Starting phenix.real_space_refine on Sat Aug 23 00:12:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihf_35443/08_2025/8ihf_35443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihf_35443/08_2025/8ihf_35443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ihf_35443/08_2025/8ihf_35443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihf_35443/08_2025/8ihf_35443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ihf_35443/08_2025/8ihf_35443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihf_35443/08_2025/8ihf_35443.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 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 61 5.16 5 C 5563 2.51 5 N 1473 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1690 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2485 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 383 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2385 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'FI7': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.59, per 1000 atoms: 0.18 Number of scatterers: 8691 At special positions: 0 Unit cell: (85.49, 117.03, 135.29, 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 61 16.00 O 1594 8.00 N 1473 7.00 C 5563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.05 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 339.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 36.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.534A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.344A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.611A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.895A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.732A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.942A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.154A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.509A 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 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.653A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 24 through 55 removed outlier: 4.038A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.608A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 Processing helix chain 'R' and resid 97 through 130 removed outlier: 5.033A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.537A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 159 removed outlier: 3.619A pdb=" N THR R 159 " --> pdb=" O THR R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 190 through 218 removed outlier: 3.682A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 4.095A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.502A pdb=" N VAL R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.505A pdb=" N ARG R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 280 removed outlier: 3.794A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 295 removed outlier: 3.876A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.537A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.530A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60 Processing sheet with id=AA4, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'S' and resid 156 through 160 Processing sheet with id=AA6, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.387A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.744A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.934A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.798A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.302A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.520A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.523A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 11 through 12 removed outlier: 4.035A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.732A pdb=" N ILE R 169 " --> pdb=" O LEU R 176 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1134 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: 1.00 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1794 1.33 - 1.46: 2819 1.46 - 1.59: 4189 1.59 - 1.72: 0 1.72 - 1.85: 86 Bond restraints: 8888 Sorted by residual: bond pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.37e-02 5.33e+03 8.29e+00 bond pdb=" C CYS B 233 " pdb=" O CYS B 233 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.24e-02 6.50e+03 7.64e+00 bond pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 1.521 1.489 0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" N15 FI7 R 602 " pdb=" O16 FI7 R 602 " ideal model delta sigma weight residual 1.363 1.415 -0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 1.521 1.488 0.033 1.28e-02 6.10e+03 6.45e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 11807 1.44 - 2.88: 195 2.88 - 4.33: 47 4.33 - 5.77: 16 5.77 - 7.21: 4 Bond angle restraints: 12069 Sorted