Starting phenix.real_space_refine on Thu Mar 13 22:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf9_60053/03_2025/8zf9_60053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf9_60053/03_2025/8zf9_60053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zf9_60053/03_2025/8zf9_60053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf9_60053/03_2025/8zf9_60053.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf9_60053/03_2025/8zf9_60053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf9_60053/03_2025/8zf9_60053.cif" } resolution = 2.56 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= 0.002 sd= 0.030 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 54 5.16 5 C 5953 2.51 5 N 1609 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9330 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1847 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 84 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': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 350 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 795 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "S" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1692 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2177 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 146 Time building chain proxies: 5.99, per 1000 atoms: 0.64 Number of scatterers: 9330 At special positions: 0 Unit cell: (83.7, 132.06, 128.34, 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 54 16.00 O 1714 8.00 N 1609 7.00 C 5953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 32.8% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.836A 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: 3.532A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.283A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.392A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 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 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.031A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.814A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 50 Proline residue: R 35 - end of helix removed outlier: 3.737A pdb=" N CYS R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU R 39 " --> pdb=" O PRO R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 65 removed outlier: 4.211A pdb=" N VAL R 56 " --> pdb=" O ASN R 52 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 70 No H-bonds generated for 'chain 'R' and resid 68 through 70' Processing helix chain 'R' and resid 71 through 81 removed outlier: 3.734A pdb=" N TRP R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 122 removed outlier: 3.591A pdb=" N ILE R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 108 " --> pdb=" O TYR R 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 131 Processing helix chain 'R' and resid 132 through 151 removed outlier: 3.503A pdb=" N ASN R 151 " --> pdb=" O GLU R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.898A pdb=" N PHE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.641A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 211 Processing helix chain 'R' and resid 219 through 253 removed outlier: 3.676A pdb=" N SER R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix Processing helix chain 'R' and resid 266 through 277 Processing helix chain 'R' and resid 279 through 290 Proline residue: R 285 - end of helix removed outlier: 3.859A pdb=" N LEU R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 6.219A pdb=" N HIS A 41 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE A 232 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 43 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N VAL A 234 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU A 45 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N ALA A 253 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG A 42 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE A 255 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 44 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 257 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 46 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASP A 259 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.565A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.700A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.476A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.665A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A 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: 6.768A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.100A 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: 6.618A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.732A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.535A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.901A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.956A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.054A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 158 through 160 Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.562A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 161 through 162 removed outlier: 3.627A pdb=" N PHE R 161 " --> pdb=" O PHE R 169 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1230 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: 2.78 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 1495 1.26 - 1.40: 2538 1.40 - 