Starting phenix.real_space_refine on Wed Sep 17 15:06:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf9_60053/09_2025/8zf9_60053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf9_60053/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zf9_60053/09_2025/8zf9_60053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf9_60053/09_2025/8zf9_60053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zf9_60053/09_2025/8zf9_60053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf9_60053/09_2025/8zf9_60053.map" } resolution = 2.56 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= 0.002 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): 0.01s 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: 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: {'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1} 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: {'GLU:plan': 6, 'ASP:plan': 4, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 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, 'ARG:plan': 2, 'GLU:plan': 4, '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: {'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 146 Time building chain proxies: 2.48, per 1000 atoms: 0.27 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: 0.91 Conformation dependent library (CDL) restraints added in 393.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.35 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: 1.52 Time building geometry restraints manager: 1.19 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- 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 9542 Z= 0.517 Angle : 0.887 23.133 13021 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 : 9.84 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 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: -0.94 (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 ARG 0.006 0.001 ARG B 256 TYR 0.040 0.002 TYR B 59 PHE 0.027 0.002 PHE B 151 TRP 0.018 0.002 TRP A 244 HIS 0.015 0.002 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00963 ( 9541) covalent geometry : angle 0.88698 (13019) SS BOND : bond 0.00513 ( 1) SS BOND : angle 0.87106 ( 2) hydrogen bonds : bond 0.19416 ( 435) hydrogen bonds : angle 7.68074 ( 1230) *********************** 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 : 0.364 Fit side-chains REVERT: B 30 LEU cc_start: 0.7314 (tp) cc_final: 0.7106 (tp) 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: 0.5779 time to fit residues: 112.6030 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 : 0.418 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 B 340 ASN G 44 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095548 restraints weight = 15069.352| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.80 r_work: 0.3319 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9542 Z= 0.237 Angle : 0.671 13.521 13021 Z= 0.353 Chirality : 0.047 0.146 1508 Planarity : 0.004 0.042 1660 Dihedral : 5.267 22.755 1368 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.01 % Allowed : 9.51 % 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 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 (0.24), residues: 1247 helix: 0.68 (0.27), residues: 381 sheet: -0.32 (0.29), residues: 315 loop : -0.90 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.027 0.002 TYR R 270 PHE 0.021 0.002 PHE B 151 TRP 0.020 0.002 TRP B 169 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 9541) covalent geometry : angle 0.67118 (13019) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.99282 ( 2) hydrogen bonds : bond 0.04929 ( 435) hydrogen bonds : angle 5.29748 ( 1230) *********************** 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 178 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.360 Fit side-chains REVERT: A 233 ASP cc_start: 0.8379 (p0) cc_final: 0.8106 (p0) REVERT: B 239 ASN cc_start: 0.8820 (m110) cc_final: 0.8558 (m110) REVERT: B 258 ASP cc_start: 0.7872 (t0) cc_final: 0.7649 (t0) REVERT: B 325 MET cc_start: 0.8852 (tpp) cc_final: 0.8351 (tpt) REVERT: S 192 MET cc_start: 0.7961 (ttp) cc_final: 0.7741 (ttp) REVERT: R 263 GLU cc_start: 0.8271 (mp0) cc_final: 0.8052 (mm-30) REVERT: R 274 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8301 (tm) outliers start: 18 outliers final: 6 residues processed: 163 average time/residue: 0.6062 time to fit residues: 105.5251 Evaluate side-chains 157 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097857 restraints weight = 15105.647| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.84 r_work: 0.3378 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9542 Z= 0.132 Angle : 0.566 11.256 13021 Z= 0.297 Chirality : 0.043 0.143 1508 Planarity : 0.004 0.035 1660 Dihedral : 4.680 21.125 1365 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.79 % Allowed : 13.65 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.20 (0.24), residues: 1247 helix: 1.07 (0.27), residues: 381 sheet: -0.36 (0.29), residues: 307 loop : -0.78 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.025 0.001 TYR R 270 PHE 0.015 0.001 PHE B 151 TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9541) covalent