by residual: angle pdb=" C LYS R 166 " pdb=" N MET R 167 " pdb=" CA MET R 167 " ideal model delta sigma weight residual 122.28 117.33 4.95 1.02e+00 9.61e-01 2.36e+01 angle pdb=" CA MET R 167 " pdb=" CB MET R 167 " pdb=" CG MET R 167 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 110.26 105.01 5.25 1.49e+00 4.50e-01 1.24e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 112.45 116.75 -4.30 1.39e+00 5.18e-01 9.59e+00 angle pdb=" N TRP R 188 " pdb=" CA TRP R 188 " pdb=" C TRP R 188 " ideal model delta sigma weight residual 110.53 106.74 3.79 1.32e+00 5.74e-01 8.25e+00 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 4774 24.88 - 49.75: 395 49.75 - 74.63: 49 74.63 - 99.50: 8 99.50 - 124.38: 1 Dihedral angle restraints: 5227 sinusoidal: 1951 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -41.94 -44.06 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA CYS R 183 " pdb=" C CYS R 183 " pdb=" N HIS R 184 " pdb=" CA HIS R 184 " ideal model delta harmonic sigma weight residual -180.00 -155.09 -24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 897 0.032 - 0.063: 327 0.063 - 0.094: 92 0.094 - 0.126: 56 0.126 - 0.157: 5 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CG LEU S 165 " pdb=" CB LEU S 165 " pdb=" CD1 LEU S 165 " pdb=" CD2 LEU S 165 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA PRO R 81 " pdb=" N PRO R 81 " pdb=" C PRO R 81 " pdb=" CB PRO R 81 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1374 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO R 81 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 R 602 " 0.032 2.00e-02 2.50e+03 1.71e-02 5.84e+00 pdb=" C08 FI7 R 602 " -0.011 2.00e-02 2.50e+03 pdb=" C09 FI7 R 602 " -0.013 2.00e-02 2.50e+03 pdb=" C10 FI7 R 602 " -0.009 2.00e-02 2.50e+03 pdb=" C11 FI7 R 602 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 R 602 " -0.009 2.00e-02 2.50e+03 pdb=" N14 FI7 R 602 " -0.015 2.00e-02 2.50e+03 pdb=" O12 FI7 R 602 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO S 75 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.032 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1277 2.75 - 3.29: 8036 3.29 - 3.83: 14167 3.83 - 4.36: 17336 4.36 - 4.90: 30354 Nonbonded interactions: 71170 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.218 3.120 nonbonded pdb=" OD1 ASN A 241 " pdb=" ND1 HIS A 244 " model vdw 2.232 3.120 nonbonded pdb=" NE2 GLN R 170 " pdb=" O GLY R 172 " model vdw 2.233 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR R 284 " pdb=" O23 FI7 R 602 " model vdw 2.260 3.040 ... (remaining 71165 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: 1.560 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.052 8892 Z= 0.170 Angle : 0.530 7.211 12078 Z= 0.289 Chirality : 0.040 0.157 1377 Planarity : 0.004 0.073 1522 Dihedral : 17.370 124.381 3100 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.11 % Allowed : 26.25 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1115 helix: 0.54 (0.28), residues: 371 sheet: 0.10 (0.33), residues: 258 loop : -1.07 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 314 TYR 0.018 0.001 TYR S 235 PHE 0.013 0.001 PHE R 10 TRP 0.014 0.001 TRP R 188 HIS 0.009 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8888) covalent geometry : angle 0.52729 (12069) SS BOND : bond 0.00849 ( 3) SS BOND : angle 1.66848 ( 6) hydrogen bonds : bond 0.26427 ( 408) hydrogen bonds : angle 8.09175 ( 1134) link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 2.55610 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.236 Fit side-chains REVERT: A 247 MET cc_start: 0.8563 (mtp) cc_final: 0.8094 (mtm) REVERT: R 51 ILE cc_start: 0.7909 (mt) cc_final: 0.7682 (mp) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.4484 time to fit residues: 66.3461 Evaluate side-chains 125 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.0050 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 161 HIS ** 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 = 0.4022 r_free = 0.4022 target = 0.170903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131359 restraints weight = 10061.035| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.04 r_work: 0.3438 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8892 Z= 0.124 Angle : 0.540 10.613 12078 Z= 0.288 Chirality : 0.041 0.173 1377 Planarity : 0.004 0.052 1522 Dihedral : 7.525 106.163 1259 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.54 % Allowed : 27.02 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.25), residues: 1115 helix: 1.42 (0.27), residues: 364 sheet: 0.16 (0.32), residues: 263 loop : -0.99 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.022 0.001 TYR S 235 PHE 0.010 0.001 PHE A 189 TRP 0.019 0.002 TRP R 188 HIS 0.003 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8888) covalent