Starting phenix.real_space_refine on Sat Aug 23 02:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxx_38764/08_2025/8xxx_38764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxx_38764/08_2025/8xxx_38764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xxx_38764/08_2025/8xxx_38764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxx_38764/08_2025/8xxx_38764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xxx_38764/08_2025/8xxx_38764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxx_38764/08_2025/8xxx_38764.map" } resolution = 3.17 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= -0.029 sd= 0.981 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 63 5.16 5 C 5786 2.51 5 N 1554 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9083 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 414 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 59} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2308 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1660 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 383 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 1.97, per 1000 atoms: 0.22 Number of scatterers: 9083 At special positions: 0 Unit cell: (89.225, 121.388, 151.475, 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 63 16.00 O 1680 8.00 N 1554 7.00 C 5786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 12 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 54 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.01 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 223.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 36.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'R' and resid 44 through 76 removed outlier: 3.544A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.681A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG R 159 " --> pdb=" O THR R 156 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 183 Proline residue: R 179 - end of helix Processing helix chain 'R' and resid 203 through 212 removed outlier: 3.576A pdb=" N TRP R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.628A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.901A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.536A pdb=" N THR R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 305 removed outlier: 3.722A pdb=" N ASP R 297 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R 305 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 removed outlier: 3.600A pdb=" N ARG R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.517A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.958A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.554A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.623A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.691A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.875A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 4.018A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 26 through 32 removed outlier: 4.504A pdb=" N VAL D 43 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 185 through 187 removed outlier: 3.668A pdb=" N ALA R 195 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.974A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.562A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.045A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.530A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.547A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.603A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.538A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.604A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.648A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.619A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.324A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.324A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1251 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: 1.28 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1585 1.32 - 1.45: 2426 1.45 - 1.57: 5166 1.57 - 1.69: 1 1.69 - 1.82: 87 Bond restraints: 9265 Sorted by residual: bond pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 1.237 1.201 0.037 1.20e-02 6.94e+03 9.34e+00 bond