Starting phenix.real_space_refine on Thu Feb 13 15:07:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxx_38764/02_2025/8xxx_38764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxx_38764/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxx_38764/02_2025/8xxx_38764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxx_38764/02_2025/8xxx_38764.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxx_38764/02_2025/8xxx_38764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxx_38764/02_2025/8xxx_38764.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.029 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, '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: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 5.37, per 1000 atoms: 0.59 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 2.77 Time building geometry restraints manager: 2.66 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: 0.010 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 9265 Z= 0.229 Angle : 0.569 8.100 12589 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (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 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 291 PHE 0.010 0.001 PHE R 130 TYR 0.024 0.002 TYR R 160 ARG 0.005 0.000 ARG R 288 *********************** 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 : 1.019 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: 0.1758 time to fit residues: 43.0041 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 : 1.056 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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** S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137159 restraints weight = 13241.522| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.73 r_work: 0.3558 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9265 Z= 0.249 Angle : 0.570 8.837 12589 Z= 0.304 Chirality : 0.043 0.196 1472 Planarity : 0.004 0.038 1595 Dihedral : 4.923 48.080 1292 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.65 % Allowed : 15.54 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1178 helix: 1.90 (0.26), residues: 389 sheet: -0.27 (0.28), residues: 331 loop : -0.78 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.010 0.001 PHE R 130 TYR 0.028 0.002 TYR S 178 ARG 0.008 0.000 ARG S 72 *********************** 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 176 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: R 319 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7617 (tm-30) REVERT: A 24 LYS cc_start: 0.7785 (tptp) cc_final: 0.7415 (tmtt) REVERT: B 59 TYR cc_start: 0.8474 (m-80) cc_final: 0.8246 (m-80) REVERT: B 75 GLN cc_start: 0.7454 (mm110) cc_final: 0.6897 (mt0) REVERT: B 76 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7852 (p0) REVERT: B 234 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: S 120 SER cc_start: 0.7871 (t) cc_final: 0.7533 (p) REVERT: S 168 ARG cc_start: 0.7961 (mpt180) cc_final: 0.7593 (mpt180) outliers start: 35 outliers final: 16 residues processed: 159 average time/residue: 0.1601 time to fit residues: 38.7752 Evaluate side-chains 149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain S residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.170183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138500 restraints weight = 13610.336| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.75 r_work: 0.3560 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9265 Z= 0.190 Angle : 0.526 8.450 12589 Z= 0.277 Chirality : 0.042 0.186 1472 Planarity : 0.003 0.038 1595 Dihedral : 4.473 44.766 1289 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.82 % Allowed : 17.00 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1178 helix: 2.02 (0.26), residues: 390 sheet: -0.20 (0.28), residues: 328 loop : -0.79 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE R 321 TYR 0.025 0.001 TYR S 178 ARG 0.010 0.000 ARG D 16 *********************** 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 169 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 ARG cc_start: 0.6315 (mtm-85) cc_final: 0.6080 (mtp-110) REVERT: R 53 ILE cc_start: 0.8251 (mt) cc_final: 0.8025 (tp) REVERT: R 319 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7594 (tm-30) REVERT: A 24 LYS cc_start: 0.7744 (tptp) cc_final: 0.7282 (tmmt) REVERT: A 218 ASP cc_start: 0.8250 (m-30) cc_final: 0.7798 (p0) REVERT: A 253 SER cc_start: 0.8350 (m) cc_final: 0.8144 (m) REVERT: B 75 GLN cc_start: 0.7389 (mm110) cc_final: 0.6851 (mt0) REVERT: B 76 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (p0) REVERT: B 188 MET cc_start: 0.8411 (mmm) cc_final: 0.8210 (mmm) REVERT: B 234 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: S 174 GLN cc_start: 0.8232 (mt0) cc_final: 0.7948 (pt0) outliers start: 27 outliers final: 16 residues processed: 155 average time/residue: 0.1739 time to fit residues: 40.4551 Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 A residue 305 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 103 CYS 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 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 89 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.169399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139155 restraints weight = 13320.894| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.48 r_work: 0.3590 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9265 Z= 0.188 Angle : 0.517 8.479 12589 Z= 0.275 Chirality : 0.042 0.187 1472 Planarity : 0.003 0.037 1595 Dihedral : 4.351 44.249 1289 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.75 % Allowed : 17.31 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1178 helix: 2.12 (0.26), residues: 389 sheet: 0.02 (0.28), residues: 318 loop : -0.77 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 322 PHE 0.012 0.001 PHE R 229 TYR 0.026 0.001 TYR S 178 ARG 0.004 0.000 ARG S 98 *********************** 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 181 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.6978 (m-70) REVERT: R 319 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7508 (tm-30) REVERT: A 24 LYS cc_start: 0.7715 (tptp) cc_final: 0.7256 (tmmt) REVERT: A 253 SER cc_start: 0.8419 (m) cc_final: 0.8215 (m) REVERT: B 76 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 234 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: