Starting phenix.real_space_refine on Mon Dec 30 00:36:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ef6_28069/12_2024/8ef6_28069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ef6_28069/12_2024/8ef6_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_28069/12_2024/8ef6_28069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ef6_28069/12_2024/8ef6_28069.map" model { file = "/net/cci-nas-00/data/ceres_data/8ef6_28069/12_2024/8ef6_28069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ef6_28069/12_2024/8ef6_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.14, per 1000 atoms: 0.61 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 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: 1.40 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: 3.67 Time building geometry restraints manager: 3.50 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: 0.470 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- 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 11970 Z= 0.301 Angle : 0.866 10.377 16303 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 *********************** 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 : 1.415 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: 0.2519 time to fit residues: 99.2634 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 : 1.380 ------------------------------------------------------------------------------- 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: 0.7980 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: 4.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN A 188 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11970 Z= 0.256 Angle : 0.577 6.656 16303 Z= 0.304 Chirality : 0.042 0.159 1910 Planarity : 0.005 0.059 1958 Dihedral : 5.622 59.891 2305 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.31 % Allowed : 6.12 % Favored : 91.57 % 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: 1.40 (0.21), residues: 1421 helix: 2.39 (0.18), residues: 665 sheet: 0.36 (0.30), residues: 287 loop : -0.87 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.008 0.002 HIS B 54 PHE 0.015 0.002 PHE A 189 TYR 0.026 0.002 TYR E 191 ARG 0.006 0.001 ARG E 67 *********************** 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 220 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8434 (m-40) cc_final: 0.8134 (m-40) REVERT: R 260 ARG cc_start: 0.7301 (tpt90) cc_final: 0.6567 (tpp80) REVERT: A 316 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8232 (p) REVERT: C 21 MET cc_start: 0.4949 (ttm) cc_final: 0.4298 (tpp) REVERT: E 187 GLN cc_start: 0.7278 (pt0) cc_final: 0.6910 (pt0) REVERT: E 231 MET cc_start: 0.7771 (ttt) cc_final: 0.6915 (ttt) REVERT: M 67 MET cc_start: 0.6131 (tmm) cc_final: 0.5460 (tpp) REVERT: M 77 TYR cc_start: 0.7562 (m-10) cc_final: 0.7281 (m-80) REVERT: M 206 PHE cc_start: 0.7844 (m-80) cc_final: 0.7567 (m-80) REVERT: M 241 PHE cc_start: 0.8318 (m-10) cc_final: 0.8071 (m-80) REVERT: M 257 MET cc_start: 0.8731 (ttp) cc_final: 0.8482 (ttt) outliers start: 29 outliers final: 20 residues processed: 211 average time/residue: 0.2472 time to fit residues: 74.6054 Evaluate side-chains 186 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 105 optimal weight: 0.0670 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 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 M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11970 Z= 0.193 Angle : 0.518 6.240 16303 Z= 0.271 Chirality : 0.040 0.149 1910 Planarity : 0.004 0.056 1958 Dihedral : 5.391 59.317 2305 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.07 % Allowed : 8.74 % Favored : 89.19 % 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: 1.87 (0.22), residues: 1421 helix: 2.88 (0.18), residues: 665 sheet: 0.37 (0.30), residues: 288 loop : -0.64 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.001 PHE E 240 TYR 0.020 0.001 TYR E 191 ARG 0.003 0.000 ARG E 67 *********************** 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 204 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8573 (m-40) cc_final: 0.8306 (m-40) REVERT: R 260 ARG cc_start: 0.7304 (tpt90) cc_final: 0.6589 (tpp80) REVERT: R 305 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8067 (ttpp) REVERT: A 33 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6832 (mm-30) REVERT: A 209 LYS cc_start: 0.8089 (ttpp) cc_final: 0.7750 (ttpt) REVERT: A 316 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 21 MET cc_start: 0.5269 (ttm) cc_final: 0.4573 (tpp) REVERT: E 87 ARG cc_start: 0.6515 (mtt180) cc_final: 0.6264 (ttm110) REVERT: E 187 GLN cc_start: 0.7284 (pt0) cc_final: 0.6971 (pt0) REVERT: E 231 MET cc_start: 0.8094 (ttt) cc_final: 0.7844 (ttt) REVERT: M 67 MET cc_start: 0.5845 (tmm) cc_final: 0.5336 (tpp) REVERT: M 205 MET cc_start: 0.7667 (ttt) cc_final: 0.7235 (tpp) REVERT: M 206 PHE cc_start: 0.7690 (m-80) cc_final: 0.7463 (m-80) REVERT: