp) REVERT: A 33 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7180 (mm-30) REVERT: A 209 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8088 (ttpt) REVERT: A 316 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8215 (p) REVERT: B 120 ILE cc_start: 0.8745 (mm) cc_final: 0.8537 (mt) REVERT: B 197 ARG cc_start: 0.6844 (mmt90) cc_final: 0.6344 (mpt180) REVERT: B 283 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6269 (tpt-90) REVERT: C 21 MET cc_start: 0.5597 (ttm) cc_final: 0.4696 (tpp) REVERT: E 113 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7460 (tp40) REVERT: E 187 GLN cc_start: 0.7624 (pt0) cc_final: 0.7126 (pt0) REVERT: E 231 MET cc_start: 0.8304 (ttt) cc_final: 0.7753 (ttt) REVERT: E 240 PHE cc_start: 0.8245 (m-10) cc_final: 0.7815 (m-10) REVERT: M 67 MET cc_start: 0.5985 (tmm) cc_final: 0.5229 (tpp) REVERT: M 72 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.6968 (p) REVERT: M 102 LYS cc_start: 0.6697 (ptpt) cc_final: 0.6407 (mttm) REVERT: M 147 SER cc_start: 0.8764 (t) cc_final: 0.8495 (m) outliers start: 31 outliers final: 23 residues processed: 198 average time/residue: 0.2607 time to fit residues: 72.9695 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 : 1.344 ------------------------------------------------------------------------------- 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 305 CYS 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 C residue 37 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 0.0020 chunk 131 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3819 r_free = 0.3819 target = 0.171058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131824 restraints weight = 12465.600| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.24 r_work: 0.3053 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11973 Z= 0.119 Angle : 0.483 6.182 16309 Z= 0.252 Chirality : 0.039 0.138 1910 Planarity : 0.004 0.048 1958 Dihedral : 4.978 53.144 2305 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.46 % Allowed : 10.65 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.22), residues: 1421 helix: 3.06 (0.19), residues: 668 sheet: 0.34 (0.29), residues: 287 loop : -0.48 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 320 HIS 0.003 0.001 HIS M 321 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR E 191 ARG 0.003 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 664) hydrogen bonds : angle 4.26155 ( 1920) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.81830 ( 6) covalent geometry : bond 0.00269 (11970) covalent geometry : angle 0.48321 (16303) *********************** 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 199 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8738 (m-40) cc_final: 0.8509 (m-40) REVERT: R 260 ARG cc_start: 0.7495 (tpt90) cc_final: 0.6577 (tpp80) REVERT: R 283 MET cc_start: 0.8255 (tpt) cc_final: 0.7891 (mmp) REVERT: R 305 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8050 (ttpp) REVERT: A 18 MET cc_start: 0.8626 (mtp) cc_final: 0.8336 (mtp) REVERT: A 33 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: A 209 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8075 (ttpt) REVERT: A 316 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 52 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.7382 (mtt90) REVERT: B 120 ILE cc_start: 0.8808 (mm) cc_final: 0.8598 (mt) REVERT: B 283 ARG cc_start: 0.7023 (ttm170) cc_final: 0.6236 (tpt-90) REVERT: C 21 MET cc_start: 0.5808 (ttm) cc_final: 0.4902 (tpp) REVERT: E 187 GLN cc_start: 0.7667 (pt0) cc_final: 0.7147 (pt0) REVERT: E 193 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7284 (ttt) REVERT: E 231 MET cc_start: 0.8370 (ttt) cc_final: 0.7875 (ttt) REVERT: E 240 PHE cc_start: 0.8309 (m-10) cc_final: 0.7750 (m-10) REVERT: M 67 MET cc_start: 0.6120 (tmm) cc_final: 0.5362 (tpp) REVERT: M 102 LYS cc_start: 0.6824 (ptpt) cc_final: 0.6528 (mttm) outliers start: 31 outliers final: 25 residues processed: 186 average time/residue: 0.3541 time to fit residues: 95.5787 Evaluate side-chains 194 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 2.268 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 ASP 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 91 THR 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 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 213 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN M 190 ASN M 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.165984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127042 restraints weight = 12603.259| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.28 r_work: 0.2976 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11973 Z= 0.166 Angle : 0.540 7.074 16309 Z= 0.280 Chirality : 0.040 0.145 1910 Planarity : 0.004 0.049 1958 Dihedral : 5.358 54.971 2305 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.86 % Allowed : 10.97 