Starting phenix.real_space_refine on Wed Feb 4 05:24:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kft_62300/02_2026/9kft_62300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kft_62300/02_2026/9kft_62300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kft_62300/02_2026/9kft_62300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kft_62300/02_2026/9kft_62300.map" model { file = "/net/cci-nas-00/data/ceres_data/9kft_62300/02_2026/9kft_62300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kft_62300/02_2026/9kft_62300.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 67 5.16 5 C 5599 2.51 5 N 1481 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1744 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2511 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 398 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2297 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 283} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "S" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1764 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.19, per 1000 atoms: 0.25 Number of scatterers: 8749 At special positions: 0 Unit cell: (87.98, 122.84, 119.52, 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 67 16.00 O 1602 8.00 N 1481 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.81 Conformation dependent library (CDL) restraints added in 338.5 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 38.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.970A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.118A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.570A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.503A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.608A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.516A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.571A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.896A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.583A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 53 Processing helix chain 'R' and resid 60 through 78 removed outlier: 4.288A pdb=" N ASN R 66 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 67 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.700A pdb=" N ARG R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 109 removed outlier: 3.603A pdb=" N CYS R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE R 100 " --> pdb=" O PHE R 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR R 103 " --> pdb=" O LYS R 99 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE R 104 " --> pdb=" O PHE R 100 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN R 108 " --> pdb=" O ILE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 129 Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 138 through 163 removed outlier: 3.952A pdb=" N ILE R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 210 Processing helix chain 'R' and resid 212 through 232 removed outlier: 3.757A pdb=" N ALA R 218 " --> pdb=" O MET R 214 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE R 224 " --> pdb=" O SER R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 267 removed outlier: 3.730A pdb=" N SER R 244 " --> pdb=" O LEU R 240 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE R 250 " --> pdb=" O VAL R 246 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 278 through 301 removed outlier: 3.990A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 315 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.709A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 188 removed outlier: 9.200A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 188 removed outlier: 9.200A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.763A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.100A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.299A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.469A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.501A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.872A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.598A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 166 through 169 removed outlier: 3.815A pdb=" N THR R 173 " --> pdb=" O GLY R 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.592A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.592A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.543A pdb=" N CYS S 159 " --> pdb=" O PHE S 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.852A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1221 