1.53: 5261 1.53 - 1.67: 171 1.67 - 1.81: 76 Bond restraints: 9541 Sorted by residual: bond pdb=" C SER R 152 " pdb=" N ALA R 153 " ideal model delta sigma weight residual 1.331 1.529 -0.198 2.07e-02 2.33e+03 9.15e+01 bond pdb=" C GLY B 310 " pdb=" O GLY B 310 " ideal model delta sigma weight residual 1.235 1.126 0.108 1.35e-02 5.49e+03 6.43e+01 bond pdb=" C GLY B 306 " pdb=" O GLY B 306 " ideal model delta sigma weight residual 1.234 1.154 0.080 1.02e-02 9.61e+03 6.12e+01 bond pdb=" CA GLY B 310 " pdb=" C GLY B 310 " ideal model delta sigma weight residual 1.514 1.410 0.104 1.41e-02 5.03e+03 5.42e+01 bond pdb=" CA ASN N 31 " pdb=" C ASN N 31 " ideal model delta sigma weight residual 1.522 1.426 0.096 1.31e-02 5.83e+03 5.32e+01 ... (remaining 9536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 12963 4.63 - 9.25: 46 9.25 - 13.88: 6 13.88 - 18.51: 2 18.51 - 23.13: 2 Bond angle restraints: 13019 Sorted by residual: angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 108.56 131.69 -23.13 1.74e+00 3.30e-01 1.77e+02 angle pdb=" N ILE B 37 " pdb=" CA ILE B 37 " pdb=" C ILE B 37 " ideal model delta sigma weight residual 109.80 126.27 -16.47 1.33e+00 5.65e-01 1.53e+02 angle pdb=" C ALA B 309 " pdb=" CA ALA B 309 " pdb=" CB ALA B 309 " ideal model delta sigma weight residual 112.03 93.20 18.83 1.56e+00 4.11e-01 1.46e+02 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 119.76 128.24 -8.48 1.03e+00 9.43e-01 6.78e+01 angle pdb=" N GLU S 42 " pdb=" CA GLU S 42 " pdb=" C GLU S 42 " ideal model delta sigma weight residual 112.88 122.19 -9.31 1.29e+00 6.01e-01 5.21e+01 ... (remaining 13014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 5005 15.45 - 30.90: 427 30.90 - 46.36: 77 46.36 - 61.81: 11 61.81 - 77.26: 6 Dihedral angle restraints: 5526 sinusoidal: 1831 harmonic: 3695 Sorted by residual: dihedral pdb=" C ILE B 37 " pdb=" N ILE B 37 " pdb=" CA ILE B 37 " pdb=" CB ILE B 37 " ideal model delta harmonic sigma weight residual -122.00 -137.65 15.65 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CA ILE B 37 " pdb=" CB ILE B 37 " ideal model delta harmonic sigma weight residual 123.40 137.98 -14.58 0 2.50e+00 1.60e-01 3.40e+01 dihedral pdb=" C ASN N 31 " pdb=" N ASN N 31 " pdb=" CA ASN N 31 " pdb=" CB ASN N 31 " ideal model delta harmonic sigma weight residual -122.60 -109.08 -13.52 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 5523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1484 0.144 - 0.288: 15 0.288 - 0.432: 6 0.432 - 0.576: 2 0.576 - 0.720: 1 Chirality restraints: 1508 Sorted by residual: chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 1.71 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ASN R 166 " pdb=" N ASN R 166 " pdb=" C ASN R 166 " pdb=" CB ASN R 166 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA HIS R 167 " pdb=" N HIS R 167 " pdb=" C HIS R 167 " pdb=" CB HIS R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 1505 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 204 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C CYS B 204 " -0.053 2.00e-02 2.50e+03 pdb=" O CYS B 204 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 205 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 153 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ALA R 153 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA R 153 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 154 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 153 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO R 154 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 154 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 154 " -0.035 5.00e-02 4.00e+02 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 17 2.35 - 2.99: 4957 2.99 - 3.62: 13820 3.62 - 4.26: 21375 4.26 - 4.90: 36706 Nonbonded interactions: 76875 Sorted by model distance: nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 1.710 3.040 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 1.770 3.120 nonbonded pdb=" O ASP A 225 " pdb=" NH2 ARG R 126 " model vdw 1.990 3.120 nonbonded pdb=" OE1 GLU A 392 " pdb=" ND2 ASN R 292 " model vdw 2.073 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.096 3.040 ... (remaining 76870 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: 1.650 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.790 Find NCS groups from input model: 0.120 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.010 0.198 9541 Z= 0.628 Angle : 0.887 23.133 13019 Z= 0.519 Chirality : 0.063 0.720 1508 Planarity : 0.005 0.063 1660 Dihedral : 12.387 77.261 3139 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.45 % Allowed : 0.67 % Favored : 98.88 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 5.00 % 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: -0.94 (0.23), residues: 1247 helix: 0.17 (0.27), residues: 376 sheet: -0.64 (0.28), residues: 319 loop : -1.07 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 244 HIS 0.015 0.002 HIS R 167 PHE 0.027 0.002 PHE B 151 TYR 0.040 0.002 TYR B 59 ARG 0.006 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 1.243 Fit side-chains REVERT: B 188 MET cc_start: 0.8845 (mmm) cc_final: 0.8598 (mmp) REVERT: B 239 ASN cc_start: 0.8545 (m110) cc_final: 0.8272 (m110) REVERT: G 24 ASN cc_start: 0.6929 (m-40) cc_final: 0.6699 (m-40) outliers start: 4 outliers final: 3 residues processed: 182 average time/residue: 1.1777 time to fit