S 87 ARG cc_start: 0.6714 (mtp85) cc_final: 0.6485 (mtp85) REVERT: S 168 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7412 (mpt180) REVERT: S 174 GLN cc_start: 0.8161 (mt0) cc_final: 0.7885 (pt0) REVERT: S 207 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7842 (pp) outliers start: 36 outliers final: 19 residues processed: 169 average time/residue: 0.1801 time to fit residues: 45.3230 Evaluate side-chains 159 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 258 LEU 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 B residue 76 ASP 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 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 113 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136940 restraints weight = 13347.083| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.54 r_work: 0.3558 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9265 Z= 0.217 Angle : 0.546 10.763 12589 Z= 0.286 Chirality : 0.042 0.202 1472 Planarity : 0.003 0.038 1595 Dihedral : 4.198 44.555 1287 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.44 % Allowed : 18.56 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1178 helix: 2.05 (0.26), residues: 392 sheet: 0.03 (0.28), residues: 315 loop : -0.72 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.005 0.001 HIS A 322 PHE 0.011 0.001 PHE R 130 TYR 0.026 0.001 TYR S 178 ARG 0.005 0.000 ARG S 98 *********************** 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 177 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 319 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7577 (tm-30) REVERT: A 24 LYS cc_start: 0.7718 (tptp) cc_final: 0.7240 (tmmt) REVERT: A 253 SER cc_start: 0.8492 (m) cc_final: 0.8286 (m) REVERT: B 59 TYR cc_start: 0.8616 (m-80) cc_final: 0.8245 (m-80) REVERT: B 76 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8118 (p0) REVERT: B 234 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: S 87 ARG cc_start: 0.6801 (mtp85) cc_final: 0.6547 (mtp85) REVERT: S 148 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.6707 (ttm-80) outliers start: 33 outliers final: 23 residues processed: 164 average time/residue: 0.1813 time to fit residues: 43.4775 Evaluate side-chains 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 R residue 39 CYS Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 258 LEU 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 50 VAL Chi-restraints excluded: chain A residue 248 LEU 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 91 THR 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 31 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.167721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138073 restraints weight = 13175.443| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.42 r_work: 0.3586 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9265 Z= 0.180 Angle : 0.521 9.874 12589 Z= 0.272 Chirality : 0.042 0.188 1472 Planarity : 0.003 0.037 1595 Dihedral : 4.108 43.968 1287 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.55 % Allowed : 18.35 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1178 helix: 2.13 (0.26), residues: 392 sheet: 0.07 (0.28), residues: 304 loop : -0.69 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 PHE 0.009 0.001 PHE R 130 TYR 0.025 0.001 TYR S 178 ARG 0.004 0.000 ARG S 98 *********************** 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 180 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8207 (mt) cc_final: 0.7888 (tp) REVERT: R 242 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7028 (m-70) REVERT: R 319 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7552 (tm-30) REVERT: A 24 LYS cc_start: 0.7705 (tptp) cc_final: 0.7222 (tmmt) REVERT: A 253 SER cc_start: 0.8485 (m) cc_final: 0.8266 (m) REVERT: B 59 TYR cc_start: 0.8574 (m-80) cc_final: 0.8272 (m-80) REVERT: B 234 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: S 87 ARG cc_start: 0.6818 (mtp85) cc_final: 0.6579 (mtp85) REVERT: S 148 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.6714 (ttm-80) outliers start: 34 outliers final: 23 residues processed: 169 average time/residue: 0.1786 time to fit residues: 44.0337 Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 258 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 190 PHE 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 189 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 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 103 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139747 restraints weight = 13363.787| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.44 r_work: 0.3596 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9265 Z= 0.167 Angle : 0.519 8.932 12589 Z= 0.271 Chirality : 0.041 0.183 1472 Planarity : 0.003 0.037 1595 Dihedral : 3.767 24.219 1285 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.13 % Allowed : 19.40 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1178 helix: 2.17 (0.26), residues: 392 sheet: 0.17 (0.29), residues: 303 loop : -0.67 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.008 0.001 PHE R 130 TYR 0.023 0.001 TYR S 178 ARG 0.004 0.000 ARG S 98 *********************** 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 173 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.7118 (m-70) REVERT: R 319 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7525 (tm-30) REVERT: A 24 LYS cc_start: 0.7673 (tptp) cc_final: 0.7219 (tmmt) REVERT: A 218 ASP cc_start: 0.8174 (m-30) cc_final: 0.7699 (p0) REVERT: A 253 SER cc_start: 0.8481 (m) cc_final: 0.8266 (m) REVERT: B 59 TYR cc_start: 0.8563 (m-80) cc_final: 0.8276 (m-80) REVERT: B 234 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: S 87 ARG cc_start: 0.6821 (mtp85) cc_final: 0.6589 (mtp85) REVERT: S 148 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.6688 (ttm-80) outliers start: 30 outliers final: 24 residues processed: 164 average time/residue: 0.1762 time to fit residues: 42.1654 Evaluate side-chains 163 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 258 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 190 PHE Chi-restraints excluded: chain A residue 318 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 148 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 104 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.168387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138696 restraints weight = 13554.643| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.46 r_work: 0.3588 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9265 Z= 0.172 Angle : 0.541 15.614 12589 Z= 0.278 Chirality : 0.042 0.184 1472 Planarity : 0.003 0.037 1595 Dihedral : 3.744 24.170 1285 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.92 % Allowed : 19.