pdb=" N LEU A 250 " pdb=" CA LEU A 250 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.29e+00 bond pdb=" CB PRO B 94 " pdb=" CG PRO B 94 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.11e+00 bond pdb=" N TYR A 354 " pdb=" CA TYR A 354 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.55e+00 bond pdb=" C ASP B 76 " pdb=" O ASP B 76 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.47e-02 4.63e+03 3.01e+00 ... (remaining 9260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12320 1.62 - 3.24: 225 3.24 - 4.86: 28 4.86 - 6.48: 11 6.48 - 8.10: 5 Bond angle restraints: 12589 Sorted by residual: angle pdb=" N THR B 102 " pdb=" CA THR B 102 " pdb=" C THR B 102 " ideal model delta sigma weight residual 107.23 115.22 -7.99 1.67e+00 3.59e-01 2.29e+01 angle pdb=" C TYR A 354 " pdb=" CA TYR A 354 " pdb=" CB TYR A 354 " ideal model delta sigma weight residual 110.10 102.00 8.10 1.90e+00 2.77e-01 1.82e+01 angle pdb=" C ASN R 203 " pdb=" N THR R 204 " pdb=" CA THR R 204 " ideal model delta sigma weight residual 120.31 114.53 5.78 1.52e+00 4.33e-01 1.45e+01 angle pdb=" CA GLN B 32 " pdb=" CB GLN B 32 " pdb=" CG GLN B 32 " ideal model delta sigma weight residual 114.10 121.43 -7.33 2.00e+00 2.50e-01 1.34e+01 angle pdb=" CA PRO B 94 " pdb=" N PRO B 94 " pdb=" CD PRO B 94 " ideal model delta sigma weight residual 112.00 106.93 5.07 1.40e+00 5.10e-01 1.31e+01 ... (remaining 12584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4869 17.92 - 35.83: 495 35.83 - 53.75: 116 53.75 - 71.67: 11 71.67 - 89.58: 8 Dihedral angle restraints: 5499 sinusoidal: 2035 harmonic: 3464 Sorted by residual: dihedral pdb=" CB CYS D 14 " pdb=" SG CYS D 14 " pdb=" SG CYS D 54 " pdb=" CB CYS D 54 " ideal model delta sinusoidal sigma weight residual -86.00 -141.96 55.96 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS R 39 " pdb=" SG CYS R 39 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual -86.00 -119.99 33.99 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1042 0.039 - 0.079: 306 0.079 - 0.118: 112 0.118 - 0.157: 9 0.157 - 0.196: 3 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA LEU A 250 " pdb=" N LEU A 250 " pdb=" C LEU A 250 " pdb=" CB LEU A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA THR B 102 " pdb=" N THR B 102 " pdb=" C THR B 102 " pdb=" CB THR B 102 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1469 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 353 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C LEU A 353 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 353 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 354 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 204 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C THR R 204 " -0.037 2.00e-02 2.50e+03 pdb=" O THR R 204 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA R 205 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 203 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ASN R 203 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN R 203 " 0.013 2.00e-02 2.50e+03 pdb=" N THR R 204 " 0.011 2.00e-02 2.50e+03 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 803 2.74 - 3.28: 8789 3.28 - 3.82: 14639 3.82 - 4.36: 16675 4.36 - 4.90: 30639 Nonbonded interactions: 71545 Sorted by model distance: nonbonded pdb=" OD1 ASP S 211 " pdb=" OH TYR S 215 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.248 3.040 ... (remaining 71540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.003 0.113 9271 Z= 0.154 Angle : 0.570 8.100 12601 Z= 0.315 Chirality : 0.043 0.196 1472 Planarity : 0.004 0.044 1595 Dihedral : 15.151 89.583 3243 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.52 % Allowed : 17.31 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1178 helix: 1.85 (0.27), residues: 388 sheet: -0.25 (0.30), residues: 315 loop : -0.69 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 288 TYR 0.024 0.002 TYR R 160 PHE 0.010 0.001 PHE R 130 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 291 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9265) covalent geometry : angle 0.56910 (12589) SS BOND : bond 0.01064 ( 6) SS BOND : angle 1.05220 ( 12) hydrogen bonds : bond 0.18210 ( 