geometry : angle 0.53797 (12069) SS BOND : bond 0.00537 ( 3) SS BOND : angle 1.12641 ( 6) hydrogen bonds : bond 0.05136 ( 408) hydrogen bonds : angle 4.95332 ( 1134) link_NAG-ASN : bond 0.00330 ( 1) link_NAG-ASN : angle 2.76265 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.270 Fit side-chains REVERT: A 29 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7897 (ttmt) REVERT: A 244 HIS cc_start: 0.7718 (m90) cc_final: 0.7291 (m90) REVERT: A 247 MET cc_start: 0.8189 (mtp) cc_final: 0.7656 (mtm) REVERT: A 349 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7775 (mmmm) REVERT: R 167 MET cc_start: 0.5678 (tpp) cc_final: 0.5315 (tpp) outliers start: 32 outliers final: 8 residues processed: 152 average time/residue: 0.3882 time to fit residues: 64.0500 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 0.0030 chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN S 113 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 237 ASN B 259 GLN R 86 ASN ** R 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.172578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133008 restraints weight = 9912.353| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.03 r_work: 0.3430 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8892 Z= 0.133 Angle : 0.526 7.292 12078 Z= 0.280 Chirality : 0.041 0.184 1377 Planarity : 0.004 0.047 1522 Dihedral : 7.689 115.135 1259 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.10 % Allowed : 26.47 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1115 helix: 1.61 (0.28), residues: 367 sheet: 0.05 (0.32), residues: 264 loop : -0.96 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.019 0.001 TYR S 235 PHE 0.018 0.001 PHE R 232 TRP 0.021 0.001 TRP R 188 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8888) covalent geometry : angle 0.52377 (12069) SS BOND : bond 0.00823 ( 3) SS BOND : angle 1.25934 ( 6) hydrogen bonds : bond 0.04562 ( 408) hydrogen bonds : angle 4.54461 ( 1134) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 2.57140 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: A 29 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7837 (ttmt) REVERT: A 244 HIS cc_start: 0.7749 (m90) cc_final: 0.7200 (m90) REVERT: A 247 MET cc_start: 0.8234 (mtp) cc_final: 0.7706 (mtm) REVERT: A 272 ASP cc_start: 0.8060 (t0) cc_final: 0.7580 (t0) REVERT: A 276 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 349 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7753 (mmmm) REVERT: S 140 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.6524 (mpp) REVERT: S 238 THR cc_start: 0.8246 (p) cc_final: 0.7962 (t) REVERT: C 38 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7163 (mtp) REVERT: C 47 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: R 167 MET cc_start: 0.5894 (tpp) cc_final: 0.5435 (tpp) REVERT: R 176 LEU cc_start: 0.8477 (pp) cc_final: 0.8264 (pp) outliers start: 37 outliers final: 11 residues processed: 150 average time/residue: 0.3764 time to fit residues: 61.1408 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN S 113 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132068 restraints weight = 10040.828| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.05 r_work: 0.3448 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8892 Z= 0.134 Angle : 0.522 6.490 12078 Z= 0.278 Chirality : 0.041 0.180 1377 Planarity : 0.004 0.050 1522 Dihedral : 7.633 116.446 1259 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.32 % Allowed : 25.91 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1115 helix: 1.66 (0.28), residues: 367 sheet: -0.03 (0.31), residues: 264 loop : -0.95 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.018 0.001 TYR S 235 PHE 0.029 0.001 PHE R 38 TRP 0.021 0.001 TRP R 188 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8888) covalent geometry : angle 0.51995 (12069) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.45644 ( 6) hydrogen bonds : bond 0.04239 ( 408) hydrogen bonds : angle 4.40304 ( 1134) link_NAG-ASN : bond 0.00175 ( 1) link_NAG-ASN : angle 2.43972 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: A 29 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7918 (ttmt) REVERT: A 244 HIS cc_start: 0.7840 (m90) cc_final: 0.7251 (m90) REVERT: A 247 MET cc_start: 0.8455 (mtp) cc_final: 0.7942 (mtm) REVERT: A 272 ASP cc_start: 0.8001 (t0) cc_final: 0.7615 (t0) REVERT: A 276 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: S 140 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6544 (mpp) REVERT: S 165 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.5997 (pp) REVERT: S 235 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6704 (t80) REVERT: S 238 THR cc_start: 0.8258 (p) cc_final: 0.8006 (t) REVERT: C 