geometry : angle 0.56600 (13019) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.56876 ( 2) hydrogen bonds : bond 0.03883 ( 435) hydrogen bonds : angle 4.79552 ( 1230) *********************** 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 173 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8202 (p0) cc_final: 0.7935 (p0) REVERT: B 101 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8473 (ptt) REVERT: B 239 ASN cc_start: 0.8800 (m110) cc_final: 0.8407 (m110) REVERT: B 258 ASP cc_start: 0.7897 (t0) cc_final: 0.7648 (t0) REVERT: B 304 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7452 (ttp-170) outliers start: 16 outliers final: 5 residues processed: 162 average time/residue: 0.5185 time to fit residues: 90.2575 Evaluate side-chains 155 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain R residue 167 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 0.0770 chunk 78 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 75 GLN B 220 GLN S 186 GLN R 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097841 restraints weight = 15224.909| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.84 r_work: 0.3379 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9542 Z= 0.130 Angle : 0.552 11.052 13021 Z= 0.290 Chirality : 0.042 0.144 1508 Planarity : 0.004 0.038 1660 Dihedral : 4.524 20.725 1364 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.91 % Allowed : 15.10 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.24), residues: 1247 helix: 1.31 (0.28), residues: 375 sheet: -0.39 (0.29), residues: 304 loop : -0.69 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.024 0.001 TYR R 78 PHE 0.019 0.001 PHE R 28 TRP 0.014 0.001 TRP A 244 HIS 0.006 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9541) covalent geometry : angle 0.55153 (13019) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.45289 ( 2) hydrogen bonds : bond 0.03646 ( 435) hydrogen bonds : angle 4.64729 ( 1230) *********************** 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 177 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8973 (ttp) cc_final: 0.8714 (ttp) REVERT: A 233 ASP cc_start: 0.8132 (p0) cc_final: 0.7890 (p0) REVERT: B 239 ASN cc_start: 0.8750 (m110) cc_final: 0.8415 (m110) REVERT: B 258 ASP cc_start: 0.7902 (t0) cc_final: 0.7634 (t0) REVERT: B 304 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7381 (ttp-170) REVERT: S 85 SER cc_start: 0.8967 (m) cc_final: 0.8699 (p) REVERT: S 140 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7966 (mtm) outliers start: 26 outliers final: 10 residues processed: 162 average time/residue: 0.6023 time to fit residues: 104.0588 Evaluate side-chains 159 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR 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 140 MET Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL 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 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 47 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 75 GLN B 110 ASN B 220 GLN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.098765 restraints weight = 15306.057| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.84 r_work: 0.3394 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9542 Z= 0.116 Angle : 0.536 10.450 13021 Z= 0.281 Chirality : 0.042 0.141 1508 Planarity : 0.004 0.042 1660 Dihedral : 4.352 20.117 1364 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.24 % Allowed : 17.23 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.24), residues: 1247 helix: 1.54 (0.28), residues: 376 sheet: -0.36 (0.29), residues: 311 loop : -0.70 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.025 0.001 TYR R 78 PHE 0.014 0.001 PHE R 99 TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9541) covalent geometry : angle 0.53601 (13019) SS BOND : bond 0.00396 ( 1) SS BOND : angle 0.90533 ( 2) hydrogen bonds : bond 0.03392 ( 435) hydrogen bonds : angle 4.50365 ( 1230) *********************** 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 171 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8950 (ttp) cc_final: 0.8705 (ttp) REVERT: B 239 ASN cc_start: 0.8711 (m110) cc_final: 0.8401 (m110) REVERT: B 258 ASP cc_start: 0.7887 (t0) cc_final: 0.7593 (t0) REVERT: S 85 SER cc_start: 0.8951 (m) cc_final: 0.8735 (p) REVERT: R 176 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.6894 (ppp) REVERT: R 204 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7879 (ttp-170) outliers start: 20 outliers final: 7 residues processed: 162 average time/residue: 0.5679 time to fit residues: 98.7590 Evaluate side-chains 157 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 204 ARG Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 114 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.110779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098475 restraints weight = 15303.843| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.85 r_work: 0.3389 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9542 Z= 0.127 Angle : 0.546 10.704 13021 Z= 0.285 Chirality : 0.042 0.139 1508 Planarity : 0.004 0.045 1660 Dihedral : 4.314 19.628 1364 