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: 1.67 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2782 1.34 - 1.46: 1836 1.46 - 1.58: 4222 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 8938 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.742 0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.759 0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C PHE R 96 " pdb=" N LEU R 97 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.40e-02 5.10e+03 7.76e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.724 0.084 3.30e-02 9.18e+02 6.45e+00 bond pdb=" N PHE R 110 " pdb=" CA PHE R 110 " ideal model delta sigma weight residual 1.460 1.429 0.031 1.27e-02 6.20e+03 6.03e+00 ... (remaining 8933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11730 2.39 - 4.78: 351 4.78 - 7.17: 40 7.17 - 9.55: 8 9.55 - 11.94: 2 Bond angle restraints: 12131 Sorted by residual: angle pdb=" C GLN S 231 " pdb=" N HIS S 232 " pdb=" CA HIS S 232 " ideal model delta sigma weight residual 122.14 112.68 9.46 1.67e+00 3.59e-01 3.21e+01 angle pdb=" C CYS A 305 " pdb=" N GLN A 306 " pdb=" CA GLN A 306 " ideal model delta sigma weight residual 122.65 115.22 7.43 1.66e+00 3.63e-01 2.01e+01 angle pdb=" CB LEU R 243 " pdb=" CG LEU R 243 " pdb=" CD1 LEU R 243 " ideal model delta sigma weight residual 110.70 98.76 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C LYS R 277 " pdb=" N GLU R 278 " pdb=" CA GLU R 278 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" CA GLY B 115 " pdb=" C GLY B 115 " pdb=" N GLY B 116 " ideal model delta sigma weight residual 115.27 118.09 -2.82 7.60e-01 1.73e+00 1.37e+01 ... (remaining 12126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4768 17.89 - 35.78: 422 35.78 - 53.67: 40 53.67 - 71.56: 11 71.56 - 89.45: 7 Dihedral angle restraints: 5248 sinusoidal: 1950 harmonic: 3298 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -175.45 89.45 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CA GLN A 306 " pdb=" C GLN A 306 " pdb=" N PHE A 307 " pdb=" CA PHE A 307 " ideal model delta harmonic sigma weight residual 180.00 146.82 33.18 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA PHE R 96 " pdb=" C PHE R 96 " pdb=" N LEU R 97 " pdb=" CA LEU R 97 " ideal model delta harmonic sigma weight residual 180.00 150.22 29.78 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 975 0.054 - 0.107: 340 0.107 - 0.161: 74 0.161 - 0.215: 7 0.215 - 0.268: 4 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA GLN A 306 " pdb=" N GLN A 306 " pdb=" C GLN A 306 " pdb=" CB GLN A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1397 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.012 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR B 105 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO B 236 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS S 232 " -0.009 2.00e-02 2.50e+03 1.54e-02 3.54e+00 pdb=" CG HIS S 232 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS S 232 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS S 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS S 232 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS S 232 " -0.003 2.00e-02 2.50e+03 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 166 2.63 - 3.20: 8610 3.20 - 3.77: 13671 3.77 - 4.33: 19009 4.33 - 4.90: 32155 Nonbonded interactions: 73611 Sorted by model distance: nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.068 3.120 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.100 3.120 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.121 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.134 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.153 3.040 ... (remaining 73606 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: 2.660 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.370 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.014 0.086 8941 Z= 0.581 Angle : 0.968 11.942 12137 Z= 0.522 Chirality : 0.056 0.268 1400 Planarity : 0.005 0.057 1527 Dihedral : 13.409 84.065 3111 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.26 (0.26), residues: 1124 helix: 0.50 (0.25), residues: 395 sheet: -1.62 (0.30), residues: 283 loop : -1.38 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 160 TYR 0.041 0.003 TYR B 105 PHE 0.023 0.003 PHE B 241 TRP 0.014 0.003 TRP R 91 HIS 0.020 0.003 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.01369 ( 8938) covalent geometry : angle 0.96755 (12131) SS BOND : bond 0.00813 ( 3) SS BOND : angle 1.49828 ( 6) hydrogen bonds : bond 0.16869 ( 416) hydrogen bonds : angle 7.76109 