Starting phenix.real_space_refine on Thu Mar 13 02:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfc_60056/03_2025/8zfc_60056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfc_60056/03_2025/8zfc_60056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfc_60056/03_2025/8zfc_60056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfc_60056/03_2025/8zfc_60056.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfc_60056/03_2025/8zfc_60056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfc_60056/03_2025/8zfc_60056.cif" } resolution = 2.68 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= 0.001 sd= 0.025 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 53 5.16 5 C 5454 2.51 5 N 1477 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8545 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1826 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2469 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 343 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1676 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2231 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 281} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 114 Time building chain proxies: 5.44, per 1000 atoms: 0.64 Number of scatterers: 8545 At special positions: 0 Unit cell: (87.98, 121.9, 127.2, 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 53 16.00 O 1561 8.00 N 1477 7.00 C 5454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 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: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 36.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.636A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.680A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.527A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.618A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.714A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.602A pdb=" N PHE R 28 " --> pdb=" O SER R 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Proline residue: R 35 - end of helix removed outlier: 3.705A pdb=" N GLN R 50 " --> pdb=" O ARG R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 70 removed outlier: 3.935A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 81 removed outlier: 4.155A pdb=" N TRP R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP R 77 " --> pdb=" O PRO R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 101 removed outlier: 3.696A pdb=" N SER R 91 " --> pdb=" O HIS R 87 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY R 96 " --> pdb=" O CYS R 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 123 removed outlier: 3.681A pdb=" N ALA R 108 " --> pdb=" O TYR R 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS R 111 " --> pdb=" O ILE R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 146 Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.580A pdb=" N HIS R 157 " --> pdb=" O PRO R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.634A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 213 removed outlier: 3.889A pdb=" N SER R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 256 removed outlier: 3.677A pdb=" N SER R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 4.060A pdb=" N TYR R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 277 removed outlier: 3.712A pdb=" N GLU R 264 " --> pdb=" O CYS R 260 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG R 265 " --> pdb=" O GLY R 261 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N SER R 268 " --> pdb=" O GLU R 264 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA R 269 " --> pdb=" O ARG R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 280 No H-bonds generated for 'chain 'R' and resid 278 through 280' Processing helix chain 'R' and resid 282 through 290 removed outlier: 3.811A pdb=" N ILE R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.645A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.554A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.552A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.752A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.602A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.509A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.319A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.509A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.982A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.458A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1200 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: 2.54 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1892 1.33 - 1.45: 2058 1.45 - 1.57: 4719 1.57 - 1.69: 0 1.69 - 1.82: 74 Bond restraints: 8743 Sorted by residual: bond pdb=" CA CYS R 170 " pdb=" C CYS R 170 " ideal model delta sigma weight residual 1.520 1.489 0.031 1.12e-02 7.97e+03 7.46e+00 bond pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.58e-02 4.01e+03 6.62e+00 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.235 1.206 0.028 1.18e-02 7.18e+03 5.73e+00 bond pdb=" CA GLU R 172 " pdb=" CB GLU R 172 " ideal model delta sigma weight residual 1.534 1.500 0.034 1.57e-02 4.06e+03 4.58e+00 bond pdb=" C PHE R 174 " pdb=" N PRO R 175 " ideal model delta sigma weight residual 1.334 1.287 0.047 2.34e-02 1.83e+03 4.09e+00 ... (remaining 8738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 11870 3.82 - 7.64: 44 7.64 - 11.47: 3 11.47 - 15.29: 2 15.29 - 19.11: 1 Bond angle restraints: 11920 Sorted by residual: angle pdb=" N LYS R 173 " pdb=" CA LYS R 173 " pdb=" C LYS R 173 " ideal model delta sigma weight residual 110.80 91.69 19.11 2.13e+00 2.20e-01 8.05e+01 angle pdb=" C LYS R 173 " pdb=" CA LYS R 173 " pdb=" CB LYS