M 241 PHE cc_start: 0.8356 (m-10) cc_final: 0.8046 (m-80) outliers start: 26 outliers final: 16 residues processed: 196 average time/residue: 0.2626 time to fit residues: 72.0501 Evaluate side-chains 177 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 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 E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11970 Z= 0.174 Angle : 0.489 6.947 16303 Z= 0.257 Chirality : 0.039 0.142 1910 Planarity : 0.004 0.051 1958 Dihedral : 5.113 49.420 2305 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.46 % Allowed : 9.70 % Favored : 87.84 % 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: 2.03 (0.22), residues: 1421 helix: 3.04 (0.18), residues: 668 sheet: 0.38 (0.29), residues: 287 loop : -0.58 (0.27), residues: 466 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 0.015 0.001 TYR E 191 ARG 0.003 0.000 ARG B 219 *********************** 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 195 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8601 (m-40) cc_final: 0.8364 (m-40) REVERT: R 155 THR cc_start: 0.8746 (m) cc_final: 0.8541 (p) REVERT: R 260 ARG cc_start: 0.7232 (tpt90) cc_final: 0.6571 (tpp80) REVERT: R 305 LYS cc_start: 0.8273 (ttpp) cc_final: 0.8033 (ttpp) REVERT: A 33 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6839 (mm-30) REVERT: A 209 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7777 (ttpt) REVERT: B 120 ILE cc_start: 0.8764 (mm) cc_final: 0.8511 (mt) REVERT: C 21 MET cc_start: 0.5273 (ttm) cc_final: 0.4538 (tpp) REVERT: E 87 ARG cc_start: 0.6507 (mtt180) cc_final: 0.6204 (ttm110) REVERT: E 187 GLN cc_start: 0.7395 (pt0) cc_final: 0.7052 (pt0) REVERT: E 193 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6175 (ttt) REVERT: M 67 MET cc_start: 0.5831 (tmm) cc_final: 0.5475 (tpp) REVERT: M 132 MET cc_start: 0.7016 (mtm) cc_final: 0.6804 (mtp) REVERT: M 206 PHE cc_start: 0.7706 (m-80) cc_final: 0.7485 (m-80) outliers start: 31 outliers final: 21 residues processed: 185 average time/residue: 0.2525 time to fit residues: 67.3214 Evaluate side-chains 179 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 260 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 156 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 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 76 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 overall best weight: 1.1520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11970 Z= 0.190 Angle : 0.495 6.732 16303 Z= 0.259 Chirality : 0.039 0.143 1910 Planarity : 0.004 0.050 1958 Dihedral : 4.983 56.186 2305 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.23 % Allowed : 10.25 % Favored : 87.52 % 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: 2.02 (0.22), residues: 1421 helix: 3.05 (0.18), residues: 668 sheet: 0.24 (0.29), residues: 288 loop : -0.53 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR E 191 ARG 0.003 0.000 ARG R 97 *********************** 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 196 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8637 (m-40) cc_final: 0.8413 (m-40) REVERT: R 260 ARG cc_start: 0.7258 (tpt90) cc_final: 0.6605 (tpp80) REVERT: A 33 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6827 (mm-30) REVERT: A 209 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7766 (ttpt) REVERT: B 120 ILE cc_start: 0.8846 (mm) cc_final: 0.8610 (mt) REVERT: C 21 MET cc_start: 0.5433 (ttm) cc_final: 0.4690 (tpp) REVERT: E 87 ARG cc_start: 0.6458 (mtt180) cc_final: 0.6159 (ttm110) REVERT: E 187 GLN cc_start: 0.7470 (pt0) cc_final: 0.7094 (pt0) REVERT: E 193 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6496 (ttt) REVERT: M 67 MET cc_start: 0.5948 (tmm) cc_final: 0.5649 (tpp) REVERT: M 72 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7480 (p) REVERT: M 206 PHE cc_start: 0.7697 (m-80) cc_final: 0.7495 (m-80) REVERT: M 245 MET cc_start: 0.7699 (mmp) cc_final: 0.7172 (mmp) REVERT: M 262 LYS cc_start: 0.7004 (mptt) cc_final: 0.6790 (mptt) outliers start: 28 outliers final: 24 residues processed: 186 average time/residue: 0.2575 time to fit residues: 68.4558 Evaluate side-chains 185 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 MET 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 49 ILE Chi-restraints excluded: chain A residue 260 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 318 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** M 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11970 Z= 0.215 Angle : 0.513 6.895 16303 Z= 0.267 Chirality : 0.039 0.143 1910 Planarity : 0.004 0.049 1958 Dihedral : 5.133 56.534 2305 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.38 % Allowed : 11.05 % Favored : 86.57 % 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: 1.95 (0.22), residues: 1421 helix: 3.00 (0.18), residues: 668 sheet: 0.15 (0.29), residues: 287 loop : -0.53 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 