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.22), residues: 1421 helix: 2.92 (0.19), residues: 665 sheet: 0.23 (0.29), residues: 286 loop : -0.56 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 321 PHE 0.015 0.002 PHE E 240 TYR 0.019 0.002 TYR R 301 ARG 0.005 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 664) hydrogen bonds : angle 4.48104 ( 1920) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.91340 ( 6) covalent geometry : bond 0.00395 (11970) covalent geometry : angle 0.54004 (16303) *********************** 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 205 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.990 Fit side-chains REVERT: R 88 ASN cc_start: 0.8816 (m-40) cc_final: 0.8593 (m-40) REVERT: R 283 MET cc_start: 0.8356 (tpt) cc_final: 0.8039 (mmp) REVERT: A 33 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: A 209 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8182 (ttmt) REVERT: A 298 GLU cc_start: 0.6631 (tp30) cc_final: 0.6296 (pt0) REVERT: A 316 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8114 (p) REVERT: B 234 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 283 ARG cc_start: 0.7055 (ttm170) cc_final: 0.6084 (tpt-90) REVERT: C 21 MET cc_start: 0.5762 (ttm) cc_final: 0.4837 (tpp) REVERT: E 63 THR cc_start: 0.7410 (p) cc_final: 0.7117 (p) REVERT: E 141 MET cc_start: 0.8657 (mmm) cc_final: 0.8364 (mmm) REVERT: E 187 GLN cc_start: 0.7780 (pt0) cc_final: 0.7218 (pt0) REVERT: E 193 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7533 (ttt) REVERT: E 231 MET cc_start: 0.8483 (ttt) cc_final: 0.8173 (ttt) REVERT: E 240 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: M 67 MET cc_start: 0.6129 (tmm) cc_final: 0.5398 (tpp) REVERT: M 98 TYR cc_start: 0.7591 (m-80) cc_final: 0.7096 (m-80) REVERT: M 102 LYS cc_start: 0.6905 (ptpt) cc_final: 0.6413 (pttm) outliers start: 36 outliers final: 26 residues processed: 191 average time/residue: 0.3093 time to fit residues: 84.1743 Evaluate side-chains 187 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 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 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP 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 91 THR 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 E residue 240 PHE Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 75 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.166990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128594 restraints weight = 12585.830| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.26 r_work: 0.2983 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4317 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= 0.141 Angle : 0.512 6.756 16309 Z= 0.267 Chirality : 0.039 0.141 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.288 57.472 2305 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.70 % Allowed : 12.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1421 helix: 2.96 (0.19), residues: 665 sheet: 0.18 (0.29), residues: 286 loop : -0.57 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS M 321 PHE 0.014 0.001 PHE A 189 TYR 0.015 0.001 TYR R 301 ARG 0.003 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 664) hydrogen bonds : angle 4.38830 ( 1920) SS BOND : bond 0.00422 ( 3) SS BOND : angle 2.10465 ( 6) covalent geometry : bond 0.00332 (11970) covalent geometry : angle 0.51059 (16303) *********************** 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 196 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.372 Fit side-chains REVERT: R 283 MET cc_start: 0.8338 (tpt) cc_final: 0.7718 (mtt) REVERT: A 18 MET cc_start: 0.8643 (mtp) cc_final: 0.8383 (mtp) REVERT: A 33 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: A 209 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8149 (ttmt) REVERT: A 298 GLU cc_start: 0.6556 (tp30) cc_final: 0.6163 (pt0) REVERT: A 316 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8142 (p) REVERT: B 52 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7391 (mtt90) REVERT: C 21 MET cc_start: 0.5711 (ttm) cc_final: 0.4820 (tpp) REVERT: E 83 MET cc_start: 0.7083 (mtm) cc_final: 0.6743 (mtt) REVERT: E 87 ARG cc_start: 0.6217 (mtt180) cc_final: 0.5721 (ttm110) REVERT: E 187 GLN cc_start: 0.7828 (pt0) cc_final: 0.7300 (pt0) REVERT: E 193 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7717 (ttt) REVERT: E 231 MET cc_start: 0.8440 (ttt) cc_final: 0.8119 (ttt) REVERT: E 240 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: M 67 MET cc_start: 0.6066 (tmm) cc_final: 0.5363 (tpp) REVERT: M 72 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7035 (p) REVERT: M 98 TYR cc_start: 0.7650 (m-80) cc_final: 0.7157 (m-80) REVERT: M 102 LYS cc_start: 0.6922 (ptpt) cc_final: 0.6419 (pttm) outliers start: 34 outliers final: 28 residues processed: 183 average time/residue: 0.3134 time to fit residues: 81.9596 Evaluate side-chains 