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.349 Fit side-chains REVERT: A 252 SER cc_start: 0.9467 (t) cc_final: 0.9255 (t) REVERT: A 306 GLN cc_start: 0.8532 (mp10) cc_final: 0.8167 (mp10) REVERT: A 350 ASP cc_start: 0.8374 (t70) cc_final: 0.8112 (t0) REVERT: B 220 GLN cc_start: 0.7745 (mm110) cc_final: 0.7356 (mm110) REVERT: R 231 GLN cc_start: 0.8320 (tt0) cc_final: 0.8070 (tt0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0954 time to fit residues: 21.3738 Evaluate side-chains 151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 6 GLN B 172 GLN B 220 GLN B 340 ASN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095287 restraints weight = 12886.803| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.96 r_work: 0.3003 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8941 Z= 0.164 Angle : 0.646 8.823 12137 Z= 0.337 Chirality : 0.044 0.165 1400 Planarity : 0.004 0.043 1527 Dihedral : 5.029 24.817 1225 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 7.82 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.82 (0.26), residues: 1124 helix: 0.84 (0.26), residues: 405 sheet: -1.26 (0.31), residues: 263 loop : -1.26 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.017 0.002 TYR S 190 PHE 0.012 0.001 PHE B 292 TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8938) covalent geometry : angle 0.64549 (12131) SS BOND : bond 0.00466 ( 3) SS BOND : angle 0.82576 ( 6) hydrogen bonds : bond 0.04468 ( 416) hydrogen bonds : angle 5.51773 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8299 (t80) cc_final: 0.7850 (t80) REVERT: A 306 GLN cc_start: 0.8278 (mp10) cc_final: 0.8012 (mt0) REVERT: A 350 ASP cc_start: 0.8493 (t70) cc_final: 0.8217 (t70) REVERT: B 59 TYR cc_start: 0.8829 (m-80) cc_final: 0.8560 (m-80) REVERT: B 153 ASP cc_start: 0.7498 (m-30) cc_final: 0.7198 (m-30) REVERT: B 220 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6755 (mm110) REVERT: C 48 ASP cc_start: 0.8280 (t0) cc_final: 0.8007 (t0) REVERT: R 152 MET cc_start: 0.7804 (tpt) cc_final: 0.7560 (mmt) REVERT: R 231 GLN cc_start: 0.8564 (tt0) cc_final: 0.8304 (tt0) REVERT: S 19 LYS cc_start: 0.8591 (tppt) cc_final: 0.8341 (tppt) REVERT: S 160 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7292 (ttp80) REVERT: S 231 GLN cc_start: 0.9172 (pp30) cc_final: 0.8911 (pp30) outliers start: 8 outliers final: 5 residues processed: 179 average time/residue: 0.0860 time to fit residues: 21.0400 Evaluate side-chains 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 172 GLN B 340 ASN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 ASN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097510 restraints weight = 12850.894| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.96 r_work: 0.3046 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8941 Z= 0.135 Angle : 0.586 10.751 12137 Z= 0.304 Chirality : 0.042 0.151 1400 Planarity : 0.004 0.041 1527 Dihedral : 4.561 24.079 1225 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.41 % Allowed : 11.94 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.59 (0.26), residues: 1124 helix: 0.97 (0.26), residues: 408 sheet: -1.16 (0.31), residues: 268 loop : -1.07 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.017 0.001 TYR S 190 PHE 0.009 0.001 PHE R 24 TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8938) covalent geometry : angle 0.58581 (12131) SS BOND : bond 0.00411 ( 3) SS BOND : angle 0.75223 ( 6) hydrogen bonds : bond 0.03939 ( 416) hydrogen bonds : angle 5.03320 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8253 (tt0) cc_final: 0.8000 (mt-10) REVERT: A 302 TYR cc_start: 0.8425 (t80) cc_final: 0.7780 (t80) REVERT: A 306 GLN cc_start: 0.8294 (mp10) cc_final: 0.7848 (mt0) REVERT: A 350 ASP cc_start: 0.8551 (t70) cc_final: 0.8257 (t70) REVERT: B 153 ASP cc_start: 0.7290 (m-30) cc_final: 0.6987 (m-30) REVERT: B 289 TYR cc_start: 0.9080 (m-80) cc_final: 0.8640 (m-80) REVERT: C 48 ASP cc_start: 0.8234 (t0) cc_final: 0.7877 (t0) REVERT: R 41 VAL cc_start: 0.8338 (t) cc_final: 0.8033 (m) REVERT: R 152 MET cc_start: 0.7745 (tpt) cc_final: 0.7534 (mmt) REVERT: R 231 GLN cc_start: 0.8539 (tt0) cc_final: 0.8272 (tt0) REVERT: S 19 LYS cc_start: 0.8603 (tppt) cc_final: 0.8165 (tppt) REVERT: S 76 LYS cc_start: 0.7937 (ptpp) cc_final: 0.7591 (ptpp) REVERT: S 192 MET cc_start: 0.8660 (ttp) cc_final: 0.8340 (ttp) REVERT: S 231 GLN cc_start: 0.9161 (pp30) cc_final: 0.8863 (pp30) REVERT: S 244 LYS cc_start: 0.8482 (tttp) cc_final: 0.8256 (tptm) outliers start: 13 outliers final: 8 residues processed: 182 average time/residue: 0.0783 time