439) hydrogen bonds : angle 6.72795 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: D 61 PHE cc_start: 0.8262 (p90) cc_final: 0.7792 (t80) REVERT: R 70 MET cc_start: 0.7732 (mmm) cc_final: 0.7446 (mmm) REVERT: R 319 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7654 (tm-30) REVERT: A 24 LYS cc_start: 0.7560 (tptp) cc_final: 0.7298 (pptt) REVERT: A 354 TYR cc_start: 0.7088 (t80) cc_final: 0.6613 (t80) REVERT: S 120 SER cc_start: 0.7808 (t) cc_final: 0.7517 (p) REVERT: S 174 GLN cc_start: 0.8162 (mt0) cc_final: 0.7836 (mt0) REVERT: S 219 GLN cc_start: 0.8373 (pp30) cc_final: 0.8083 (pp30) outliers start: 5 outliers final: 4 residues processed: 168 average time/residue: 0.0605 time to fit residues: 15.1130 Evaluate side-chains 140 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.168441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136201 restraints weight = 13321.220| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.91 r_work: 0.3556 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9271 Z= 0.164 Angle : 0.573 9.069 12601 Z= 0.305 Chirality : 0.044 0.199 1472 Planarity : 0.004 0.038 1595 Dihedral : 4.966 48.561 1292 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.34 % Allowed : 15.75 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.25), residues: 1178 helix: 1.87 (0.26), residues: 389 sheet: -0.28 (0.28), residues: 331 loop : -0.80 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 16 TYR 0.028 0.002 TYR S 178 PHE 0.010 0.001 PHE R 130 TRP 0.019 0.001 TRP B 211 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9265) covalent geometry : angle 0.57259 (12589) SS BOND : bond 0.00444 ( 6) SS BOND : angle 1.08610 ( 12) hydrogen bonds : bond 0.04284 ( 439) hydrogen bonds : angle 4.74911 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: R 319 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7623 (tm-30) REVERT: A 24 LYS cc_start: 0.7763 (tptp) cc_final: 0.7383 (tmtt) REVERT: A 218 ASP cc_start: 0.8257 (m-30) cc_final: 0.7826 (p0) REVERT: B 59 TYR cc_start: 0.8498 (m-80) cc_final: 0.8248 (m-80) REVERT: B 75 GLN cc_start: 0.7466 (mm110) cc_final: 0.6895 (mt0) REVERT: B 76 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7968 (p0) REVERT: B 234 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: S 120 SER cc_start: 0.7872 (t) cc_final: 0.7534 (p) REVERT: S 168 ARG cc_start: 0.7976 (mpt180) cc_final: 0.7614 (mpt180) outliers start: 32 outliers final: 15 residues processed: 160 average time/residue: 0.0549 time to fit residues: 13.4859 Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 0.0070 chunk 28 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** 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 = 0.4152 r_free = 0.4152 target = 0.172124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140567 restraints weight = 13365.107| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.70 r_work: 0.3607 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9271 Z= 0.108 Angle : 0.510 8.254 12601 Z= 0.269 Chirality : 0.041 0.175 1472 Planarity : 0.003 0.037 1595 Dihedral : 4.404 44.977 1289 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.61 % Allowed : 17.41 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.25), residues: 1178 helix: 2.05 (0.27), residues: 389 sheet: -0.11 (0.28), residues: 326 loop : -0.81 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 72 TYR 0.023 0.001 TYR S 178 PHE 0.008 0.001 PHE R 321 TRP 0.016 0.001 TRP B 211 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9265) covalent geometry : angle 0.50986 (12589) SS BOND : bond 0.00389 ( 6) SS BOND : angle 0.79173 ( 12) hydrogen bonds : bond 0.03760 ( 439) hydrogen bonds : angle 4.36773 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 ARG cc_start: 0.6292 (mtm-85) cc_final: 0.6025 (mtp-110) REVERT: D 61 PHE cc_start: 0.8298 (p90) cc_final: 0.7946 (t80) REVERT: R 53 ILE cc_start: 0.8251 (mt) cc_final: 0.8032 (tp) REVERT: R 319 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7590 (tm-30) REVERT: A 24 LYS cc_start: 0.7773 (tptp) cc_final: 0.7326 (tmmt) REVERT: A 218 ASP cc_start: 0.8222 (m-30) cc_final: 0.7819 (p0) REVERT: A 253 SER cc_start: 0.8314 (m) cc_final: 0.8110 (m) REVERT: B 75 GLN cc_start: 0.7291 (mm110) cc_final: 0.6799 (mt0) REVERT: B 76 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8036 (p0) REVERT: B 188 MET cc_start: 0.8351 (mmm) cc_final: 0.8150 (mmm) REVERT: B 234 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: S 174 GLN cc_start: 0.8196 (mt0) cc_final: 0.7932 (pt0) outliers start: 25 outliers final: 15 residues processed: 155 average time/residue: 0.0552 time to fit residues: 13.0550 Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 ASN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 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 = 0.4056 r_free = 0.4056 target = 0.162654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133416 restraints weight = 13551.066| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.62 r_work: 0.3505 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9271 Z= 0.228 Angle : 0.639 9.402 12601 Z= 0.336 Chirality : 0.046 0.236 1472 Planarity : 0.004 0.045 1595 Dihedral : 4.878 43.265 1289 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.96 % Allowed : 17.62 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1178 helix: 1.76 (0.26), residues: 392 sheet: -0.20 (0.28), residues: 317 loop : -0.78 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 98 TYR 0.034 0.002 TYR S 178 PHE 0.016 0.002 PHE R 130 TRP 0.019 0.002 TRP B 211 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 9265) covalent geometry : angle 0.63828 (12589) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.14148 ( 12) hydrogen bonds : bond 0.04714 ( 439) hydrogen bonds : angle 4.68595 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 319 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7709 (tm-30) REVERT: A 24 LYS cc_start: 0.7761 (tptp) cc_final: 0.7319 (tmmt) REVERT: A 210 LYS cc_start: 0.7947 (mttt) cc_final: 0.7204 (pttt) REVERT: A 218 ASP cc_start: 0.8262 (m-30) cc_final: 0.7844 (p0) REVERT: A 245 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5755 (t-90) REVERT: A 253 SER cc_start: 0.8524 (m) cc_final: 0.8294 (m) REVERT: B 59 TYR cc_start: 0.8525 (m-80) cc_final: 0.8297 (m-80) REVERT: B 75 GLN cc_start: 0.7432 (mm110) cc_final: 0.6934 (mt0) REVERT: B 76 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8020 (p0) REVERT: B 234 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: S 38 ARG cc_start: 0.8159 (ptt-90) cc_final: 0.7911 (ptt-90) REVERT: S 87 ARG cc_start: 0.6905 (mtp85) cc_final: 0.6647 (mtp85) REVERT: S 207 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7824 (pp) REVERT: S 211 ASP cc_start: 0.7731 (t70) cc_final: 0.7521 (t70) outliers start: 38 outliers final: 24 residues processed: 168 average time/residue: 0.0591 time to fit residues: 14.6824 Evaluate side-chains 158 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134855 restraints weight = 13469.231| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.59 r_work: 0.3539 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9271 Z= 0.146 Angle : 0.557 9.884 12601 Z= 0.293 Chirality : 0.043 0.206 1472 Planarity : 0.003 0.039 1595 Dihedral : 4.398 44.946 1287 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.02 % Allowed : 19.19 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1178 helix: 1.91 (0.26), residues: 392 sheet: -0.16 (0.28), residues: 319 loop : -0.71 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 98 TYR 0.027 0.001 TYR S 178 PHE 0.012 0.001 PHE B 241 TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9265) covalent geometry : angle 0.55609 (12589) SS BOND : bond 0.00471 ( 6) SS BOND : angle 0.89740 ( 12) hydrogen bonds : bond 0.04012 ( 439) hydrogen bonds : angle 4.40055 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7136 (m-70) REVERT: R 319 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7685 (tm-30) REVERT: A 24 LYS cc_start: 0.7659 (tptp) cc_final: 0.7183 (tmmt) REVERT: A 211 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7516 (mmtt) REVERT: A 218 ASP cc_start: 0.8251 (m-30) cc_final: 0.7810 (p0) REVERT: A 249 MET cc_start: 0.7838 (tpp) cc_final: 0.7610 (tpp) REVERT: A 253 SER cc_start: 0.8522 (m) cc_final: 0.8285 (m) REVERT: A 349 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7492 (ttm-80) REVERT: B 17 GLN cc_start: 0.8782 (mt0) cc_final: 0.8527 (mt0) REVERT: B 59 TYR cc_start: 0.8536 (m-80) cc_final: 0.8239 (m-80) REVERT: B 75 GLN cc_start: 0.7293 (mm110) cc_final: 0.6817 (mt0) REVERT: B 76 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8160 (p0) REVERT: B 234 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: S 87 ARG cc_start: 0.6860 (mtp85) cc_final: 0.6633 (mtp85) REVERT: S 148 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.6644 (ttm-80) REVERT: S 168 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7860 (mpt180) REVERT: S 207 LEU cc_start: 0.8128 (pp) cc_final: 0.7902 (pp) outliers start: 29 outliers final: 20 residues processed: 163 average time/residue: 0.0689 time to fit residues: 16.2819 Evaluate side-chains 158 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.0070 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.165241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134641 restraints weight = 13471.435| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.50 r_work: 0.3529 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9271 Z= 0.155 Angle : 0.552 8.863 12601 Z= 0.292 Chirality : 0.043 0.208 1472 Planarity : 0.003 0.040 1595 Dihedral : 4.372 44.283 1287 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.96 % Allowed : 18.46 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1178 helix: 1.98 (0.26), residues: 392 sheet: -0.15 (0.28), residues: 321 loop : -0.69 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 98 TYR 0.028 0.001 TYR S 178 PHE 0.011 0.001 PHE R 130 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9265) covalent geometry : angle 0.55193 (12589) SS BOND : bond 0.00468 ( 6) SS BOND : angle 0.89678 ( 12) hydrogen bonds : bond 0.03994 ( 439) hydrogen bonds : angle 4.36819 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 ARG cc_start: 0.6685 (mtp-110) cc_final: 0.6417 (mtp-110) REVERT: R 53 ILE cc_start: 0.8264 (mt) cc_final: 0.7969 (tp) REVERT: R 242 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: R 319 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7647 (tm-30) REVERT: A 24 LYS cc_start: 0.7688 (tptp) cc_final: 0.7220 (tmmt) REVERT: A 218 ASP cc_start: 0.8264 (m-30) cc_final: 0.7811 (p0) REVERT: A 253 SER cc_start: 0.8555 (m) cc_final: 0.8332 (m) REVERT: A 349 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7511 (ttm-80) REVERT: B 17 GLN cc_start: 0.8806 (mt0) cc_final: 0.8347 (pt0) REVERT: B 59 TYR cc_start: 0.8576 (m-80) cc_final: 0.8148 (m-80) REVERT: B 75 GLN cc_start: 0.7380 (mm110) cc_final: 0.6867 (mt0) REVERT: B 234 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: S 87 ARG cc_start: 0.6864 (mtp85) cc_final: 0.6628 (mtp85) REVERT: S 148 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.6679 (ttm-80) REVERT: S 207 LEU cc_start: 0.8234 (pp) cc_final: 0.8034 (pp) REVERT: S 211 ASP cc_start: 0.7743 (t70) cc_final: 0.7536 (t70) outliers start: 38 outliers final: 28 residues processed: 165 average time/residue: 0.0648 time to fit residues: 15.5492 Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN ** A 322 HIS ** 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 = 0.4086 r_free = 0.4086 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134570 restraints weight = 13434.903| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.56 r_work: 0.3530 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9271 Z= 0.148 Angle : 0.552 8.895 12601 Z= 0.291 Chirality : 0.043 0.207 1472 Planarity : 0.003 0.038 1595 Dihedral : 4.084 27.440 1285 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.34 % Allowed : 20.02 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1178 helix: 1.99 (0.26), residues: 392 sheet: -0.04 (0.29), residues: 305 loop : -0.70 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 98 TYR 0.028 0.001 TYR S 178 PHE 0.013 0.001 PHE S 200 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9265) covalent geometry : angle 0.55126 (12589) SS BOND : bond 0.00460 ( 6) SS BOND : angle 0.88892 ( 12) hydrogen bonds : bond 0.03911 ( 439) hydrogen bonds : angle 4.34230 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8279 (mt) cc_final: 0.7981 (tp) REVERT: R 242 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7293 (m-70) REVERT: R 319 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7675 (tm-30) REVERT: A 24 LYS cc_start: 0.7716 (tptp) cc_final: 0.7255 (tmmt) REVERT: A 218 ASP cc_start: 0.8250 (m-30) cc_final: 0.7821 (p0) REVERT: A 253 SER cc_start: 0.8554 (m) cc_final: 0.8325 (m) REVERT: A 349 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7522 (ttm-80) REVERT: B 17 GLN cc_start: 0.8848 (mt0) cc_final: 0.8378 (pt0) REVERT: B 59 TYR cc_start: 0.8571 (m-80) cc_final: 0.8211 (m-80) REVERT: B 75 GLN cc_start: 0.7337 (mm110) cc_final: 0.6792 (mt0) REVERT: B 234 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: G 38 MET cc_start: 0.6795 (ppp) cc_final: 0.6145 (ptp) REVERT: S 87 ARG cc_start: 0.6866 (mtp85) cc_final: 0.6639 (mtp85) REVERT: S 148 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.6734 (ttm-80) REVERT: S 211 ASP cc_start: 0.7704 (t70) cc_final: 0.7479 (t70) outliers start: 32 outliers final: 28 residues processed: 156 average time/residue: 0.0620 time to fit residues: 14.0633 Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130841 restraints weight = 13400.353| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.59 r_work: 0.3437 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9271 Z= 0.265 Angle : 0.664 9.319 12601 Z= 0.349 Chirality : 0.046 0.242 1472 Planarity : 0.004 0.041 1595 Dihedral : 4.525 31.685 1285 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.38 % Allowed : 20.23 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.24), residues: 1178 helix: 1.72 (0.26), residues: 392 sheet: -0.23 (0.28), residues: 311 loop : -0.82 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 98 TYR 0.036 0.002 TYR S 178 PHE 0.019 0.002 PHE R 130 TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 9265) covalent geometry : angle 0.66356 (12589) SS BOND : bond 0.00601 ( 6) SS BOND : angle 1.21206 ( 12) hydrogen bonds : bond 0.04726 ( 439) hydrogen bonds : angle 4.70674 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8221 (mt) cc_final: 0.8001 (tp) REVERT: R 319 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7724 (tm-30) REVERT: A 24 LYS cc_start: 0.7792 (tptp) cc_final: 0.7340 (tmmt) REVERT: A 218 ASP cc_start: 0.8279 (m-30) cc_final: 0.7879 (p0) REVERT: A 253 SER cc_start: 0.8629 (m) cc_final: 0.8414 (m) REVERT: B 17 GLN cc_start: 0.8807 (mt0) cc_final: 0.8355 (pt0) REVERT: B 234 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: G 38 MET cc_start: 0.6832 (ppp) cc_final: 0.5645 (ptm) REVERT: S 87 ARG cc_start: 0.6959 (mtp85) cc_final: 0.6693 (mtp85) REVERT: S 148 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.6807 (ttm-80) REVERT: S 180 MET cc_start: 0.7575 (tpt) cc_final: 0.7217 (mmm) REVERT: S 211 ASP cc_start: 0.7784 (t70) cc_final: 0.7463 (t0) outliers start: 42 outliers final: 35 residues processed: 154 average time/residue: 0.0609 time to fit residues: 14.0467 Evaluate side-chains 160 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN A 245 HIS B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.166823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136802 restraints weight = 13298.983| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.44 r_work: 0.3561 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9271 Z= 0.113 Angle : 0.543 8.667 12601 Z= 0.285 Chirality : 0.042 0.186 1472 Planarity : 0.003 0.039 1595 Dihedral : 4.074 27.975 1285 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.13 % Allowed : 20.96 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1178 helix: 2.02 (0.26), residues: 392 sheet: -0.05 (0.29), residues: 296 loop : -0.72 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 72 TYR 0.025 0.001 TYR S 178 PHE 0.011 0.001 PHE S 200 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9265) covalent geometry : angle 0.54240 (12589) SS BOND : bond 0.00402 ( 6) SS BOND : angle 0.76548 ( 12) hydrogen bonds : bond 0.03758 ( 439) hydrogen bonds : angle 4.32714 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8202 (mt) cc_final: 0.7942 (tp) REVERT: R 242 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7311 (m-70) REVERT: R 319 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7671 (tm-30) REVERT: A 