47 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: R 25 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6961 (m-10) REVERT: R 167 MET cc_start: 0.6173 (tpp) cc_final: 0.5935 (mmm) outliers start: 48 outliers final: 13 residues processed: 158 average time/residue: 0.3783 time to fit residues: 65.0593 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN S 113 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135973 restraints weight = 9879.296| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.96 r_work: 0.3479 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8892 Z= 0.110 Angle : 0.508 10.617 12078 Z= 0.267 Chirality : 0.040 0.168 1377 Planarity : 0.004 0.048 1522 Dihedral : 7.353 114.666 1259 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.98 % Allowed : 26.91 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.25), residues: 1115 helix: 1.79 (0.28), residues: 367 sheet: 0.03 (0.31), residues: 261 loop : -0.97 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.018 0.001 TYR S 235 PHE 0.021 0.001 PHE R 38 TRP 0.025 0.001 TRP R 188 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8888) covalent geometry : angle 0.50586 (12069) SS BOND : bond 0.00731 ( 3) SS BOND : angle 1.21877 ( 6) hydrogen bonds : bond 0.03787 ( 408) hydrogen bonds : angle 4.22609 ( 1134) link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 2.38642 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: A 29 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7938 (ttmt) REVERT: A 247 MET cc_start: 0.8483 (mtp) cc_final: 0.7988 (mtm) REVERT: A 272 ASP cc_start: 0.7947 (t0) cc_final: 0.7545 (t0) REVERT: A 276 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 349 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7837 (mmmm) REVERT: S 140 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.6564 (mpp) REVERT: S 165 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.5940 (pp) REVERT: S 235 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6697 (t80) REVERT: S 238 THR cc_start: 0.8194 (p) cc_final: 0.7991 (t) REVERT: C 19 LEU cc_start: 0.8524 (mm) cc_final: 0.8048 (mm) REVERT: R 25 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: R 165 LYS cc_start: 0.7306 (mtpt) cc_final: 0.6942 (tttm) outliers start: 45 outliers final: 16 residues processed: 159 average time/residue: 0.5059 time to fit residues: 86.6693 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN S 113 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130575 restraints weight = 9935.678| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.01 r_work: 0.3401 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8892 Z= 0.150 Angle : 0.545 8.537 12078 Z= 0.287 Chirality : 0.042 0.184 1377 Planarity : 0.004 0.050 1522 Dihedral : 7.480 116.205 1259 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.20 % Allowed : 26.91 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1115 helix: 1.71 (0.28), residues: 367 sheet: -0.05 (0.31), residues: 267 loop : -1.00 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 128 TYR 0.018 0.001 TYR S 235 PHE 0.031 0.002 PHE R 38 TRP 0.028 0.001 TRP R 188 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8888) covalent geometry : angle 0.54347 (12069) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.28958 ( 6) hydrogen bonds : bond 0.04153 ( 408) hydrogen bonds : angle 4.29828 ( 1134) link_NAG-ASN : bond 0.00160 ( 1) link_NAG-ASN : angle 2.21068 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: A 29 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7861 (ttmt) REVERT: A 247 MET cc_start: 0.8361 (mtp) cc_final: 0.7807 (mtm) REVERT: A 272 ASP cc_start: 0.7986 (t0) cc_final: 0.7583 (t0) REVERT: A 275 GLU cc_start: 0.8379 (tp30) cc_final: 0.7529 (tp30) REVERT: A 276 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: S 165 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.5892 (pp) REVERT: S 235 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6719 (t80) REVERT: S 238 THR cc_start: 0.8369 (p) cc_final: 0.8063 (t) REVERT: B 42 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7578 (ttm-80) REVERT: C 19 LEU cc_start: 0.8430 (mm) cc_final: 0.8002 (mm) REVERT: R 25 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6907 (m-10) REVERT: R 28 LYS cc_start: 0.6473 (tttt) cc_final: 0.5776 (tttp) REVERT: R 167 MET cc_start: 0.6318 (mmm) cc_final: 0.5795 (tpp) outliers start: 47 outliers final: 18 residues processed: 162 average time/residue: 0.4674 time to fit residues: 82.0927 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131208 restraints weight = 10130.097| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.04 r_work: 0.3382 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8892 Z= 0.157 Angle : 0.557 7.732 12078 Z= 0.292 