to fit residues: 19.8115 Evaluate side-chains 171 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 172 GLN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098530 restraints weight = 12956.541| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.13 r_work: 0.3042 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 0.037 8941 Z= 0.136 Angle : 0.578 11.094 12137 Z= 0.298 Chirality : 0.042 0.147 1400 Planarity : 0.004 0.041 1527 Dihedral : 4.459 22.873 1225 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.06 % Allowed : 14.12 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.35 (0.26), residues: 1124 helix: 1.13 (0.26), residues: 406 sheet: -0.86 (0.31), residues: 272 loop : -1.01 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.017 0.001 TYR S 190 PHE 0.009 0.001 PHE R 110 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8938) covalent geometry : angle 0.57831 (12131) SS BOND : bond 0.00453 ( 3) SS BOND : angle 0.83696 ( 6) hydrogen bonds : bond 0.03788 ( 416) hydrogen bonds : angle 4.83880 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8254 (tt0) cc_final: 0.7975 (mt-10) REVERT: A 302 TYR cc_start: 0.8453 (t80) cc_final: 0.7618 (t80) REVERT: A 306 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: A 350 ASP cc_start: 0.8570 (t70) cc_final: 0.8293 (t70) REVERT: B 153 ASP cc_start: 0.7266 (m-30) cc_final: 0.6976 (m-30) REVERT: B 277 SER cc_start: 0.8715 (p) cc_final: 0.8365 (p) REVERT: B 289 TYR cc_start: 0.9102 (m-80) cc_final: 0.8630 (m-80) REVERT: C 48 ASP cc_start: 0.8245 (t0) cc_final: 0.7933 (t0) REVERT: R 152 MET cc_start: 0.7781 (tpt) cc_final: 0.7575 (mmt) REVERT: R 231 GLN cc_start: 0.8523 (tt0) cc_final: 0.8236 (tt0) REVERT: S 2 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7848 (p) REVERT: S 19 LYS cc_start: 0.8878 (tppt) cc_final: 0.8677 (tppt) REVERT: S 76 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7610 (ptpp) REVERT: S 192 MET cc_start: 0.8672 (ttp) cc_final: 0.8366 (ttp) REVERT: S 226 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7959 (m) REVERT: S 231 GLN cc_start: 0.9151 (pp30) cc_final: 0.8814 (pp30) REVERT: S 244 LYS cc_start: 0.8444 (tttp) cc_final: 0.8193 (tptm) outliers start: 19 outliers final: 10 residues processed: 183 average time/residue: 0.0741 time to fit residues: 19.2899 Evaluate side-chains 176 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 24 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 0.0270 chunk 87 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 172 GLN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100063 restraints weight = 12774.462| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.89 r_work: 0.3098 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8941 Z= 0.108 Angle : 0.560 11.795 12137 Z= 0.286 Chirality : 0.042 0.156 1400 Planarity : 0.004 0.038 1527 Dihedral : 4.307 25.963 1225 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.71 % Allowed : 15.53 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.22 (0.26), residues: 1124 helix: 1.22 (0.27), residues: 407 sheet: -0.68 (0.32), residues: 267 loop : -1.00 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 160 TYR 0.014 0.001 TYR R 30 PHE 0.009 0.001 PHE B 253 TRP 0.014 0.001 TRP B 339 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8938) covalent geometry : angle 0.55965 (12131) SS BOND : bond 0.00354 ( 3) SS BOND : angle 0.73991 ( 6) hydrogen bonds : bond 0.03512 ( 416) hydrogen bonds : angle 4.63173 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8092 (tt0) cc_final: 0.7820 (mt-10) REVERT: A 302 TYR cc_start: 0.8443 (t80) cc_final: 0.7669 (t80) REVERT: A 306 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: A 350 ASP cc_start: 0.8574 (t70) cc_final: 0.8286 (t70) REVERT: B 153 ASP cc_start: 0.7151 (m-30) cc_final: 0.6827 (m-30) REVERT: B 220 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7213 (mm110) REVERT: B 277 SER cc_start: 0.8673 (p) cc_final: 0.8327 (p) REVERT: B 289 TYR cc_start: 0.9045 (m-80) cc_final: 0.8573 (m-80) REVERT: C 32 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8869 (ttpp) REVERT: C 48 ASP cc_start: 0.8236 (t0) cc_final: 0.7914 (t0) REVERT: S 2 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7872 (p) REVERT: S 76 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7537 (ptpp) REVERT: S 87 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8175 (mtm-85) REVERT: S 226 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7977 (m) REVERT: S 231 GLN cc_start: 0.9125 (pp30) cc_final: 0.8786 (pp30) REVERT: S 244 LYS cc_start: 0.8427 (tttp) cc_final: 0.8196 (tptm) outliers start: 25 outliers final: 15 residues processed: 185 average time/residue: 0.0740 time to fit residues: 19.5020 Evaluate side-chains 183 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 24 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099268 restraints weight = 12869.169| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.98 r_work: 0.3070 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8941 Z= 0.132 Angle : 0.580 11.554 12137 Z= 0.295 Chirality : 0.043 0.163 1400 Planarity : 0.004 0.039 1527 Dihedral : 4.316 24.594 1225 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.71 % Allowed : 16.72 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.15 (0.26), residues: 1124 helix: 1.27 (0.26), residues: 406 sheet: -0.57 (0.31), residues: 283 loop : -1.00 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.016 0.001 TYR S 190 PHE 0.009 0.001 PHE S 27 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8938) covalent geometry : angle 0.58001 (12131) SS BOND : bond 0.00497 ( 3) SS BOND : angle 0.93454 ( 6) hydrogen bonds : bond 0.03626 ( 416) hydrogen bonds : angle 4.65798 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8145 (tt0) cc_final: 0.7850 (mt-10) REVERT: A 302 TYR cc_start: 0.8481 (t80) cc_final: 0.7766 (t80) REVERT: A 306 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: A 308 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 313 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7640 (ptp90) REVERT: A 350 ASP cc_start: 0.8605 (t70) cc_final: 0.8312 (t70) REVERT: B 153 ASP cc_start: 0.7236 (m-30) cc_final: 0.6900 (m-30) REVERT: B 220 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7288 (mm110) REVERT: B 277 SER cc_start: 0.8674 (p) cc_final: 0.8304 (p) REVERT: B 289 TYR cc_start: 0.9011 (m-80) cc_final: 0.8463 (m-80) REVERT: B 338 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8270 (mm) REVERT: C 32 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8801 (ttpp) REVERT: C 48 ASP cc_start: 0.8277 (t0) cc_final: 0.7984 (t0) REVERT: S 2 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7900 (p) REVERT: S 18 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7780 (tpp80) REVERT: S 76 LYS cc_start: 0.7880 (ptpp) cc_final: 0.7537 (ptpp) REVERT: S 163 LYS cc_start: 0.7645 (tttt) cc_final: 0.7438 (tttt) REVERT: S 226 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8036 (m) REVERT: L 2 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8349 (tt) outliers start: 25 outliers final: 18 residues processed: 181 average time/residue: 0.0789 time to fit residues: 20.2587 Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 24 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100459 restraints weight = 12873.116| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.00 r_work: 0.3084 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8941 Z= 0.120 Angle : 0.568 10.700 12137 Z= 0.290 Chirality : 0.042 0.162 1400 Planarity : 0.004 0.038 1527 Dihedral : 4.289 24.827 1225 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.04 % Allowed : 16.94 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.10 (0.26), residues: 1124 helix: 1.32 (0.26), residues: 408 sheet: -0.54 (0.31), residues: 274 loop : -0.99 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.015 0.001 TYR S 190 PHE 0.009 0.001 PHE B 253 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8938) covalent geometry : angle 0.56758 (12131) SS BOND : bond 0.00427 ( 3) SS BOND : angle 0.85738 ( 6) hydrogen bonds : bond 0.03500 ( 416) hydrogen bonds : angle 4.58869 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8065 (tt0) cc_final: 0.7824 (mt-10) REVERT: A 302 TYR cc_start: 0.8460 (t80) cc_final: 0.7777 (t80) REVERT: A 306 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: A 313 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7662 (ptp90) REVERT: A 350 ASP cc_start: 0.8598 (t70) cc_final: 0.8299 (t70) REVERT: B 153 ASP cc_start: 0.7176 (m-30) cc_final: 0.6852 (m-30) REVERT: B 234 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 277 SER cc_start: 0.8702 (p) cc_final: 0.8320 (p) REVERT: B 289 TYR cc_start: 0.9012 (m-80) cc_final: 0.8449 (m-80) REVERT: B 338 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8292 (mm) REVERT: C 32 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8780 (ttpp) REVERT: C 48 ASP cc_start: 0.8268 (t0) cc_final: 0.7991 (t0) REVERT: S 2 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (p) REVERT: S 18 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7851 (tpp80) REVERT: S 19 LYS