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.57 % Allowed : 17.90 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.17 (0.25), residues: 1247 helix: 1.58 (0.28), residues: 377 sheet: -0.21 (0.29), residues: 315 loop : -0.65 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.025 0.001 TYR R 78 PHE 0.019 0.001 PHE R 99 TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9541) covalent geometry : angle 0.54592 (13019) SS BOND : bond 0.00321 ( 1) SS BOND : angle 1.43497 ( 2) hydrogen bonds : bond 0.03450 ( 435) hydrogen bonds : angle 4.46278 ( 1230) *********************** 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 172 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.366 Fit side-chains REVERT: A 231 MET cc_start: 0.8944 (ttp) cc_final: 0.8702 (ttp) REVERT: B 239 ASN cc_start: 0.8704 (m110) cc_final: 0.8403 (m110) REVERT: B 258 ASP cc_start: 0.7886 (t0) cc_final: 0.7563 (t0) REVERT: B 280 LYS cc_start: 0.8735 (tttp) cc_final: 0.8346 (mttp) REVERT: S 85 SER cc_start: 0.8974 (m) cc_final: 0.8655 (p) REVERT: S 140 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8017 (mtm) REVERT: R 204 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7873 (ttp-170) outliers start: 23 outliers final: 12 residues processed: 161 average time/residue: 0.5839 time to fit residues: 100.6644 Evaluate side-chains 160 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 301 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 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 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095599 restraints weight = 15152.930| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.81 r_work: 0.3320 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9542 Z= 0.240 Angle : 0.638 12.970 13021 Z= 0.332 Chirality : 0.046 0.147 1508 Planarity : 0.004 0.049 1660 Dihedral : 4.806 21.444 1364 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.13 % Allowed : 18.12 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.24), residues: 1247 helix: 1.24 (0.28), residues: 379 sheet: -0.33 (0.29), residues: 316 loop : -0.73 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.028 0.002 TYR R 270 PHE 0.026 0.002 PHE R 99 TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 9541) covalent geometry : angle 0.63799 (13019) SS BOND : bond 0.00233 ( 1) SS BOND : angle 1.71436 ( 2) hydrogen bonds : bond 0.04194 ( 435) hydrogen bonds : angle 4.77015 ( 1230) *********************** 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 182 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.412 Fit side-chains REVERT: A 231 MET cc_start: 0.8974 (ttp) cc_final: 0.8720 (ttp) REVERT: B 239 ASN cc_start: 0.8760 (m110) cc_final: 0.8474 (m110) REVERT: B 258 ASP cc_start: 0.7932 (t0) cc_final: 0.7641 (t0) REVERT: S 85 SER cc_start: 0.8993 (m) cc_final: 0.8661 (p) REVERT: R 176 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7705 (ptt) outliers start: 28 outliers final: 13 residues processed: 168 average time/residue: 0.5850 time to fit residues: 105.2935 Evaluate side-chains 167 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 252 VAL 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 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.110308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098067 restraints weight = 15058.040| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.82 r_work: 0.3379 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9542 Z= 0.137 Angle : 0.566 11.070 13021 Z= 0.297 Chirality : 0.043 0.141 1508 Planarity : 0.004 0.049 1660 Dihedral : 4.471 19.703 1364 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.01 % Allowed : 20.02 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1247 helix: 1.54 (0.28), residues: 373 sheet: -0.35 (0.29), residues: 315 loop : -0.69 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.027 0.001 TYR R 78 PHE 0.026 0.002 PHE R 99 TRP 0.015 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9541) covalent geometry : angle 0.56540 (13019) SS BOND : bond 0.00411 ( 1) SS BOND : angle 1.38554 ( 2) hydrogen bonds : bond 0.03558 ( 435) hydrogen bonds : angle 4.58837 ( 1230) *********************** 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 181 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.361 Fit side-chains REVERT: A 231 MET cc_start: 0.8945 (ttp) cc_final: 0.8719 (ttp) REVERT: B 239 ASN cc_start: 0.8733 (m110) cc_final: 0.8440 (m110) REVERT: B 258 ASP cc_start: 0.7907 (t0) cc_final: 0.7597 (t0) REVERT: B 280 LYS cc_start: 0.8710 (tttp) cc_final: 0.8354 (mttp) REVERT: S 85 SER cc_start: 0.8970 (m) cc_final: 0.8656 (p) REVERT: R 127 PHE cc_start: 0.8758 (m-80) cc_final: 0.8542 (m-80) REVERT: R 176 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7139 (ppp) outliers start: 18 outliers final: 13 residues processed: 169 average time/residue: 0.5278 time to fit residues: 95.7392 Evaluate side-chains 168 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 219 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain R residue 176 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 71 optimal weight: 0.0970 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 75 GLN B 220 GLN N 31 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 = 0.3660 r_free = 0.3660 target = 0.110163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097901 restraints weight = 15085.761| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.82 r_work: 0.3377 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9542 Z= 0.147 Angle : 0.581 11.273 13021 Z= 0.302 Chirality : 0.043 0.144 1508 Planarity : 0.004 0.051 1660 Dihedral : 4.440 19.680 1364 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.57 % Allowed : 19.