Chirality : 0.042 0.193 1377 Planarity : 0.004 0.046 1522 Dihedral : 7.189 116.595 1257 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.87 % Allowed : 28.02 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1115 helix: 1.69 (0.28), residues: 366 sheet: -0.27 (0.30), residues: 278 loop : -0.91 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 128 TYR 0.019 0.001 TYR S 235 PHE 0.026 0.002 PHE R 38 TRP 0.034 0.002 TRP R 188 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8888) covalent geometry : angle 0.55503 (12069) SS BOND : bond 0.00633 ( 3) SS BOND : angle 1.53696 ( 6) hydrogen bonds : bond 0.04201 ( 408) hydrogen bonds : angle 4.30697 ( 1134) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 2.34593 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: A 29 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7849 (ttmt) REVERT: A 247 MET cc_start: 0.8365 (mtp) cc_final: 0.7834 (mtm) REVERT: A 272 ASP cc_start: 0.7991 (t0) cc_final: 0.7585 (t0) REVERT: A 275 GLU cc_start: 0.8406 (tp30) cc_final: 0.7586 (tp30) REVERT: A 276 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: A 349 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7893 (mmmm) REVERT: S 165 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.5859 (pp) REVERT: S 235 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6923 (t80) REVERT: B 42 ARG cc_start: 0.7876 (tpt170) cc_final: 0.7605 (ttm-80) REVERT: C 19 LEU cc_start: 0.8447 (mm) cc_final: 0.8033 (mm) REVERT: R 25 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: R 167 MET cc_start: 0.6511 (mmm) cc_final: 0.5992 (tpp) outliers start: 44 outliers final: 23 residues processed: 158 average time/residue: 0.4685 time to fit residues: 80.2106 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.0270 chunk 73 optimal weight: 7.9990 chunk 62 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 113 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.175143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135582 restraints weight = 9819.870| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.00 r_work: 0.3497 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8892 Z= 0.102 Angle : 0.510 7.420 12078 Z= 0.267 Chirality : 0.040 0.157 1377 Planarity : 0.004 0.050 1522 Dihedral : 6.863 113.334 1257 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.65 % Allowed : 29.46 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1115 helix: 1.90 (0.28), residues: 367 sheet: 0.01 (0.31), residues: 266 loop : -0.99 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 128 TYR 0.017 0.001 TYR S 235 PHE 0.025 0.001 PHE R 38 TRP 0.037 0.001 TRP R 188 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8888) covalent geometry : angle 0.50776 (12069) SS BOND : bond 0.00596 ( 3) SS BOND : angle 1.41844 ( 6) hydrogen bonds : bond 0.03501 ( 408) hydrogen bonds : angle 4.11224 ( 1134) link_NAG-ASN : bond 0.00130 ( 1) link_NAG-ASN : angle 2.21909 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: A 28 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7055 (pt0) REVERT: A 29 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7868 (ttmt) REVERT: A 247 MET cc_start: 0.8342 (mtp) cc_final: 0.7717 (mtm) REVERT: A 272 ASP cc_start: 0.7938 (t0) cc_final: 0.7567 (t0) REVERT: A 275 GLU cc_start: 0.8327 (tp30) cc_final: 0.7550 (tp30) REVERT: A 276 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 349 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7828 (mmmm) REVERT: S 165 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.5888 (pp) REVERT: S 235 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6728 (t80) REVERT: S 238 THR cc_start: 0.8209 (p) cc_final: 0.7890 (t) REVERT: B 42 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7486 (ttm-80) REVERT: C 19 LEU cc_start: 0.8503 (mm) cc_final: 0.8082 (mm) REVERT: R 167 MET cc_start: 0.6466 (mmm) cc_final: 0.5978 (tpp) outliers start: 33 outliers final: 17 residues processed: 151 average time/residue: 0.4670 time to fit residues: 76.3661 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 86 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 39 GLN S 113 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131985 restraints weight = 9790.938| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.06 r_work: 0.3401 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8892 Z= 0.140 Angle : 0.542 7.406 12078 Z= 0.284 Chirality : 0.042 0.178 1377 Planarity : 0.004 0.049 1522 Dihedral : 6.967 115.666 1257 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.54 % Allowed : 29.79 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.26), residues: 1115 helix: 1.80 (0.28), residues: 368 sheet: -0.03 (0.31), residues: 267 loop : -1.00 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 128 