186 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 49 ILE 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 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 247 ASP 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 91 THR 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 E residue 240 PHE 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 101 MET Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 0.0030 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.166525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127909 restraints weight = 12453.531| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.19 r_work: 0.2982 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11973 Z= 0.142 Angle : 0.518 6.690 16309 Z= 0.269 Chirality : 0.039 0.140 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.317 58.766 2305 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.02 % Allowed : 12.64 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1421 helix: 2.97 (0.19), residues: 665 sheet: 0.21 (0.29), residues: 284 loop : -0.61 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS M 321 PHE 0.014 0.001 PHE A 189 TYR 0.016 0.001 TYR R 301 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 664) hydrogen bonds : angle 4.38095 ( 1920) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.99309 ( 6) covalent geometry : bond 0.00334 (11970) covalent geometry : angle 0.51673 (16303) *********************** 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 195 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.737 Fit side-chains REVERT: R 283 MET cc_start: 0.8321 (tpt) cc_final: 0.7729 (mtt) REVERT: A 18 MET cc_start: 0.8619 (mtp) cc_final: 0.8358 (mtp) REVERT: A 33 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 209 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8164 (ttmt) REVERT: A 298 GLU cc_start: 0.6541 (tp30) cc_final: 0.6165 (pt0) REVERT: B 52 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7450 (mtt90) REVERT: B 214 ARG cc_start: 0.7258 (mpt180) cc_final: 0.6991 (mmt-90) REVERT: B 234 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: B 322 ASP cc_start: 0.8281 (t0) cc_final: 0.7870 (m-30) REVERT: C 21 MET cc_start: 0.5816 (ttm) cc_final: 0.4907 (tpp) REVERT: E 83 MET cc_start: 0.7061 (mtm) cc_final: 0.6554 (mtt) REVERT: E 87 ARG cc_start: 0.6238 (mtt180) cc_final: 0.5731 (ttm110) REVERT: E 187 GLN cc_start: 0.7805 (pt0) cc_final: 0.7266 (pt0) REVERT: E 193 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7776 (ttt) REVERT: E 231 MET cc_start: 0.8433 (ttt) cc_final: 0.8120 (ttt) REVERT: E 240 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: M 67 MET cc_start: 0.6056 (tmm) cc_final: 0.5365 (tpp) REVERT: M 72 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7015 (p) REVERT: M 98 TYR cc_start: 0.7614 (m-80) cc_final: 0.7117 (m-80) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.3824 time to fit residues: 104.5196 Evaluate side-chains 186 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 340 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP 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 91 THR 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 E residue 240 PHE Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.168544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129939 restraints weight = 12520.279| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.24 r_work: 0.3036 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4445 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= 0.109 Angle : 0.483 7.319 16309 Z= 0.252 Chirality : 0.038 0.135 1910 Planarity : 0.004 0.044 1958 Dihedral : 5.130 59.204 2305 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.07 % Allowed : 13.35 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1421 helix: 3.10 (0.19), residues: 668 sheet: 0.29 (0.29), residues: 284 loop : -0.53 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS M 321 PHE 0.013 0.001 PHE E 68 TYR 0.013 0.001 TYR M 130 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 664) hydrogen bonds : angle 4.22869 ( 1920) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.45792 ( 6) covalent geometry : bond 0.00239 (11970) covalent geometry : angle 0.48187 (16303) *********************** 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 178 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 2.034 Fit side-chains REVERT: R 152 ASN cc_start: 0.8491 (m110) cc_final: 0.8233 (m-40) REVERT: R 283 MET cc_start: 0.8198 (tpt) cc_final: 0.7646 (mtt) REVERT: A 18 MET cc_start: 0.8624 (mtp) cc_final: 0.8377 (mtp) REVERT: A 33 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: A 209 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8140 (ttmt) REVERT: A 298 GLU cc_start: 0.6409 (tp30) cc_final: 0.6037 (pt0) REVERT: B 52 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7476 (mtt90) REVERT: B 234 