residues: 231.8559 Evaluate side-chains 164 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain R residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.0070 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 88 ASN B 220 GLN B 340 ASN G 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.110325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098216 restraints weight = 15242.857| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.82 r_work: 0.3362 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9541 Z= 0.216 Angle : 0.608 11.737 13019 Z= 0.320 Chirality : 0.044 0.141 1508 Planarity : 0.004 0.040 1660 Dihedral : 4.908 21.755 1368 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.68 % Allowed : 9.84 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.31 (0.24), residues: 1247 helix: 0.92 (0.27), residues: 381 sheet: -0.36 (0.28), residues: 317 loop : -0.83 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.022 0.002 PHE R 262 TYR 0.024 0.002 TYR R 270 ARG 0.010 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.045 Fit side-chains REVERT: A 233 ASP cc_start: 0.8311 (p0) cc_final: 0.8033 (p0) REVERT: B 188 MET cc_start: 0.8952 (mmm) cc_final: 0.8557 (mmm) REVERT: B 237 ASN cc_start: 0.7546 (t0) cc_final: 0.7311 (t160) REVERT: B 239 ASN cc_start: 0.8745 (m110) cc_final: 0.8428 (m110) REVERT: B 258 ASP cc_start: 0.7934 (t0) cc_final: 0.7721 (t0) REVERT: B 304 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7501 (ttp-170) REVERT: B 325 MET cc_start: 0.8850 (tpp) cc_final: 0.8446 (tpt) REVERT: R 263 GLU cc_start: 0.8227 (mp0) cc_final: 0.7987 (mm-30) outliers start: 15 outliers final: 3 residues processed: 168 average time/residue: 1.0774 time to fit residues: 195.1285 Evaluate side-chains 151 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 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 292 ASN B 220 GLN S 186 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097136 restraints weight = 15253.380| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.85 r_work: 0.3346 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9541 Z= 0.244 Angle : 0.584 11.693 13019 Z= 0.306 Chirality : 0.043 0.144 1508 Planarity : 0.004 0.035 1660 Dihedral : 4.689 20.878 1364 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 13.65 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.17 (0.24), residues: 1247 helix: 1.09 (0.27), residues: 381 sheet: -0.34 (0.29), residues: 305 loop : -0.74 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.002 PHE B 151 TYR 0.024 0.002 TYR R 78 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.017 Fit side-chains REVERT: A 233 ASP cc_start: 0.8248 (p0) cc_final: 0.7991 (p0) REVERT: B 101 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (ptt) REVERT: B 188 MET cc_start: 0.8941 (mmm) cc_final: 0.8538 (mmm) REVERT: B 239 ASN cc_start: 0.8809 (m110) cc_final: 0.8456 (m110) REVERT: B 258 ASP cc_start: 0.7905 (t0) cc_final: 0.7650 (t0) REVERT: B 325 MET cc_start: 0.8882 (tpp) cc_final: 0.8565 (tpt) REVERT: S 34 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8233 (mmm) outliers start: 17 outliers final: 8 residues processed: 160 average time/residue: 1.1013 time to fit residues: 189.9038 Evaluate side-chains 159 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 271 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 95 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 390 GLN B 220 GLN B 237 ASN S 186 GLN R 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097687 restraints weight = 15110.295| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.83 r_work: 0.3377 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9541 Z= 0.214 Angle : 0.551 11.114 13019 Z= 0.291 Chirality : 0.042 0.143 1508 Planarity : 0.004 0.039 1660 Dihedral : 4.518 20.365 1364 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.91 % Allowed : 15.44 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.06 (0.24), residues: 1247 helix: 1.31 (0.28), residues: 375 sheet: -0.38 (0.29), residues: 309 loop : -0.69 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE R 28 TYR 0.024 0.001 TYR R 78 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.030 Fit side-chains REVERT: A 233 ASP cc_start: 0.8141 (p0) cc_final: 0.7901 (p0) REVERT: B 101 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8667 (ptt) REVERT: B 188 MET cc_start: 0.8907 (mmm) cc_final: 0.8703 (mmp) REVERT: B 239 ASN cc_start: 0.8775 (m110) cc_final: 0.8386 (m110) REVERT: B 258 ASP cc_start: 0.7934 (t0) cc_final: 0.7675 (t0) REVERT: S 34 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: S 83 MET cc_start: 0.8103 (mtm) cc_final: 0.7395 (mtm) REVERT: S 140 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8185 (mtm) REVERT: R 127 PHE cc_start: 0.8811 (m-80) cc_final: 0.8531 (m-80) outliers start: 26 outliers final: 15 residues processed: 166 average time/residue: 1.0882 time to fit residues: 194.3169 Evaluate side-chains 163 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.110718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.098473 restraints weight = 15064.368| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.83 r_work: 0.3388 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9541 Z= 0.183 Angle : 0.537 10.648 13019 Z= 0.282 Chirality : 0.042 0.141 1508 Planarity : 0.004 0.044 1660 Dihedral : 4.360 19.606 1364 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.68 % Allowed : 17.11 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.04 (0.24), residues: 1247 helix: 1.52 (0.28), residues: 376 sheet: -0.35 (0.29), residues: 311 loop : -0.72 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 99 TYR 0.025 0.001 TYR R 78 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.067 Fit side-chains REVERT: A 233 ASP cc_start: 0.8059 (p0) cc_final: 0.7811 (p0) REVERT: B 188 MET cc_start: 0.8903 (mmm) cc_final: 0.8503 (mmm) REVERT: B 239 ASN cc_start: 0.8705 (m110) cc_final: 0.8402 (m110) REVERT: B 258 ASP cc_start: 0.7932 (t0) cc_final: 0.7619 (t0) REVERT: B 280 LYS cc_start: 0.8733 (tttp) cc_final: 0.8323 (mttp) REVERT: B 304 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7398 (ttp-170) REVERT: S 34 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: S 83 MET cc_start: 0.8109 (mtm) cc_final: 0.7460 (mtm) REVERT: S 140 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: R 176 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.6910 (ppp) REVERT: R 204 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7829 (ttp-170) outliers start: 24 outliers final: 9 residues processed: 160 average time/residue: 1.1976 time to fit residues: 205.6975 Evaluate side-chains 159 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 271 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 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 390 GLN B 220 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.109897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097638 restraints weight = 15066.464| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.82 r_work: 0.3354 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9541 Z= 0.239 Angle : 0.563 11.341 13019 Z= 0.294 Chirality : 0.043 0.139 1508 Planarity : 0.004 0.047 1660 Dihedral : 4.455 19.399 1364 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 17.67 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1247 helix: 1.48 (0.28), residues: 373 sheet: -0.35 (0.29), residues: 310 loop : -0.73 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE R 28 TYR 0.025 0.002 TYR R 270 ARG 0.010 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.979 Fit side-chains REVERT: B 188 MET cc_start: 0.8905 (mmm) cc_final: 0.8501 (mmm) REVERT: B 239 ASN cc_start: 0.8737 (m110) cc_final: 0.8424 (m110) REVERT: B 258 ASP cc_start: 0.7931 (t0) cc_final: 0.7625 (t0) REVERT: S 34 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8165 (mtm) REVERT: S 140 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8258 (mtm) REVERT: R 204 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7858 (ttp-170) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 1.1324 time to fit residues: 192.0305 Evaluate side-chains 163 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 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 390 GLN B 110 ASN B 220 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097674 restraints weight = 15168.426| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.85 r_work: 0.3373 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9541 Z= 0.223 Angle : 0.560 11.120 13019 Z= 0.292 Chirality : 0.043 0.139 1508 Planarity : 0.004 0.049 1660 Dihedral : 4.410 19.316 1364 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.02 % Allowed : 17.79 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.06 (0.24), residues: 1247 helix: 1.52 (0.28), residues: 373 sheet: -0.31 (0.29), residues: 314 loop : -0.70 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.022 0.002 PHE R 99 TYR 0.025 0.001 TYR R 270 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.063 Fit side-chains REVERT: A 392 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: B 188 MET cc_start: 0.8903 (mmm) cc_final: 0.8498 (mmm) REVERT: B 234 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: B 239 ASN cc_start: 0.8721 (m110) cc_final: 0.8410 (m110) REVERT: B 258 ASP cc_start: 0.7953 (t0) cc_final: 0.7644 (t0) REVERT: S 34 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: S 140 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8276 (mtm) REVERT: R 176 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7109 (ppp) REVERT: R 204 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7891 (ttp-170) outliers start: 27 outliers final: 15 residues processed: 168 average time/residue: 1.7820 time to fit residues: 323.3944 Evaluate side-chains 171 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN S 186 GLN R 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097585 restraints weight = 15258.427| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.82 r_work: 0.3353 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9541 Z= 0.252 Angle : 0.577 11.458 13019 Z= 0.301 Chirality : 0.043 0.139 1508 Planarity : 0.004 0.050 1660 Dihedral : 4.468 19.079 1364 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.02 % Allowed : 18.90 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.05 (0.24), residues: 1247 helix: 1.52 (0.28), residues: 373 sheet: -0.33 (0.29), residues: 315 loop : -0.70 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.029 0.002 PHE R 99 TYR 0.026 0.002 TYR R 78 ARG 0.012 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.977 Fit side-chains REVERT: A 231 MET cc_start: 0.8901 (ttp) cc_final: 0.8691 (ttp) REVERT: A 392 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: B 188 MET cc_start: 0.8898 (mmm) cc_final: 