R 173 " ideal model delta sigma weight residual 110.42 124.89 -14.47 1.99e+00 2.53e-01 5.29e+01 angle pdb=" C PHE R 174 " pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta sigma weight residual 110.17 121.65 -11.48 1.97e+00 2.58e-01 3.39e+01 angle pdb=" N CYS R 170 " pdb=" CA CYS R 170 " pdb=" C CYS R 170 " ideal model delta sigma weight residual 108.13 100.51 7.62 1.72e+00 3.38e-01 1.96e+01 angle pdb=" C GLU R 172 " pdb=" N LYS R 173 " pdb=" CA LYS R 173 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 11915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 4670 17.36 - 34.71: 358 34.71 - 52.07: 45 52.07 - 69.42: 9 69.42 - 86.78: 4 Dihedral angle restraints: 5086 sinusoidal: 1745 harmonic: 3341 Sorted by residual: dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 145.43 -52.43 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" C PHE R 174 " pdb=" N PHE R 174 " pdb=" CA PHE R 174 " pdb=" CB PHE R 174 " ideal model delta harmonic sigma weight residual -122.60 -135.40 12.80 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" CA THR R 216 " pdb=" C THR R 216 " pdb=" N GLU R 217 " pdb=" CA GLU R 217 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 5083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1259 0.089 - 0.177: 110 0.177 - 0.266: 4 0.266 - 0.354: 0 0.354 - 0.443: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA PHE R 174 " pdb=" N PHE R 174 " pdb=" C PHE R 174 " pdb=" CB PHE R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PHE R 171 " pdb=" N PHE R 171 " pdb=" C PHE R 171 " pdb=" CB PHE R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1371 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 174 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 175 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " 0.027 2.00e-02 2.50e+03 2.26e-02 8.91e+00 pdb=" CG PHE R 174 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 102 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C ASN R 102 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN R 102 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE R 103 " 0.017 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 81 2.62 - 3.19: 7481 3.19 - 3.76: 13072 3.76 - 4.33: 18710 4.33 - 4.90: 31346 Nonbonded interactions: 70690 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.051 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.095 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.148 3.120 nonbonded pdb=" OG SER A 6 " pdb=" OD1 ASP A 9 " model vdw 2.166 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.190 3.040 ... (remaining 70685 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.370 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.006 0.047 8743 Z= 0.418 Angle : 0.736 19.110 11920 Z= 0.406 Chirality : 0.050 0.443 1374 Planarity : 0.005 0.080 1517 Dihedral : 12.449 86.778 2924 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.53 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.86 % 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: -0.79 (0.24), residues: 1133 helix: 0.54 (0.27), residues: 372 sheet: -0.40 (0.31), residues: 281 loop : -1.39 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 244 HIS 0.011 0.002 HIS A 230 PHE 0.052 0.002 PHE R 174 TYR 0.026 0.002 TYR R 104 ARG 0.006 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 1.2675 time to fit residues: 229.2050 Evaluate side-chains 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 278 ASN A 294 GLN B 32 GLN B 75 GLN B 237 ASN B 259 GLN B 340 ASN G 24 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086826 restraints weight = 14659.895| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.91 r_work: 0.3158 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8743 Z= 0.238 Angle : 0.602 8.497 11920 Z= 0.322 Chirality : 0.044 0.174 1374 Planarity : 0.004 0.047 1517 Dihedral : 5.019 28.967 1236 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.61 % Allowed : 9.85 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.40 (0.25), residues: 1133 helix: 0.81 (0.27), residues: 389 sheet: -0.00 (0.31), residues: 285 loop : -1.34 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 62 PHE 0.027 0.002 PHE R 28 TYR 0.019 0.001 TYR R 270 ARG 0.007 0.001 ARG R 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.784 Fit side-chains REVERT: A 343 ASP cc_start: 0.7983 (m-30) cc_final: 0.7579 (m-30) REVERT: B 17 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8384 (tp-100) REVERT: B 239 ASN cc_start: 0.8960 (m110) cc_final: 0.8638 (m110) REVERT: R 179 TRP cc_start: 0.8391 (p-90) cc_final: 0.8109 (p-90) outliers start: 22 outliers final: 13 residues processed: 166 average time/residue: 1.4784 time to fit residues: 260.3608 Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 75 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085563 restraints weight = 14797.302| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.93 r_work: 0.3137 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8743 Z= 0.295 Angle : 0.596 7.448 11920 Z= 0.318 Chirality : 0.044 0.153 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.964 29.487 1236 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 12.93 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.33 (0.24), residues: 1133 helix: 0.90 (0.27), residues: 390 sheet: 0.04 (0.31), residues: 261 loop : -1.27 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.006 0.001 HIS A 230 PHE 0.028 0.002 PHE R 28 TYR 0.020 0.002 TYR R 253 ARG 0.008 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.983 Fit side-chains REVERT: A 343 ASP cc_start: 0.7986 (m-30) cc_final: 0.7535 (m-30) REVERT: B 239 ASN cc_start: 0.8997 (m110) cc_final: 