Starting phenix.real_space_refine on Wed Sep 17 11:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfc_60056/09_2025/8zfc_60056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfc_60056/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zfc_60056/09_2025/8zfc_60056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfc_60056/09_2025/8zfc_60056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zfc_60056/09_2025/8zfc_60056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfc_60056/09_2025/8zfc_60056.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 7, 'ARG:plan': 5, 'TYR:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 1} 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: {'GLU:plan': 6, 'ASP:plan': 4, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 2} 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, 'ARG:plan': 2, 'GLU:plan': 5, '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: {'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3} 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: {'ARG:plan': 8, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 114 Time building chain proxies: 2.09, per 1000 atoms: 0.24 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: 0.70 Conformation dependent library (CDL) restraints added in 456.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.28 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: 1.42 Time building geometry restraints manager: 0.97 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: 1.830 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- 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 8745 Z= 0.270 Angle : 0.736 19.110 11924 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (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 ARG 0.006 0.001 ARG S 98 TYR 0.026 0.002 TYR R 104 PHE 0.052 0.002 PHE R 174 TRP 0.013 0.002 TRP A 244 HIS 0.011 0.002 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 8743) covalent geometry : angle 0.73570 (11920) SS BOND : bond 0.01669 ( 2) SS BOND : angle 1.89958 ( 4) hydrogen bonds : bond 0.17772 ( 416) hydrogen bonds : angle 7.23422 ( 1200) *********************** 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 : 0.337 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.5738 time to fit residues: 103.4748 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 : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 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 237 GLN A 278 ASN A 294 GLN B 32 GLN B 75 GLN B 259 GLN B 340 ASN G 24 ASN S 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.099328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.087134 restraints weight = 14660.658| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.90 r_work: 0.3160 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8745 Z= 0.169 Angle : 0.611 8.553 11924 Z= 0.327 Chirality : 0.045 0.175 1374 Planarity : 0.004 0.047 1517 Dihedral : 5.081 29.567 1236 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.73 % Allowed : 9.96 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.25), residues: 1133 helix: 0.76 (0.27), residues: 389 sheet: -0.01 (0.31), residues: 285 loop : -1.36 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 132 TYR 0.018 0.002 TYR R 270 PHE 0.027 0.002 PHE R 28 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8743) covalent geometry : angle 0.61111 (11920) SS BOND : bond 0.00431 ( 2) SS BOND : angle 1.16043 ( 4) hydrogen bonds : bond 0.04384 ( 416) hydrogen bonds : angle 5.18862 ( 1200) *********************** 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 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.236 Fit side-chains REVERT: A 343 ASP cc_start: 0.7967 (m-30) cc_final: 0.7608 (m-30) REVERT: B 17 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8395 (tp-100) REVERT: B 239 ASN cc_start: 0.8983 (m110) cc_final: 0.8680 (m110) REVERT: R 179 TRP cc_start: 0.8409 (p-90) cc_final: 0.8100 (p-90) outliers start: 23 outliers final: 13 residues processed: 166 average time/residue: 0.5917 time to fit residues: 104.1829 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 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 277 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 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 294 GLN B 75 GLN B 259 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.099000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086950 restraints weight = 14568.084| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.90 r_work: 0.3157 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8745 Z= 0.148 Angle : 0.574 8.497 11924 Z= 0.305 Chirality : 0.043 0.145 1374 Planarity : 0.004 0.048 1517 Dihedral : 4.826 28.588 1236 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.25 % Allowed : 13.29 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.25), residues: 1133 helix: 1.00 (0.27), residues: 389 sheet: 0.07 (0.31), residues: 268 loop : -1.25 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 126 TYR 0.019 0.002 TYR R 253 PHE 0.029 0.002 PHE R 28 TRP 0.012 0.001 TRP A 244 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8743) covalent geometry : angle 0.57336 (11920) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.16923 ( 4) hydrogen bonds : bond 0.03965 ( 416) hydrogen bonds : angle 4.85742 ( 1200) *********************** 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 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.337 Fit side-chains REVERT: A 343 ASP cc_start: 0.7939 (m-30) cc_final: 0.7509 (m-30) REVERT: B 239 ASN cc_start: 0.8955 (m110) cc_final: 0.8655 (m110) REVERT: R 126 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7856 (mtt90) REVERT: R 179 TRP cc_start: 0.8316 (p-90) cc_final: 0.8105 (p-90) outliers start: 19 outliers final: 13 residues processed: 168 average time/residue: 0.6213 time to fit residues: 110.6906 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 32 GLN B 75 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083429 restraints weight = 14987.905| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.93 r_work: 0.3101 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 8745 Z= 0.295 Angle : 0.661 8.159 11924 Z= 0.351 Chirality : 0.047 0.154 1374 Planarity : 0.005 0.089 1517 Dihedral : 5.237 32.550 1236 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.08 % Allowed : 15.54 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.24), residues: 1133 helix: 0.84 (0.27), residues: 388 sheet: -0.28 (0.30), residues: 281 loop : -1.28 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 187 TYR 0.023 0.002 TYR R 253 PHE 0.025 0.002 PHE R 28 TRP 0.014 0.002 TRP B 99 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 8743) covalent geometry : angle 0.66101 (11920) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.32890 ( 4) hydrogen bonds : bond 0.04738 ( 416) hydrogen bonds : angle 5.04542 ( 1200) *********************** 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 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.366 Fit side-chains REVERT: A 9 ASP cc_start: 0.8301 (m-30) cc_final: 0.7981 (m-30) REVERT: B 57 LYS cc_start: 0.9089 (ptpt) cc_final: 0.8767 (mtmt) REVERT: R 179 TRP cc_start: 0.8350 (p-90) cc_final: 0.8134 (p-90) REVERT: R 226 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7743 (mtm110) outliers start: 26 outliers final: 16 residues processed: 162 average time/residue: 0.6014 time to fit residues: 103.4571 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3432 r_free = 0.3432 target = 0.097176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085084 restraints weight = 14735.441| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.93 r_work: 0.3131 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8745 Z= 0.187 Angle : 0.587 9.348 11924 Z= 0.313 Chirality : 0.043 0.134 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.970 29.638 1236 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.68 % Allowed : 16.01 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.25), residues: 1133 helix: 1.07 (0.27), residues: 387 sheet: -0.08 (0.31), residues: 263 loop : -1.21 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 126 TYR 0.019 0.002 TYR R 253 PHE 0.019 0.002 PHE R 174 TRP 0.012 0.002 TRP A 244 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8743) covalent geometry : angle 0.58695 (11920) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.97235 ( 4) hydrogen bonds : bond 0.04106 ( 416) hydrogen bonds : angle 4.85516 ( 1200) *********************** 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: 31 poor density : 151 time to evaluate : 0.376 Fit side-chains REVERT: B 17 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8421 (tp-100) REVERT: B 57 LYS cc_start: 0.9079 (ptpt) cc_final: 0.8709 (mtmt) REVERT: B 59 TYR cc_start: 0.8802 (m-80) cc_final: 0.8448 (m-80) REVERT: R 226 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7690 (mtm110) outliers start: 31 outliers final: 15 residues processed: 162 average time/residue: 0.6544 time to fit residues: 112.1514 Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN 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 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 108 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 46 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.0010 chunk 96 optimal weight: 1.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 32 GLN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 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 = 0.3467 r_free = 0.3467 target = 0.099276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087152 restraints weight = 14609.620| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.93 r_work: 0.3172 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8745 Z= 0.115 Angle : 0.541 9.182 11924 Z= 0.287 Chirality : 0.042 0.155 1374 Planarity : 0.004 0.048 1517 Dihedral : 4.559 26.773 1236 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.44 % Allowed : 17.67 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1133 helix: 1.39 (0.28), residues: 390 sheet: 0.14 (0.31), residues: 276 loop : -1.10 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 249 TYR 0.019 0.001 TYR R 253 PHE 0.030 0.001 PHE R 28 TRP 0.042 0.002 TRP R 179 HIS 0.003 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8743) covalent geometry : angle 0.54130 (11920) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.79509 ( 4) hydrogen bonds : bond 0.03428 ( 416) hydrogen bonds : angle 4.59690 ( 1200) *********************** 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 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.350 Fit side-chains REVERT: B 57 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8712 (mtmp) REVERT: B 59 TYR cc_start: 0.8722 (m-80) cc_final: 0.8427 (m-80) REVERT: B 239 ASN cc_start: 0.8913 (m110) cc_final: 0.8685 (m110) REVERT: B 243 THR cc_start: 0.8829 (p) cc_final: 0.8566 (p) REVERT: S 183 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: R 226 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6443 (mmm160) outliers start: 29 outliers final: 12 residues processed: 165 average time/residue: 0.5837 time to fit residues: 102.5075 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN 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 234 PHE 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 S residue 183 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 46 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086906 restraints weight = 14871.360| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.95 r_work: 0.3162 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8745 Z= 0.133 Angle : 0.560 9.540 11924 Z= 0.295 Chirality : 0.042 0.134 1374 Planarity : 0.004 0.049 1517 Dihedral : 4.540 27.000 1236 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.44 % Allowed : 18.74 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1133 helix: 1.44 (0.27), residues: 394 sheet: 0.15 (0.31), residues: 270 loop : -1.09 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 126 TYR 0.016 0.001 TYR R 104 PHE 0.017 0.002 PHE R 21 TRP 0.042 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8743) covalent geometry : angle 0.56012 (11920) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.91797 ( 4) hydrogen bonds : bond 0.03517 ( 416) hydrogen bonds : angle 4.59690 ( 1200) *********************** 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 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.355 Fit side-chains REVERT: B 57 LYS cc_start: 0.9065 (ptpt) cc_final: 0.8710 (mtmp) REVERT: B 59 TYR cc_start: 0.8704 (m-80) cc_final: 0.8418 (m-80) REVERT: S 183 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: R 226 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.6445 (mmm160) outliers start: 29 outliers final: 18 residues processed: 171 average time/residue: 0.5557 time to fit residues: 101.2207 Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 