24 LYS cc_start: 0.7729 (tptp) cc_final: 0.7276 (tmmt) REVERT: A 218 ASP cc_start: 0.8228 (m-30) cc_final: 0.7802 (p0) REVERT: A 248 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8790 (tt) REVERT: A 253 SER cc_start: 0.8517 (m) cc_final: 0.8292 (m) REVERT: A 323 MET cc_start: 0.8320 (mmm) cc_final: 0.7758 (mtt) REVERT: A 349 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7494 (ttm-80) REVERT: B 17 GLN cc_start: 0.8741 (mt0) cc_final: 0.8335 (pt0) REVERT: B 59 TYR cc_start: 0.8357 (m-80) cc_final: 0.7980 (m-80) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: G 38 MET cc_start: 0.6831 (ppp) cc_final: 0.6103 (ptm) REVERT: S 87 ARG cc_start: 0.6886 (mtp85) cc_final: 0.6681 (mtp85) REVERT: S 148 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.6778 (ttm-80) outliers start: 30 outliers final: 21 residues processed: 155 average time/residue: 0.0603 time to fit residues: 13.7021 Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 86 optimal weight: 0.0040 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 216 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.168505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136502 restraints weight = 13308.670| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.61 r_work: 0.3523 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9271 Z= 0.114 Angle : 0.538 8.355 12601 Z= 0.282 Chirality : 0.042 0.182 1472 Planarity : 0.003 0.039 1595 Dihedral : 3.908 25.841 1285 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.71 % Allowed : 21.27 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1178 helix: 2.11 (0.26), residues: 392 sheet: 0.15 (0.30), residues: 286 loop : -0.73 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 168 TYR 0.023 0.001 TYR S 178 PHE 0.011 0.001 PHE S 200 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9265) covalent geometry : angle 0.53825 (12589) SS BOND : bond 0.00405 ( 6) SS BOND : angle 0.73360 ( 12) hydrogen bonds : bond 0.03600 ( 439) hydrogen bonds : angle 4.22529 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7319 (m-70) REVERT: R 319 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7598 (tm-30) REVERT: A 24 LYS cc_start: 0.7681 (tptp) cc_final: 0.7208 (tmmt) REVERT: A 253 SER cc_start: 0.8517 (m) cc_final: 0.8302 (m) REVERT: A 323 MET cc_start: 0.8284 (mmm) cc_final: 0.7773 (mtt) REVERT: A 349 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7497 (ttm-80) REVERT: B 17 GLN cc_start: 0.8701 (mt0) cc_final: 0.8312 (pt0) REVERT: B 59 TYR cc_start: 0.8397 (m-80) cc_final: 0.7897 (m-80) REVERT: B 234 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: G 38 MET cc_start: 0.6866 (ppp) cc_final: 0.6296 (ptm) REVERT: S 87 ARG cc_start: 0.6839 (mtp85) cc_final: 0.6621 (mtp85) REVERT: S 148 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.6740 (ttm-80) REVERT: S 180 MET cc_start: 0.7557 (mmm) cc_final: 0.7219 (tpp) outliers start: 26 outliers final: 23 residues processed: 144 average time/residue: 0.0603 time to fit residues: 12.9105 Evaluate side-chains 148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 0.9990 chunk 33 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 216 GLN R 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136972 restraints weight = 13116.694| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.53 r_work: 0.3530 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9271 Z= 0.116 Angle : 0.549 14.190 12601 Z= 0.283 Chirality : 0.042 0.186 1472 Planarity : 0.003 0.038 1595 Dihedral : 3.877 25.586 1285 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.50 % Allowed : 21.58 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1178 helix: 2.21 (0.26), residues: 382 sheet: 0.08 (0.29), residues: 296 loop : -0.67 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 168 TYR 0.023 0.001 TYR S 178 PHE 0.010 0.001 PHE S 200 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9265) covalent geometry : angle 0.54891 (12589) SS BOND : bond 0.00397 ( 6) SS BOND : angle 0.71654 ( 12) hydrogen bonds : bond 0.03546 ( 439) hydrogen bonds : angle 4.23035 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.21 seconds wall clock time: 31 minutes 25.75 seconds (1885.75 seconds total)