0.8666 (m110) REVERT: R 179 TRP cc_start: 0.8316 (p-90) cc_final: 0.8106 (p-90) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 1.7532 time to fit residues: 309.6375 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 294 GLN B 32 GLN B 75 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085734 restraints weight = 14717.657| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.93 r_work: 0.3141 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8743 Z= 0.274 Angle : 0.575 7.841 11920 Z= 0.307 Chirality : 0.043 0.137 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.833 30.052 1236 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.20 % Allowed : 15.07 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.22 (0.25), residues: 1133 helix: 1.08 (0.27), residues: 391 sheet: 0.00 (0.31), residues: 261 loop : -1.24 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS R 167 PHE 0.018 0.002 PHE R 171 TYR 0.021 0.002 TYR R 253 ARG 0.008 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.912 Fit side-chains REVERT: A 219 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 343 ASP cc_start: 0.7980 (m-30) cc_final: 0.7623 (m-30) REVERT: B 17 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8376 (tp-100) REVERT: B 57 LYS cc_start: 0.9068 (ptpt) cc_final: 0.8740 (mtmt) REVERT: B 239 ASN cc_start: 0.8987 (m110) cc_final: 0.8689 (m110) REVERT: R 179 TRP cc_start: 0.8301 (p-90) cc_final: 0.8099 (p-90) REVERT: R 226 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7695 (mtm110) outliers start: 27 outliers final: 15 residues processed: 168 average time/residue: 1.1741 time to fit residues: 210.0506 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 32 GLN B 75 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 186 GLN R 84 ASN R 167 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086045 restraints weight = 14602.140| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.92 r_work: 0.3145 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8743 Z= 0.255 Angle : 0.568 7.941 11920 Z= 0.301 Chirality : 0.043 0.134 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.742 28.428 1236 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.32 % Allowed : 16.61 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.08 (0.25), residues: 1133 helix: 1.27 (0.27), residues: 387 sheet: -0.02 (0.31), residues: 269 loop : -1.15 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS A 230 PHE 0.029 0.002 PHE R 28 TYR 0.023 0.002 TYR R 104 ARG 0.008 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.921 Fit side-chains REVERT: A 219 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 57 LYS cc_start: 0.9063 (ptpt) cc_final: 0.8689 (mtmt) REVERT: B 59 TYR cc_start: 0.8773 (m-80) cc_final: 0.8397 (m-80) REVERT: B 239 ASN cc_start: 0.8951 (m110) cc_final: 0.8687 (m110) REVERT: B 268 ASN cc_start: 0.8413 (p0) cc_final: 0.8163 (p0) REVERT: R 226 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7667 (mtm110) outliers start: 28 outliers final: 15 residues processed: 166 average time/residue: 1.1615 time to fit residues: 205.3306 Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 32 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086671 restraints weight = 14494.006| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.92 r_work: 0.3156 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8743 Z= 0.225 Angle : 0.555 8.077 11920 Z= 0.295 Chirality : 0.042 0.132 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.638 27.833 1236 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.80 % Allowed : 16.84 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.01 (0.25), residues: 1133 helix: 1.32 (0.27), residues: 394 sheet: 0.05 (0.31), residues: 262 loop : -1.12 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 PHE 0.019 0.002 PHE R 171 TYR 0.018 0.001 TYR R 104 ARG 0.009 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.930 Fit side-chains REVERT: A 219 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: A 238 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (mtm110) REVERT: B 17 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8494 (tp40) REVERT: B 57 LYS cc_start: 0.9058 (ptpt) cc_final: 0.8709 (mtmt) REVERT: B 59 TYR cc_start: 0.8739 (m-80) cc_final: 0.8433 (m-80) REVERT: B 239 ASN cc_start: 0.8934 (m110) cc_final: 0.8702 (m110) REVERT: S 183 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: R 226 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7638 (mtm110) outliers start: 32 outliers final: 17 residues processed: 168 average time/residue: 1.2466 time to fit residues: 223.1365 Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 237 ASN B 266 HIS B 340 ASN G 24 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085784 restraints weight = 14645.113| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.93 r_work: 0.3139 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8743 Z= 0.279 Angle : 0.580 8.427 11920 Z= 0.309 Chirality : 0.043 0.136 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.732 28.114 1236 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.91 % Allowed : 18.39 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.02 (0.25), residues: 1133 helix: 1.31 (0.27), residues: 394 sheet: 0.07 (0.31), residues: 269 loop : -1.11 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 PHE 0.029 0.002 PHE R 28 TYR 0.017 0.002 TYR R 104 ARG 0.009 0.001 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.006 Fit side-chains REVERT: A 219 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 57 LYS cc_start: 0.9061 (ptpt) cc_final: 0.8741 (mtmt) REVERT: B 59 TYR cc_start: 0.8782 (m-80) cc_final: 0.8558 (m-80) REVERT: B 239 ASN cc_start: 0.8938 (m110) cc_final: 0.8728 (m110) REVERT: S 183 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8605 (pm20) REVERT: R 226 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7654 (mtm110) outliers start: 33 outliers final: 21 residues processed: 173 average time/residue: 1.1572 time to fit residues: 213.3893 Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 32 GLN B 237 ASN B 340 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085952 restraints weight = 14844.151| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.95 r_work: 0.3152 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8743 Z= 0.231 Angle : 0.574 10.231 11920 Z= 0.302 Chirality : 0.043 0.133 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.632 27.850 1236 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.91 % Allowed : 18.86 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.12 (0.25), residues: 1133 helix: 1.40 (0.27), residues: 394 sheet: 0.14 (0.31), residues: 268 loop : -1.08 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 179 HIS 0.004 0.001 HIS A 230 PHE 0.018 0.002 PHE R 21 TYR 0.017 0.001 TYR R 270 ARG 0.009 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.918 Fit side-chains REVERT: A 219 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: B 57 LYS cc_start: 0.9060 (ptpt) cc_final: 0.8743 (mtmp) REVERT: B 59 TYR cc_start: 0.8768 (m-80) cc_final: 0.8547 (m-80) REVERT: S 183 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: R 152 SER cc_start: 0.8452 (p) cc_final: 0.8245 (t) REVERT: R 226 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7638 (mtm110) outliers start: 33 outliers final: 25 residues processed: 174 average time/residue: 1.1447 time to fit residues: 212.4948 Evaluate side-chains 185 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 237 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 186 GLN R 167 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.087118 restraints weight = 14604.263| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.92 r_work: 0.3159 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8743 Z= 0.235 Angle : 0.587 12.514 11920 Z= 0.308 Chirality : 0.043 0.133 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.639 26.187 1236 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.56 % Allowed : 19.57 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.15 (0.25), residues: 1133 helix: 1.47 (0.28), residues: 387 sheet: 0.16 (0.31), residues: 268 loop : -1.07 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 PHE 0.016 0.001 PHE R 171 TYR 0.018 0.001 TYR R 270 ARG 0.009 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.890 Fit side-chains REVERT: A 219 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: B 57 LYS cc_start: 0.9049 (ptpt) cc_final: 0.8738 (mtmp) REVERT: B 59 TYR cc_start: 0.8771 (m-80) cc_final: 0.8537 (m-80) REVERT: S 183 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8581 (pm20) REVERT: R 152 SER cc_start: 0.8403 (p) cc_final: 0.8194 (t) REVERT: R 226 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6474 (mmm160) outliers start: 30 outliers final: 23 residues processed: 170 average time/residue: 1.1429 time to fit residues: 207.4807 Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 106 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 104 optimal weight: 0.9980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 237 ASN B 340 ASN S 186 GLN R 167 HIS R 271 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089363 restraints weight = 14483.681| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.92 r_work: 0.3193 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8743 Z= 0.167 Angle : 0.572 14.696 11920 Z= 0.297 Chirality : 0.042 0.160 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.434 24.874 1236 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 20.40 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.25), residues: 1133 helix: 1.63 (0.28), residues: 390 sheet: 0.18 (0.31), residues: 271 loop : -1.04 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 PHE 0.023 0.001 PHE R 21 TYR 0.017 0.001 TYR R 104 ARG 0.009 0.001 ARG R 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.997 Fit side-chains REVERT: A 219 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: B 243 THR cc_start: 0.8806 (p) cc_final: 0.8536 (p) REVERT: R 152 SER cc_start: 0.8383 (p) cc_final: 0.8178 (t) REVERT: R 226 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.6467 (mmm160) outliers start: 23 outliers final: 14 residues processed: 181 average time/residue: 1.1329 time to fit residues: 219.1683 Evaluate side-chains 182 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 237 ASN B 340 ASN S 186 GLN R 82 HIS R 167 HIS R 271 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.100121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087874 restraints weight = 14745.397| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.94 r_work: 0.3171 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8743 Z= 0.239 Angle : 0.601 14.875 11920 Z= 0.312 Chirality : 0.043 0.158 1374 Planarity : 0.004 0.051 1517 Dihedral : 4.584 24.571 1236 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.49 % Allowed : 21.23 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.23 (0.25), residues: 1133 helix: 1.58 (0.28), residues: 387 sheet: 0.17 (0.31), residues: 276 loop : -1.06 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP R 179 HIS 0.006 0.001 HIS A 230 PHE 0.030 0.002 PHE R 99 TYR 0.022 0.002 TYR R 186 ARG 0.008 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7424.89 seconds wall clock time: 128 minutes 16.76 seconds (7696.76 seconds total)