321 PHE 0.013 0.001 PHE A 189 TYR 0.018 0.001 TYR E 94 ARG 0.003 0.000 ARG R 181 *********************** 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 194 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: R 88 ASN cc_start: 0.8650 (m-40) cc_final: 0.8430 (m-40) REVERT: R 260 ARG cc_start: 0.7271 (tpt90) cc_final: 0.6623 (tpp80) REVERT: A 18 MET cc_start: 0.7853 (mtp) cc_final: 0.7598 (mtp) REVERT: A 33 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6867 (mm-30) REVERT: A 209 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7833 (ttmt) REVERT: B 52 ARG cc_start: 0.7243 (mtt-85) cc_final: 0.6808 (mtt90) REVERT: B 120 ILE cc_start: 0.8839 (mm) cc_final: 0.8621 (mt) REVERT: C 21 MET cc_start: 0.5392 (ttm) cc_final: 0.4636 (tpp) REVERT: E 87 ARG cc_start: 0.6430 (mtt180) cc_final: 0.6142 (ttm110) REVERT: E 113 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7380 (tp40) REVERT: E 187 GLN cc_start: 0.7498 (pt0) cc_final: 0.7092 (pt0) REVERT: E 193 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6661 (ttt) REVERT: M 67 MET cc_start: 0.5913 (tmm) cc_final: 0.5628 (tpp) REVERT: M 72 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7159 (p) REVERT: M 206 PHE cc_start: 0.7669 (m-80) cc_final: 0.7447 (m-80) REVERT: M 245 MET cc_start: 0.7449 (mmp) cc_final: 0.6988 (mmt) outliers start: 30 outliers final: 24 residues processed: 183 average time/residue: 0.2512 time to fit residues: 65.7893 Evaluate side-chains 182 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 MET 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 49 ILE 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 195 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** M 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11970 Z= 0.178 Angle : 0.489 6.495 16303 Z= 0.255 Chirality : 0.039 0.140 1910 Planarity : 0.004 0.047 1958 Dihedral : 5.063 57.802 2305 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.38 % Allowed : 11.69 % Favored : 85.93 % 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: 2.01 (0.22), residues: 1421 helix: 3.09 (0.18), residues: 668 sheet: 0.16 (0.29), residues: 286 loop : -0.55 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR E 94 ARG 0.004 0.000 ARG B 219 *********************** 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 187 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7887 (mtp) cc_final: 0.7644 (mtp) REVERT: A 33 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6868 (mm-30) REVERT: A 209 LYS cc_start: 0.8096 (ttpp) cc_final: 0.7817 (ttmt) REVERT: B 52 ARG cc_start: 0.7233 (mtt-85) cc_final: 0.6803 (mtt90) REVERT: B 120 ILE cc_start: 0.8848 (mm) cc_final: 0.8636 (mt) REVERT: B 234 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: C 21 MET cc_start: 0.5434 (ttm) cc_final: 0.4694 (tpp) REVERT: E 87 ARG cc_start: 0.6382 (mtt180) cc_final: 0.6116 (ttm110) REVERT: E 187 GLN cc_start: 0.7500 (pt0) cc_final: 0.7088 (pt0) REVERT: E 193 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6658 (ttt) REVERT: M 67 MET cc_start: 0.5956 (tmm) cc_final: 0.5717 (tpp) REVERT: M 98 TYR cc_start: 0.7224 (m-80) cc_final: 0.6717 (m-80) REVERT: M 206 PHE cc_start: 0.7661 (m-80) cc_final: 0.7431 (m-80) outliers start: 30 outliers final: 25 residues processed: 176 average time/residue: 0.2465 time to fit residues: 62.8087 Evaluate side-chains 183 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 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 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL 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 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 53 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 122 optimal weight: 0.5980 chunk 129 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11970 Z= 0.126 Angle : 0.465 8.086 16303 Z= 0.243 Chirality : 0.038 0.134 1910 Planarity : 0.003 0.045 1958 Dihedral : 4.883 59.597 2305 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.91 % Allowed : 12.32 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.20 (0.22), residues: 1421 helix: 3.25 (0.19), residues: 668 sheet: 0.30 (0.29), residues: 284 loop : -0.50 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS M 321 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR E 191 ARG 0.004 0.000 ARG E 67 *********************** 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 187 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.470 Fit side-chains REVERT: A 18 MET cc_start: 0.7850 (mtp) cc_final: 0.7630 (mtp) REVERT: A 33 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6864 (mm-30) REVERT: A 209 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7777 (ttmt) REVERT: B 52 ARG cc_start: 0.7307 (mtt-85) cc_final: 0.6923 (mtt90) REVERT: B 234 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: C 21 MET cc_start: 0.5518 (ttm) cc_final: 0.4771 (tpp) REVERT: E 87 ARG