0.8477 (mmm) REVERT: B 234 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: B 239 ASN cc_start: 0.8730 (m110) cc_final: 0.8438 (m110) REVERT: B 258 ASP cc_start: 0.7950 (t0) cc_final: 0.7634 (t0) REVERT: B 280 LYS cc_start: 0.8695 (tttp) cc_final: 0.8422 (mttp) REVERT: S 34 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8184 (mtm) REVERT: S 140 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8278 (mtm) REVERT: R 176 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7655 (ptt) REVERT: R 199 MET cc_start: 0.8244 (mtm) cc_final: 0.8043 (ttm) REVERT: R 204 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7879 (ttp-170) outliers start: 27 outliers final: 15 residues processed: 167 average time/residue: 1.0609 time to fit residues: 191.2693 Evaluate side-chains 167 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 271 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.110582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098273 restraints weight = 15113.879| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.83 r_work: 0.3384 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9541 Z= 0.200 Angle : 0.556 10.883 13019 Z= 0.291 Chirality : 0.042 0.140 1508 Planarity : 0.004 0.050 1660 Dihedral : 4.333 18.748 1364 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.02 % Allowed : 19.35 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.13 (0.24), residues: 1247 helix: 1.63 (0.28), residues: 373 sheet: -0.32 (0.29), residues: 314 loop : -0.68 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.027 0.001 PHE R 99 TYR 0.026 0.001 TYR R 78 ARG 0.011 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8935 (ttp) cc_final: 0.8706 (ttp) REVERT: B 188 MET cc_start: 0.8880 (mmm) cc_final: 0.8480 (mmm) REVERT: B 234 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: B 239 ASN cc_start: 0.8699 (m110) cc_final: 0.8440 (m110) REVERT: B 258 ASP cc_start: 0.7933 (t0) cc_final: 0.7626 (t0) REVERT: S 34 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8199 (mmm) REVERT: S 140 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8099 (mtm) REVERT: R 176 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7558 (ptt) REVERT: R 204 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7829 (ttp-170) outliers start: 27 outliers final: 17 residues processed: 168 average time/residue: 1.0465 time to fit residues: 189.8433 Evaluate side-chains 173 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.0470 chunk 98 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 104 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 110 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN N 31 ASN S 82 GLN S 186 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.112002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099772 restraints weight = 15265.197| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.84 r_work: 0.3405 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9541 Z= 0.171 Angle : 0.553 10.441 13019 Z= 0.287 Chirality : 0.042 0.141 1508 Planarity : 0.004 0.050 1660 Dihedral : 4.198 18.506 1364 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.80 % Allowed : 20.81 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.20 (0.25), residues: 1247 helix: 1.58 (0.27), residues: 378 sheet: -0.24 (0.29), residues: 316 loop : -0.59 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS S 35 PHE 0.028 0.001 PHE R 99 TYR 0.025 0.001 TYR R 78 ARG 0.010 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8924 (ttp) cc_final: 0.8693 (ttp) REVERT: B 188 MET cc_start: 0.8881 (mmm) cc_final: 0.8578 (mmp) REVERT: B 234 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8871 (m-80) REVERT: B 258 ASP cc_start: 0.7917 (t0) cc_final: 0.7613 (t0) REVERT: G 42 GLU cc_start: 0.7733 (pp20) cc_final: 0.7359 (pm20) REVERT: S 34 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8164 (mmm) REVERT: S 83 MET cc_start: 0.8039 (mtm) cc_final: 0.7837 (ptt) REVERT: S 140 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: R 127 PHE cc_start: 0.8714 (m-80) cc_final: 0.8493 (m-80) REVERT: R 176 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7605 (ptt) REVERT: R 204 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7850 (ttp-170) REVERT: R 290 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8898 (mp) outliers start: 25 outliers final: 14 residues processed: 166 average time/residue: 1.1005 time to fit residues: 196.9008 Evaluate side-chains 167 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 271 HIS Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN N 31 ASN S 186 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098705 restraints weight = 15176.143| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.83 r_work: 0.3372 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9541 Z= 0.217 Angle : 0.571 10.988 13019 Z= 0.297 Chirality : 0.043 0.145 1508 Planarity : 0.004 0.050 1660 Dihedral : 4.266 18.648 1364 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.46 % Allowed : 21.25 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.22 (0.25), residues: 1247 helix: 1.61 (0.28), residues: 378 sheet: -0.24 (0.29), residues: 316 loop : -0.58 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE B 151 TYR 0.026 0.002 TYR R 78 ARG 0.010 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7956.08 seconds wall clock time: 138 minutes 38.46 seconds (8318.46 seconds total)