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.24), residues: 1247 helix: 1.54 (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 ARG 0.006 0.000 ARG B 137 TYR 0.026 0.002 TYR R 78 PHE 0.024 0.002 PHE R 99 TRP 0.015 0.001 TRP A 244 HIS 0.004 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9541) covalent geometry : angle 0.58110 (13019) SS BOND : bond 0.00388 ( 1) SS BOND : angle 1.54886 ( 2) hydrogen bonds : bond 0.03573 ( 435) hydrogen bonds : angle 4.55185 ( 1230) *********************** 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 178 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.388 Fit side-chains REVERT: A 231 MET cc_start: 0.8948 (ttp) cc_final: 0.8706 (ttp) REVERT: B 239 ASN cc_start: 0.8724 (m110) cc_final: 0.8436 (m110) REVERT: B 258 ASP cc_start: 0.7927 (t0) cc_final: 0.7612 (t0) REVERT: S 85 SER cc_start: 0.8988 (m) cc_final: 0.8666 (p) REVERT: R 176 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7758 (ptt) outliers start: 23 outliers final: 17 residues processed: 165 average time/residue: 0.6295 time to fit residues: 110.8054 Evaluate side-chains 169 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 219 ARG 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 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain R residue 176 MET 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 17 optimal weight: 0.0870 chunk 70 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.111631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099365 restraints weight = 15121.648| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.83 r_work: 0.3396 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9542 Z= 0.122 Angle : 0.560 10.690 13021 Z= 0.293 Chirality : 0.042 0.142 1508 Planarity : 0.004 0.049 1660 Dihedral : 4.322 19.432 1364 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.90 % Allowed : 21.03 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.13 (0.24), residues: 1247 helix: 1.55 (0.28), residues: 378 sheet: -0.32 (0.29), residues: 310 loop : -0.63 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 96 TYR 0.026 0.001 TYR R 78 PHE 0.023 0.001 PHE R 99 TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9541) covalent geometry : angle 0.55987 (13019) SS BOND : bond 0.00271 ( 1) SS BOND : angle 1.25996 ( 2) hydrogen bonds : bond 0.03372 ( 435) hydrogen bonds : angle 4.51760 ( 1230) ********************** 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 168 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.375 Fit side-chains REVERT: B 239 ASN cc_start: 0.8720 (m110) cc_final: 0.8482 (m110) REVERT: B 258 ASP cc_start: 0.7909 (t0) cc_final: 0.7609 (t0) REVERT: G 42 GLU cc_start: 0.7736 (pp20) cc_final: 0.7370 (pm20) REVERT: S 85 SER cc_start: 0.8973 (m) cc_final: 0.8675 (p) REVERT: R 127 PHE cc_start: 0.8737 (m-80) cc_final: 0.8511 (m-80) REVERT: R 176 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7584 (ptt) REVERT: R 290 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8893 (mp) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.5676 time to fit residues: 96.1732 Evaluate side-chains 161 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL 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 219 ARG 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 11 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain R residue 176 MET 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 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 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 = 0.3662 r_free = 0.3662 target = 0.110483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098290 restraints weight = 15052.006| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.81 r_work: 0.3382 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9542 Z= 0.150 Angle : 0.574 11.188 13021 Z= 0.301 Chirality : 0.043 0.146 1508 Planarity : 0.004 0.055 1660 Dihedral : 4.380 19.573 1364 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.24 % Allowed : 20.81 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.12 (0.24), residues: 1247 helix: 1.53 (0.27), residues: 378 sheet: -0.31 (0.29), residues: 312 loop : -0.64 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 96 TYR 0.026 0.002 TYR R 270 PHE 0.023 0.002 PHE R 99 TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9541) covalent geometry : angle 0.57429 (13019) SS BOND : bond 0.00336 ( 1) SS BOND : angle 1.30991 ( 2) hydrogen bonds : bond 0.03553 ( 435) hydrogen bonds : angle 4.55564 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.78 seconds wall clock time: 70 minutes 35.65 seconds (4235.65 seconds total)