cc_start: 0.6445 (mtt180) cc_final: 0.6154 (ttm110) REVERT: M 98 TYR cc_start: 0.7072 (m-80) cc_final: 0.6607 (m-80) REVERT: M 206 PHE cc_start: 0.7618 (m-80) cc_final: 0.7404 (m-80) outliers start: 24 outliers final: 20 residues processed: 180 average time/residue: 0.2361 time to fit residues: 61.9851 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 : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain 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 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 118 LEU 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 117 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11970 Z= 0.282 Angle : 0.557 8.058 16303 Z= 0.289 Chirality : 0.041 0.175 1910 Planarity : 0.004 0.047 1958 Dihedral : 5.359 58.391 2305 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.99 % Allowed : 12.96 % Favored : 85.06 % 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: 2.99 (0.19), residues: 665 sheet: 0.16 (0.29), residues: 285 loop : -0.60 (0.28), residues: 471 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 68 TYR 0.021 0.002 TYR E 94 ARG 0.003 0.000 ARG R 265 *********************** 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 176 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.395 Fit side-chains REVERT: A 18 MET cc_start: 0.7914 (mtp) cc_final: 0.7661 (mtp) REVERT: A 33 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6926 (mm-30) REVERT: A 209 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7840 (ttmt) REVERT: B 52 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.6874 (mtt90) REVERT: B 234 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: C 21 MET cc_start: 0.5452 (ttm) cc_final: 0.4752 (tpp) REVERT: E 87 ARG cc_start: 0.6493 (mtt180) cc_final: 0.6209 (ttm110) REVERT: E 187 GLN cc_start: 0.8152 (pt0) cc_final: 0.7843 (pt0) REVERT: M 98 TYR cc_start: 0.7195 (m-80) cc_final: 0.6741 (m-80) REVERT: M 206 PHE cc_start: 0.7717 (m-80) cc_final: 0.7478 (m-80) outliers start: 25 outliers final: 19 residues processed: 168 average time/residue: 0.2287 time to fit residues: 56.1726 Evaluate side-chains 166 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 231 MET 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 81 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 152 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11970 Z= 0.212 Angle : 0.521 7.801 16303 Z= 0.271 Chirality : 0.040 0.155 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.248 59.729 2305 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.67 % Allowed : 13.43 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.96 (0.19), residues: 667 sheet: 0.18 (0.30), residues: 284 loop : -0.60 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.013 0.001 PHE A 189 TYR 0.019 0.001 TYR E 94 ARG 0.004 0.000 ARG R 181 ********************** 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 169 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.258 Fit side-chains REVERT: A 18 MET cc_start: 0.7863 (mtp) cc_final: 0.7619 (mtp) REVERT: A 33 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6911 (mm-30) REVERT: A 53 MET cc_start: 0.7883 (mtt) cc_final: 0.7629 (mtm) REVERT: A 209 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7841 (ttmt) REVERT: B 52 ARG cc_start: 0.7291 (mtt-85) cc_final: 0.6866 (mtt90) REVERT: B 234 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: C 21 MET cc_start: 0.5444 (ttm) cc_final: 0.4767 (tpp) REVERT: E 87 ARG cc_start: 0.6455 (mtt180) cc_final: 0.6153 (ttm110) REVERT: E 187 GLN cc_start: 0.8105 (pt0) cc_final: 0.7817 (pt0) REVERT: M 98 TYR cc_start: 0.7183 (m-80) cc_final: 0.6662 (m-80) REVERT: M 206 PHE cc_start: 0.7709 (m-80) cc_final: 0.7421 (m-80) outliers start: 21 outliers final: 19 residues processed: 164 average time/residue: 0.2634 time to fit residues: 62.6874 Evaluate side-chains 167 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 231 MET 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 34 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 = 0.3798 r_free = 0.3798 target = 0.169191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130136 restraints weight = 12351.462| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.15 r_work: 0.3036 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11970 Z= 0.161 Angle : 0.491 6.987 16303 Z= 0.257 Chirality : 0.039 0.151 1910 Planarity : 0.004 0.045 1958 Dihedral : 5.083 59.368 2305 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.67 % Allowed : 13.28 % Favored : 85.06 % 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: 2.02 (0.22), residues: 1421 helix: 3.09 (0.19), residues: 668 sheet: 0.23 (0.30), residues: 284 loop : -0.57 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.001 TYR E 94 ARG 0.009 0.000 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.19 seconds wall clock time: 47 minutes 16.69 seconds (2836.69 seconds total)