cc_start: 0.8561 (tppt) cc_final: 0.8319 (tppt) REVERT: S 76 LYS cc_start: 0.7892 (ptpp) cc_final: 0.7546 (ptpp) REVERT: S 140 MET cc_start: 0.8585 (mmm) cc_final: 0.8213 (mmm) REVERT: S 226 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8069 (m) REVERT: S 231 GLN cc_start: 0.9102 (pp30) cc_final: 0.8754 (pp30) REVERT: L 2 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8334 (tt) outliers start: 28 outliers final: 19 residues processed: 183 average time/residue: 0.0785 time to fit residues: 20.3914 Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 24 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098569 restraints weight = 12784.489| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.12 r_work: 0.3047 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8941 Z= 0.150 Angle : 0.596 12.091 12137 Z= 0.303 Chirality : 0.043 0.174 1400 Planarity : 0.004 0.039 1527 Dihedral : 4.378 27.693 1225 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.15 % Allowed : 16.94 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.07 (0.26), residues: 1124 helix: 1.33 (0.26), residues: 408 sheet: -0.45 (0.31), residues: 276 loop : -1.03 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.016 0.001 TYR S 190 PHE 0.010 0.001 PHE S 27 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8938) covalent geometry : angle 0.59620 (12131) SS BOND : bond 0.00450 ( 3) SS BOND : angle 0.88597 ( 6) hydrogen bonds : bond 0.03648 ( 416) hydrogen bonds : angle 4.67533 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8162 (tt0) cc_final: 0.7849 (mt-10) REVERT: A 302 TYR cc_start: 0.8479 (t80) cc_final: 0.7818 (t80) REVERT: A 306 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: A 313 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7725 (ptp90) REVERT: A 350 ASP cc_start: 0.8610 (t70) cc_final: 0.8308 (t70) REVERT: B 153 ASP cc_start: 0.7308 (m-30) cc_final: 0.6975 (m-30) REVERT: B 234 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: B 277 SER cc_start: 0.8720 (p) cc_final: 0.8336 (p) REVERT: B 289 TYR cc_start: 0.9024 (m-80) cc_final: 0.8498 (m-80) REVERT: B 338 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8264 (mm) REVERT: C 32 LYS cc_start: 0.9115 (ptmm) cc_final: 0.8777 (ttpp) REVERT: C 48 ASP cc_start: 0.8297 (t0) cc_final: 0.8040 (t0) REVERT: S 2 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7932 (p) REVERT: S 18 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7818 (tpp80) REVERT: S 76 LYS cc_start: 0.7881 (ptpp) cc_final: 0.7536 (ptpp) REVERT: S 226 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8053 (m) REVERT: S 231 GLN cc_start: 0.9108 (pp30) cc_final: 0.8764 (pp30) REVERT: L 2 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8414 (tt) outliers start: 29 outliers final: 19 residues processed: 177 average time/residue: 0.0801 time to fit residues: 19.7737 Evaluate side-chains 182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 24 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100807 restraints weight = 12747.471| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.95 r_work: 0.3090 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8941 Z= 0.119 Angle : 0.587 11.340 12137 Z= 0.297 Chirality : 0.042 0.159 1400 Planarity : 0.004 0.037 1527 Dihedral : 4.285 28.488 1225 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.82 % Allowed : 17.81 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.05 (0.26), residues: 1124 helix: 1.39 (0.26), residues: 407 sheet: -0.40 (0.31), residues: 275 loop : -1.08 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.015 0.001 TYR S 190 PHE 0.031 0.001 PHE R 96 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8938) covalent geometry : angle 0.58696 (12131) SS BOND : bond 0.00427 ( 3) SS BOND : angle 0.82795 ( 6) hydrogen bonds : bond 0.03436 ( 416) hydrogen bonds : angle 4.60942 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8048 (tt0) cc_final: 0.7804 (mt-10) REVERT: A 302 TYR cc_start: 0.8468 (t80) cc_final: 0.7827 (t80) REVERT: A 306 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: A 313 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7664 (ptp90) REVERT: A 350 ASP cc_start: 0.8608 (t70) cc_final: 0.8315 (t70) REVERT: B 153 ASP cc_start: 0.7140 (m-30) cc_final: 0.6797 (m-30) REVERT: B 234 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: B 277 SER cc_start: 0.8733 (p) cc_final: 0.8322 (p) REVERT: B 289 TYR cc_start: 0.8983 (m-80) cc_final: 0.8411 (m-80) REVERT: B 338 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8307 (mm) REVERT: C 32 LYS cc_start: 0.9108 (ptmm) cc_final: 0.8773 (ttpp) REVERT: C 48 ASP cc_start: 0.8308 (t0) cc_final: 0.8054 (t0) REVERT: S 2 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7916 (p) REVERT: S 18 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7836 (tpp80) REVERT: S 19 LYS cc_start: 0.8579 (tppt) cc_final: 0.8308 (tppt) REVERT: S 76 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7496 (ptpp) REVERT: S 226 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8091 (m) REVERT: S 231 GLN cc_start: 0.9103 (pp30) cc_final: 0.8759 (pp30) REVERT: L 2 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8394 (tt) outliers start: 26 outliers final: 18 residues processed: 179 average time/residue: 0.0794 time to fit residues: 19.7360 Evaluate side-chains 184 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098457 restraints weight = 12779.042| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.98 r_work: 0.3059 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8941 Z= 0.150 Angle : 0.609 11.347 12137 Z= 0.310 Chirality : 0.043 0.183 1400 Planarity : 0.004 0.039 1527 Dihedral : 4.349 27.898 1225 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.82 % Allowed : 18.24 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.03 (0.26), residues: 1124 helix: 1.42 (0.26), residues: 403 sheet: -0.42 (0.31), residues: 274 loop : -1.04 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.016 0.001 TYR S 190 PHE 0.009 0.001 PHE S 27 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8938) covalent geometry : angle 0.60871 (12131) SS BOND : bond 0.00434 ( 3) SS BOND : angle 0.82096 ( 6) hydrogen bonds : bond 0.03609 ( 416) hydrogen bonds : angle 4.64393 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: A 186 GLU cc_start: 0.8124 (tt0) cc_final: 0.7843 (mt-10) REVERT: A 302 TYR cc_start: 0.8496 (t80) cc_final: 0.7863 (t80) REVERT: A 306 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: A 308 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 313 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7743 (ptp90) REVERT: A 350 ASP cc_start: 0.8599 (t70) cc_final: 0.8300 (t70) REVERT: B 153 ASP cc_start: 0.7298 (m-30) cc_final: 0.6964 (m-30) REVERT: B 234 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: B 277 SER cc_start: 0.8712 (p) cc_final: 0.8332 (p) REVERT: B 289 TYR cc_start: 0.9024 (m-80) cc_final: 0.8417 (m-80) REVERT: B 338 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8276 (mm) REVERT: C 21 MET cc_start: 0.8518 (mtm) cc_final: 0.8297 (mpp) REVERT: C 48 ASP cc_start: 0.8332 (t0) cc_final: 0.8102 (t0) REVERT: S 2 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (p) REVERT: S 18 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7832 (tpp80) REVERT: S 19 LYS cc_start: 0.8630 (tppt) cc_final: 0.8375 (tppt) REVERT: S 76 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7526 (ptpp) REVERT: S 226 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8086 (m) REVERT: S 231 GLN cc_start: 0.9085 (pp30) cc_final: 0.8752 (pp30) REVERT: L 2 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8426 (tt) outliers start: 26 outliers final: 17 residues processed: 169 average time/residue: 0.0796 time to fit residues: 18.5250 Evaluate side-chains 178 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 PHE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain R residue 312 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.0000 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 0.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 172 GLN ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100360 restraints weight = 12642.111| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.89 r_work: 0.3101 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.119 Angle : 0.591 11.139 12137 Z= 0.300 Chirality : 0.042 0.170 1400 Planarity : 0.004 0.037 1527 Dihedral : 4.265 32.318 1225 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.71 % Allowed : 18.78 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: -0.01 (0.26), residues: 1124 helix: 1.45 (0.26), residues: 407 sheet: -0.41 (0.31), residues: 280 loop : -1.06 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 160 TYR 0.015 0.001 TYR S 190 PHE 0.008 0.001 PHE B 253 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8938) covalent geometry : angle 0.59129 (12131) SS BOND : bond 0.00407 ( 3) SS BOND : angle 0.75651 ( 6) hydrogen bonds : bond 0.03414 ( 416) hydrogen bonds : angle 4.58552 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.08 seconds wall clock time: 35 minutes 36.61 seconds (2136.61 seconds total)