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: B 322 ASP cc_start: 0.8259 (t0) cc_final: 0.7849 (m-30) REVERT: C 21 MET cc_start: 0.5820 (ttm) cc_final: 0.4917 (tpp) REVERT: E 83 MET cc_start: 0.7045 (mtm) cc_final: 0.6535 (mtt) REVERT: E 87 ARG cc_start: 0.6184 (mtt180) cc_final: 0.5674 (ttm110) REVERT: E 187 GLN cc_start: 0.7910 (pt0) cc_final: 0.7662 (pt0) REVERT: E 231 MET cc_start: 0.8302 (ttt) cc_final: 0.7901 (ttt) REVERT: E 240 PHE cc_start: 0.8518 (m-10) cc_final: 0.7822 (m-10) REVERT: M 67 MET cc_start: 0.6088 (tmm) cc_final: 0.5432 (tpp) REVERT: M 72 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7014 (p) REVERT: M 98 TYR cc_start: 0.7576 (m-80) cc_final: 0.7085 (m-80) REVERT: M 102 LYS cc_start: 0.6709 (ptpt) cc_final: 0.6337 (mmtt) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.3139 time to fit residues: 78.4454 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 : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 210 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 340 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP 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 91 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.168411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129910 restraints weight = 12422.327| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.18 r_work: 0.3012 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4485 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= 0.113 Angle : 0.487 7.269 16309 Z= 0.254 Chirality : 0.038 0.136 1910 Planarity : 0.004 0.045 1958 Dihedral : 5.122 59.779 2305 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 13.51 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1421 helix: 3.13 (0.19), residues: 668 sheet: 0.28 (0.29), residues: 285 loop : -0.53 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.014 0.001 PHE E 68 TYR 0.013 0.001 TYR E 191 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 664) hydrogen bonds : angle 4.20092 ( 1920) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.56188 ( 6) covalent geometry : bond 0.00254 (11970) covalent geometry : angle 0.48624 (16303) ********************** 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 178 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.210 Fit side-chains REVERT: R 283 MET cc_start: 0.8255 (tpt) cc_final: 0.7678 (mtt) REVERT: A 18 MET cc_start: 0.8662 (mtp) cc_final: 0.8413 (mtp) REVERT: A 33 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: A 209 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8176 (ttmt) REVERT: A 298 GLU cc_start: 0.6408 (tp30) cc_final: 0.6124 (mt-10) REVERT: B 52 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.7499 (mtt90) REVERT: B 234 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: B 322 ASP cc_start: 0.8269 (t0) cc_final: 0.7863 (m-30) REVERT: C 21 MET cc_start: 0.5964 (ttm) cc_final: 0.5020 (tpp) REVERT: E 187 GLN cc_start: 0.7966 (pt0) cc_final: 0.7714 (pt0) REVERT: E 231 MET cc_start: 0.8324 (ttt) cc_final: 0.7942 (ttt) REVERT: E 240 PHE cc_start: 0.8493 (m-10) cc_final: 0.7796 (m-10) REVERT: M 67 MET cc_start: 0.6211 (tmm) cc_final: 0.5490 (tpp) REVERT: M 72 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7026 (p) REVERT: M 98 TYR cc_start: 0.7607 (m-80) cc_final: 0.7091 (m-80) REVERT: M 102 LYS cc_start: 0.6661 (ptpt) cc_final: 0.6229 (pttm) outliers start: 25 outliers final: 18 residues processed: 172 average time/residue: 0.2578 time to fit residues: 64.2009 Evaluate side-chains 174 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP 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 91 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 198 SER 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 122 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.168597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129932 restraints weight = 12474.531| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.20 r_work: 0.3022 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4535 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= 0.112 Angle : 0.484 6.873 16309 Z= 0.252 Chirality : 0.038 0.136 1910 Planarity : 0.004 0.044 1958 Dihedral : 5.099 59.473 2305 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.99 % Allowed : 13.43 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.22), residues: 1421 helix: 3.15 (0.19), residues: 668 sheet: 0.28 (0.29), residues: 285 loop : -0.53 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.013 0.001 PHE E 68 TYR 0.013 0.001 TYR E 191 ARG 0.004 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 664) hydrogen bonds : angle 4.17983 ( 1920) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.46493 ( 6) covalent geometry : bond 0.00251 (11970) covalent geometry : angle 0.48292 (16303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6805.44 seconds wall clock time: 127 minutes 54.19 seconds (7674.19 seconds total)