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1178 helix: 2.23 (0.26), residues: 392 sheet: 0.22 (0.29), residues: 303 loop : -0.64 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.009 0.001 PHE R 59 TYR 0.023 0.001 TYR S 178 ARG 0.005 0.000 ARG S 168 *********************** 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 167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7105 (m-70) REVERT: R 319 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7532 (tm-30) REVERT: A 24 LYS cc_start: 0.7680 (tptp) cc_final: 0.7235 (tmmt) REVERT: A 218 ASP cc_start: 0.8189 (m-30) cc_final: 0.7724 (p0) REVERT: A 253 SER cc_start: 0.8485 (m) cc_final: 0.8267 (m) REVERT: B 59 TYR cc_start: 0.8537 (m-80) cc_final: 0.8280 (m-80) REVERT: B 118 ASP cc_start: 0.8200 (m-30) cc_final: 0.7936 (m-30) REVERT: B 234 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: S 87 ARG cc_start: 0.6843 (mtp85) cc_final: 0.6621 (mtp85) REVERT: S 148 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.6735 (ttm-80) outliers start: 28 outliers final: 23 residues processed: 159 average time/residue: 0.1778 time to fit residues: 41.5294 Evaluate side-chains 159 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 242 HIS Chi-restraints excluded: chain R residue 258 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 190 PHE Chi-restraints excluded: chain A residue 318 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.0020 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.169689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139527 restraints weight = 13262.020| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.47 r_work: 0.3599 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9265 Z= 0.168 Angle : 0.539 15.165 12589 Z= 0.277 Chirality : 0.041 0.179 1472 Planarity : 0.003 0.037 1595 Dihedral : 3.696 23.935 1285 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.92 % Allowed : 19.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1178 helix: 2.22 (0.26), residues: 393 sheet: 0.22 (0.29), residues: 298 loop : -0.61 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.010 0.001 PHE R 59 TYR 0.023 0.001 TYR S 178 ARG 0.003 0.000 ARG S 168 *********************** 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 167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7159 (m-70) REVERT: R 319 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7573 (tm-30) REVERT: A 24 LYS cc_start: 0.7684 (tptp) cc_final: 0.7239 (tmmt) REVERT: A 218 ASP cc_start: 0.8207 (m-30) cc_final: 0.7766 (p0) REVERT: A 253 SER cc_start: 0.8475 (m) cc_final: 0.8270 (m) REVERT: B 118 ASP cc_start: 0.8191 (m-30) cc_final: 0.7942 (m-30) REVERT: B 234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: S 87 ARG cc_start: 0.6867 (mtp85) cc_final: 0.6645 (mtp85) outliers start: 28 outliers final: 23 residues processed: 158 average time/residue: 0.1851 time to fit residues: 42.1731 Evaluate side-chains 162 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 318 GLU 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 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 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 114 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.168902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138404 restraints weight = 13410.514| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.52 r_work: 0.3579 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9265 Z= 0.190 Angle : 0.552 14.343 12589 Z= 0.285 Chirality : 0.042 0.185 1472 Planarity : 0.003 0.037 1595 Dihedral : 3.756 24.435 1285 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.92 % Allowed : 19.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1178 helix: 2.15 (0.26), residues: 393 sheet: 0.26 (0.29), residues: 303 loop : -0.62 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.020 0.001 PHE S 200 TYR 0.025 0.001 TYR S 178 ARG 0.005 0.000 ARG S 168 ********************** 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 158 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 242 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7185 (m-70) REVERT: R 319 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7587 (tm-30) REVERT: A 24 LYS cc_start: 0.7650 (tptp) cc_final: 0.7197 (tmmt) REVERT: A 218 ASP cc_start: 0.8228 (m-30) cc_final: 0.7739 (p0) REVERT: A 253 SER cc_start: 0.8498 (m) cc_final: 0.8293 (m) REVERT: B 118 ASP cc_start: 0.8188 (m-30) cc_final: 0.7933 (m-30) REVERT: B 234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: S 87 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6611 (mtp85) outliers start: 28 outliers final: 24 residues processed: 151 average time/residue: 0.1930 time to fit residues: 42.5174 Evaluate side-chains 155 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 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 55 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 318 GLU 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 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 81 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 105 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.170252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139729 restraints weight = 13345.645| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.54 r_work: 0.3601 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9265 Z= 0.163 Angle : 0.541 14.328 12589 Z= 0.277 Chirality : 0.042 0.190 1472 Planarity : 0.003 0.037 1595 Dihedral : 3.694 23.566 1285 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.71 % Allowed : 19.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1178 helix: 2.18 (0.26), residues: 393 sheet: 0.27 (0.29), residues: 298 loop : -0.58 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.018 0.001 PHE S 200 TYR 0.023 0.001 TYR S 178 ARG 0.005 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4370.48 seconds wall clock time: 78 minutes 28.31 seconds (4708.31 seconds total)