TYR 0.017 0.001 TYR S 235 PHE 0.021 0.001 PHE R 38 TRP 0.033 0.001 TRP R 188 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8888) covalent geometry : angle 0.54033 (12069) SS BOND : bond 0.00565 ( 3) SS BOND : angle 1.39610 ( 6) hydrogen bonds : bond 0.03938 ( 408) hydrogen bonds : angle 4.20500 ( 1134) link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 2.18898 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: A 29 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7868 (ttmt) REVERT: A 247 MET cc_start: 0.8280 (mtp) cc_final: 0.7705 (mtm) REVERT: A 272 ASP cc_start: 0.7938 (t0) cc_final: 0.7556 (t0) REVERT: A 275 GLU cc_start: 0.8362 (tp30) cc_final: 0.7587 (tp30) REVERT: A 276 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: A 349 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7811 (mmmm) REVERT: S 165 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.5927 (pp) REVERT: S 235 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6509 (t80) REVERT: B 42 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7523 (ttm-80) REVERT: C 19 LEU cc_start: 0.8469 (mm) cc_final: 0.8075 (mm) REVERT: R 167 MET cc_start: 0.6502 (mmm) cc_final: 0.5942 (tpp) outliers start: 32 outliers final: 16 residues processed: 146 average time/residue: 0.4902 time to fit residues: 77.2944 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 113 GLN B 259 GLN R 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134473 restraints weight = 9946.027| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.09 r_work: 0.3431 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 8892 Z= 0.107 Angle : 0.521 8.303 12078 Z= 0.276 Chirality : 0.041 0.300 1377 Planarity : 0.004 0.050 1522 Dihedral : 6.840 113.632 1257 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.66 % Allowed : 30.90 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.26), residues: 1115 helix: 1.87 (0.28), residues: 367 sheet: 0.08 (0.31), residues: 271 loop : -0.97 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 128 TYR 0.017 0.001 TYR S 235 PHE 0.022 0.001 PHE R 38 TRP 0.038 0.001 TRP R 188 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8888) covalent geometry : angle 0.51824 (12069) SS BOND : bond 0.00881 ( 3) SS BOND : angle 1.77943 ( 6) hydrogen bonds : bond 0.03534 ( 408) hydrogen bonds : angle 4.12211 ( 1134) link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 2.35470 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: A 28 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7004 (pt0) REVERT: A 29 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7817 (ttmt) REVERT: A 247 MET cc_start: 0.8270 (mtp) cc_final: 0.7647 (mtm) REVERT: A 272 ASP cc_start: 0.7946 (t0) cc_final: 0.7619 (t0) REVERT: A 275 GLU cc_start: 0.8372 (tp30) cc_final: 0.7589 (tp30) REVERT: A 276 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: A 349 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7848 (mmmm) REVERT: S 165 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.5953 (pp) REVERT: S 235 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6355 (t80) REVERT: S 238 THR cc_start: 0.8220 (p) cc_final: 0.7939 (t) REVERT: B 42 ARG cc_start: 0.7778 (tpt170) cc_final: 0.7506 (ttm-80) REVERT: C 19 LEU cc_start: 0.8393 (mm) cc_final: 0.7999 (mm) REVERT: R 103 MET cc_start: 0.7663 (tmt) cc_final: 0.7349 (tmt) REVERT: R 167 MET cc_start: 0.6522 (mmm) cc_final: 0.6040 (tpp) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.4629 time to fit residues: 70.8202 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 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 = 0.4021 r_free = 0.4021 target = 0.170570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132854 restraints weight = 9992.406| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.06 r_work: 0.3426 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8892 Z= 0.117 Angle : 0.532 8.791 12078 Z= 0.279 Chirality : 0.041 0.170 1377 Planarity : 0.004 0.051 1522 Dihedral : 6.832 114.030 1257 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.10 % Allowed : 30.45 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1115 helix: 1.90 (0.28), residues: 367 sheet: 0.07 (0.31), residues: 272 loop : -0.95 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.016 0.001 TYR S 235 PHE 0.021 0.001 PHE R 38 TRP 0.037 0.001 TRP R 188 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8888) covalent geometry : angle 0.52973 (12069) SS BOND : bond 0.00682 ( 3) SS BOND : angle 1.66148 ( 6) hydrogen bonds : bond 0.03659 ( 408) hydrogen bonds : angle 4.12969 ( 1134) link_NAG-ASN : bond 0.00073 ( 1) link_NAG-ASN : angle 2.22199 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.81 seconds wall clock time: 59 minutes 24.60 seconds (3564.60 seconds total)