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 193 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 237 VAL 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 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085616 restraints weight = 14714.136| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.93 r_work: 0.3145 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8745 Z= 0.170 Angle : 0.584 9.794 11924 Z= 0.309 Chirality : 0.043 0.139 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.700 27.561 1236 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.97 % Allowed : 20.28 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.25), residues: 1133 helix: 1.36 (0.27), residues: 394 sheet: 0.12 (0.31), residues: 268 loop : -1.13 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 126 TYR 0.017 0.002 TYR R 270 PHE 0.017 0.002 PHE R 171 TRP 0.052 0.002 TRP R 179 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8743) covalent geometry : angle 0.58348 (11920) SS BOND : bond 0.00166 ( 2) SS BOND : angle 1.04750 ( 4) hydrogen bonds : bond 0.03808 ( 416) hydrogen bonds : angle 4.69373 ( 1200) *********************** 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 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.318 Fit side-chains REVERT: B 17 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8527 (tp40) REVERT: B 57 LYS cc_start: 0.9079 (ptpt) cc_final: 0.8729 (mtmp) REVERT: B 59 TYR cc_start: 0.8752 (m-80) cc_final: 0.8460 (m-80) REVERT: S 183 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: R 152 SER cc_start: 0.8461 (p) cc_final: 0.8260 (t) REVERT: R 226 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7634 (mtm110) outliers start: 25 outliers final: 18 residues processed: 168 average time/residue: 0.5700 time to fit residues: 101.9718 Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 24 ASN 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 193 LEU Chi-restraints excluded: chain R residue 226 ARG Chi-restraints excluded: chain R residue 237 VAL 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 63 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 46 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 237 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088152 restraints weight = 14503.256| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.91 r_work: 0.3178 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8745 Z= 0.123 Angle : 0.563 10.539 11924 Z= 0.296 Chirality : 0.042 0.153 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.540 27.087 1236 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.85 % Allowed : 20.40 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1133 helix: 1.56 (0.28), residues: 387 sheet: 0.16 (0.30), residues: 283 loop : -1.04 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 126 TYR 0.021 0.001 TYR R 270 PHE 0.021 0.001 PHE R 21 TRP 0.060 0.002 TRP R 179 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8743) covalent geometry : angle 0.56309 (11920) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.79882 ( 4) hydrogen bonds : bond 0.03438 ( 416) hydrogen bonds : angle 4.60217 ( 1200) *********************** 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 187 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.321 Fit side-chains REVERT: B 17 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 59 TYR cc_start: 0.8696 (m-80) cc_final: 0.8457 (m-80) REVERT: S 183 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: R 226 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6487 (mmm160) outliers start: 24 outliers final: 17 residues processed: 172 average time/residue: 0.5565 time to fit residues: 102.1323 Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 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 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 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 105 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087923 restraints weight = 14493.995| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.91 r_work: 0.3175 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8745 Z= 0.131 Angle : 0.576 13.497 11924 Z= 0.301 Chirality : 0.042 0.132 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.529 26.882 1236 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.37 % Allowed : 22.42 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.25), residues: 1133 helix: 1.61 (0.27), residues: 387 sheet: 0.13 (0.31), residues: 277 loop : -1.02 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 126 TYR 0.016 0.001 TYR R 104 PHE 0.032 0.002 PHE R 99 TRP 0.059 0.002 TRP R 179 HIS 0.008 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8743) covalent geometry : angle 0.57616 (11920) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.87225 ( 4) hydrogen bonds : bond 0.03468 ( 416) hydrogen bonds : angle 4.57984 ( 1200) ********************** 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 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.375 Fit side-chains REVERT: B 59 TYR cc_start: 0.8697 (m-80) cc_final: 0.8476 (m-80) REVERT: R 226 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.6532 (mmm160) outliers start: 20 outliers final: 15 residues processed: 168 average time/residue: 0.6057 time to fit residues: 108.4003 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 101 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 237 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 24 ASN S 186 GLN R 82 HIS R 167 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088135 restraints weight = 14425.574| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8745 Z= 0.130 Angle : 0.578 14.731 11924 Z= 0.302 Chirality : 0.042 0.149 1374 Planarity : 0.004 0.050 1517 Dihedral : 4.555 27.677 1236 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.25 % Allowed : 22.42 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.25), residues: 1133 helix: 1.66 (0.28), residues: 383 sheet: 0.14 (0.31), residues: 277 loop : -1.05 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.018 0.001 TYR R 270 PHE 0.030 0.002 PHE R 99 TRP 0.068 0.002 TRP R 179 HIS 0.010 0.001 HIS R 157 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8743) covalent geometry : angle 0.57785 (11920) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.72487 ( 4) hydrogen bonds : bond 0.03436 ( 416) hydrogen bonds : angle 4.54619 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3727.90 seconds wall clock time: 64 minutes 10.72 seconds (3850.72 seconds total)